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Update tests for extended phylip format

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* Update expected output for test_AlignIO, test_SeqIO
* Apply most of the same exceptions affecting the phylip format to
  extended phylip
* Add a sample extended phylip format-file (primates.phyx, from the
  Bodega Phylogenetics Wiki:
  http://bodegaphylo.wikispot.org/RAxML_Tutorial)
This commit is contained in:
Connor McCoy
2011-06-07 17:12:17 -07:00
committed by peterjc
parent f4d2001340
commit 4d5e57aa19
6 changed files with 442 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files

234
Tests/ExtendedPhylip/primates.phyx Normal file
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@ -0,0 +1,234 @@
12 898
Tarsius_syrichta AAGTTTCATT GGAGCCACCA CTCTTATAAT TGCCCATGGC CTCACCTCCT
Lemur_catta AAGCTTCATA GGAGCAACCA TTCTAATAAT CGCACATGGC CTTACATCAT
Homo_sapiens AAGCTTCACC GGCGCAGTCA TTCTCATAAT CGCCCACGGG CTTACATCCT
Pan AAGCTTCACC GGCGCAATTA TCCTCATAAT CGCCCACGGA CTTACATCCT
Gorilla AAGCTTCACC GGCGCAGTTG TTCTTATAAT TGCCCACGGA CTTACATCAT
Pongo AAGCTTCACC GGCGCAACCA CCCTCATGAT TGCCCATGGA CTCACATCCT
Hylobates AAGCTTTACA GGTGCAACCG TCCTCATAAT CGCCCACGGA CTAACCTCTT
Macaca_fuscus AAGCTTTTCC GGCGCAACCA TCCTTATGAT CGCTCACGGA CTCACCTCTT
Macaca_mulatta AAGCTTTTCT GGCGCAACCA TCCTCATGAT TGCTCACGGA CTCACCTCTT
Macaca_fascicularis AAGCTTCTCC GGCGCAACCA CCCTTATAAT CGCCCACGGG CTCACCTCTT
Macaca_sylvanus AAGCTTCTCC GGTGCAACTA TCCTTATAGT TGCCCATGGA CTCACCTCTT
Saimiri_sciureus AAGCTTCACC GGCGCAATGA TCCTAATAAT CGCTCACGGG TTTACTTCGT
CCCTATTATT TTGCCTAGCA AATACAAACT ACGAACGAGT CCACAGTCGA
CCATATTATT CTGTCTAGCC AACTCTAACT ACGAACGAAT CCATAGCCGT
CATTACTATT CTGCCTAGCA AACTCAAACT ACGAACGCAC TCACAGTCGC
CATTATTATT CTGCCTAGCA AACTCAAATT ATGAACGCAC CCACAGTCGC
CATTATTATT CTGCCTAGCA AACTCAAACT ACGAACGAAC CCACAGCCGC
CCCTACTGTT CTGCCTAGCA AACTCAAACT ACGAACGAAC CCACAGCCGC
CCCTGCTATT CTGCCTTGCA AACTCAAACT ACGAACGAAC TCACAGCCGC
CCATATATTT CTGCCTAGCC AATTCAAACT ATGAACGCAC TCACAACCGT
CCATATATTT CTGCCTAGCC AATTCAAACT ATGAACGCAC TCACAACCGT
CCATGTATTT CTGCTTGGCC AATTCAAACT ATGAGCGCAC TCATAACCGT
CCATATACTT CTGCTTGGCC AACTCAAACT ACGAACGCAC CCACAGCCGC
CTATGCTATT CTGCCTAGCA AACTCAAATT ACGAACGAAT TCACAGCCGA
ACAATAGCAC TAGCCCGTGG CCTTCAAACC CTATTACCTC TTGCAGCAAC
ACAATACTAC TAGCACGAGG GATCCAAACC ATTCTCCCTC TTATAGCCAC
ATCATAATCC TCTCTCAAGG ACTTCAAACT CTACTCCCAC TAATAGCTTT
ATCATAATTC TCTCCCAAGG ACTTCAAACT CTACTCCCAC TAATAGCCTT
ATCATAATTC TCTCTCAAGG ACTCCAAACC CTACTCCCAC TAATAGCCCT
ATCATAATCC TCTCTCAAGG CCTTCAAACT CTACTCCCCC TAATAGCCCT
ATCATAATCC TATCTCGAGG GCTCCAAGCC TTACTCCCAC TGATAGCCTT
ACCATACTAC TGTCCCGAGG ACTTCAAATC CTACTTCCAC TAACAGCCTT
ACCATACTAC TGTCCCGGGG ACTTCAAATC CTACTTCCAC TAACAGCTTT
ACCATACTAC TATCCCGAGG ACTTCAAATT CTACTTCCAT TGACAGCCTT
ATCATACTAC TATCCCGAGG ACTCCAAATC CTACTCCCAC TAACAGCCTT
ACAATAACAT TTACTCGAGG GCTCCAAACA CTATTCCCGC TTATAGGCCT
ATGATGACTC CTCGCCAGCT TAACCAACCT GGCCCTTCCC CCAACAATTA
CTGATGACTA CTCGCCAGCC TAACTAACCT AGCCCTACCC ACCTCTATCA
TTGATGACTT CTAGCAAGCC TCGCTAACCT CGCCTTACCC CCCACTATTA
TTGATGACTC CTAGCAAGCC TCGCTAACCT CGCCCTACCC CCTACCATTA
TTGATGACTT CTGGCAAGCC TCGCCAACCT CGCCTTACCC CCCACCATTA
CTGATGACTT CTAGCAAGCC TCACTAACCT TGCCCTACCA CCCACCATCA
CTGATGACTC GCAGCAAGCC TCGCTAACCT CGCCCTACCC CCCACTATTA
TTGATGATTA ACAGCAAGCC TTACTAACCT TGCCCTACCC CCCACTATCA
CTGATGATTA ACAGCAAGCC TTACTAACCT TGCCCTACCC CCCACTATCA
CTGATGACTC ACAGCAAGCC TTACTAACCT TGCCCTACCC CCCACTATTA
CTGATGATTC ACAGCAAGCC TTACTAATCT TGCTCTACCC TCCACTATTA
CTGATGACTC CTAGCAAATC TCGCTAACCT CGCCCTACCC ACAGCTATTA
ATTTAATCGG TGAACTGTCC GTAATAATAG CAGCATTTTC ATGGTCACAC
ATTTAATTGG CGAACTATTC GTCACTATAG CATCCTTCTC ATGATCAAAC
ACCTACTGGG AGAACTCTCT GTGCTAGTAA CCACGTTCTC CTGATCAAAT
ATCTCCTAGG GGAACTCTCC GTGCTAGTAA CCTCATTCTC CTGATCAAAT
ACCTACTAGG AGAGCTCTCC GTACTAGTAA CCACATTCTC CTGATCAAAC
ACCTTCTAGG AGAACTCTCC GTACTAATAG CCATATTCTC TTGATCTAAC
ACCTCCTAGG TGAACTCTTC GTACTAATGG CCTCCTTCTC CTGGGCAAAC
ATCTACTAGG TGAACTCTTT GTAATCGCAA CCTCATTCTC CTGATCCCAT
ACCTACTAGG TGAACTCTTT GTAATCGCGA CCTCATTCTC CTGGTCCCAT
ATCTACTAGG CGAACTCTTT GTAATCACAA CTTCATTTTC CTGATCCCAT
ATCTACTGGG CGAACTCTTC GTAATCGCAA CCTCATTTTC CTGATCCCAC
ATCTAGTAGG AGAATTACTC ACAATCGTAT CTTCCTTCTC TTGATCCAAC
CTAACTATTA TCTTAGTAGG CCTTAACACC CTTATCACCG CCCTATATTC
ATTACAATTA TCTTAATAGG CTTAAATATG CTCATCACCG CTCTCTATTC
ATCACTCTCC TACTTACAGG ACTCAACATA CTAGTCACAG CCCTATACTC
ACCACTCTCC TACTCACAGG ATTCAACATA CTAATCACAG CCCTGTACTC
ACCACCCTTT TACTTACAGG ATCTAACATA CTAATTACAG CCCTGTACTC
ATCACCATCC TACTAACAGG ACTCAACATA CTAATCACAA CCCTATACTC
ACTACTATTA CACTCACCGG GCTCAACGTA CTAATCACGG CCCTATACTC
ATCACCATTA TGCTAACAGG ACTTAACATA TTAATTACGG CCCTCTACTC
ATCACCATTA TATTAACAGG ATTTAACATA CTAATTACGG CCCTCTACTC
ATCACCATTG TGTTAACGGG CCTTAATATA CTAATCACAG CCCTCTACTC
ATCACCATCA TACTAACAGG ACTGAACATA CTAATTACAG CCCTCTACTC
TTTACTATTA TATTCACAGG ACTTAATATA CTAATTACAG CACTCTACTC
CCTATATATA CTAATCATAA CTCAACGAGG AAAATACACA TATCATATCA
CCTCTATATA TTAACTACTA CACAACGAGG AAAACTCACA TATCATTCGC
CCTCTACATA TTTACCACAA CACAATGGGG CTCACTCACC CACCACATTA
CCTCTACATG TTTACCACAA CACAATGAGG CTCACTCACC CACCACATTA
CCTTTATATA TTTACCACAA CACAATGAGG CCCACTCACA CACCACATCA
TCTCTATATA TTCACCACAA CACAACGAGG TACACCCACA CACCACATCA
CCTTTACATA TTTATCATAA CACAACGAGG CACACTTACA CACCACATTA
TCTCCACATA TTCACTACAA CACAACGAGG AACACTCACA CATCACATAA
CCTCCACATA TTCACCACAA CACAACGAGG AGCACTCACA CATCACATAA
TCTCCACATG TTCATTACAG TACAACGAGG AACACTCACA CACCACATAA
TCTTCACATA TTCACCACAA CACAACGAGG AGCGCTCACA CACCACATAA
ACTTCATATG TATGCCTCTA CACAGCGAGG TCCACTTACA TACAGCACCA
ACAATATCAT GCCCCCTTTC ACCCGAGAAA ATACATTAAT AATCATACAC
ACAACCTAAA CCCATCCTTT ACACGAGAAA ACACCCTTAT ATCCATACAC
ACAACATAAA ACCCTCATTC ACACGAGAAA ACACCCTCAT GTTCATACAC
ATAACATAAA GCCCTCATTC ACACGAGAAA ATACTCTCAT ATTTTTACAC
CCAACATAAA ACCCTCATTT ACACGAGAAA ACATCCTCAT ATTCATGCAC
ACAACATAAA ACCTTCTTTC ACACGCGAAA ATACCCTCAT GCTCATACAC
AAAACATAAA ACCCTCACTC ACACGAGAAA ACATATTAAT ACTTATGCAC
TCAACATAAA GCCCCCCTTC ACACGAGAAA ACACATTAAT ATTCATACAC
TCAACATAAA ACCCCCCTTC ACACGAGAAA ACATATTAAT ATTCATACAC
TCAATATAAA ACCCCCCTTC ACACGAGAAA ACATATTAAT ATTCATACAC
TTAACATAAA ACCACCTTTC ACACGAGAAA ACATATTAAT ACTCATACAC
GCAATATAAA ACCAATATTT ACACGAGAAA ATACGCTAAT ATTTATACAT
CTATTTCCCT TAATCCTACT ATCTACCAAC CCCAAAGTAA TTATAGGAAC
ATACTCCCCC TTCTCCTATT TACCTTAAAC CCCAAAATTA TTCTAGGACC
CTATCCCCCA TTCTCCTCCT ATCCCTCAAC CCCGACATCA TTACCGGGTT
CTATCCCCCA TCCTCCTTCT ATCCCTCAAT CCTGATATCA TCACTGGATT
CTATCCCCCA TCCTCCTCCT ATCCCTCAAC CCCGATATTA TCACCGGGTT
CTATCCCCCA TCCTCCTCTT ATCCCTCAAC CCCAGCATCA TCGCTGGGTT
CTCTTCCCCC TCCTCCTCCT AACCCTCAAC CCTAACATCA TTACTGGCTT
CTCGCTCCAA TTATCCTTCT ATCCCTCAAC CCCAACATCA TCCTGGGGTT
CTCGCTCCAA TCATCCTCCT ATCTCTCAAC CCCAACATCA TCCTGGGGTT
CTCGCTCCAA TTATCCTTCT ATCTCTCAAC CCCAACATCA TCCTGGGGTT
CTCGCTCCAA TTATTCTTCT ATCTCTTAAC CCCAACATCA TTCTAGGATT
ATAACACCAA TCCTCCTCCT TACCTTGAGC CCCAAGGTAA TTATAGGACC
CATGTACTGT AAATATAGTT TAAACAAAAC ATTAGATTGT GAGTCTAATA
CACGTACTGT AAATATAGTT TAAA-AAAAC ACTAGATTGT GAATCCAGAA
TTCCTCTTGT AAATATAGTT TAACCAAAAC ATCAGATTGT GAATCTGACA
CACCTCCTGT AAATATAGTT TAACCAAAAC ATCAGATTGT GAATCTGACA
CACCTCCTGT AAATATAGTT TAACCAAAAC ATCAGATTGT GAATCTGATA
CGCCTACTGT AAATATAGTT TAACCAAAAC ATTAGATTGT GAATCTAATA
TACTCCCTGT AAACATAGTT TAATCAAAAC ATTAGATTGT GAATCTAACA
TACCTCCTGT AGATATAGTT TAACTAAAAC ACTAGATTGT GAATCTAACC
TACTTCCTGT AGATATAGTT TAACTAAAAC ATTAGATTGT GAATCTAACC
TACCTCCTGT AAATATAGTT TAACTAAAAC ATTAGATTGT GAATCTAACT
TACTTCCTGT AAATATAGTT TAATTAAAAC ATTAGACTGT GAATCTAACT
CTCACCTTGT AATTATAGTT TAGCTAAAAC ATTAGATTGT GAATCTAATA
ATAGAAGCCC AAAGATTTCT TATTTACCAA GAAAGTA-TG CAAGAACTGC
ATAGAAGCTC AAAC-CTTCT TATTTACCGA GAAAGTAATG TATGAACTGC
ACAGAGGCTT A-CGACCCCT TATTTACCGA GAAAGCT-CA CAAGAACTGC
ACAGAGGCTC A-CGACCCCT TATTTACCGA GAAAGCT-TA TAAGAACTGC
ACAGAGGCTC A-CAACCCCT TATTTACCGA GAAAGCT-CG TAAGAGCTGC
ATAGGGCCCC A-CAACCCCT TATTTACCGA GAAAGCT-CA CAAGAACTGC
ATAGAGGCTC G-AAACCTCT TGCTTACCGA GAAAGCC-CA CAAGAACTGC
ATAGAGACTC A-CCACCTCT TATTTACCGA GAAAACT-CG CAAGGACTGC
ATAGAGACTT A-CCACCTCT TATTTACCGA GAAAACT-CG CGAGGACTGC
ATAGAGGCCT A-CCACTTCT TATTTACCGA GAAAACT-CG CAAGGACTGC
ATAGAAGCTT A-CCACTTCT TATTTACCGA GAAAACT-TG CAAGGACCGC
ATAGAAGAAT A-TAACTTCT TAATTACCGA GAAAGTG-CG CAAGAACTGC
TAACTCATGC CTCCATATAT AACAATGTGG CTTTCTT-AC TTTTAAAGGA
TAACTCTGCA CTCCGTATAT AAAAATACGG CTATCTCAAC TTTTAAAGGA
TAACTCATGC CCCCATGTCT AACAACATGG CTTTCTCAAC TTTTAAAGGA
TAATTCATAT CCCCATGCCT GACAACATGG CTTTCTCAAC TTTTAAAGGA
TAACTCATAC CCCCGTGCTT GACAACATGG CTTTCTCAAC TTTTAAAGGA
TAACTCTCAC T-CCATGTGT GACAACATGG CTTTCTCAGC TTTTAAAGGA
TAACTCACTA TCCCATGTAT GACAACATGG CTTTCTCAAC TTTTAAAGGA
TAACCCATGT ACCCGTACCT AAAATTACGG TTTTCTCAAC TTTTAAAGGA
TAACCCATGT ATCCGTACCT AAAATTACGG TTTTCTCAAC TTTTAAAGGA
TAATCCATGC CTCCGTACTT AAAACTACGG TTTCCTCAAC TTTTAAAGGA
TAATCCACAC CTCCGTACTT AAAACTACGG TTTTCTCAAC TTTTAAAGGA
TAATTCATGC TCCCAAGACT AACAACTTGG CTTCCTCAAC TTTTAAAGGA
TAGAAGTAAT CCATCGGTCT TAGGAACCGA AAA-ATTGGT GCAACTCCAA
TAGAAGTAAT CCATTGGCCT TAGGAGCCAA AAA-ATTGGT GCAACTCCAA
TAACAGCTAT CCATTGGTCT TAGGCCCCAA AAATTTTGGT GCAACTCCAA
TAACAGCCAT CCGTTGGTCT TAGGCCCCAA AAATTTTGGT GCAACTCCAA
TAACAGCTAT CCATTGGTCT TAGGACCCAA AAATTTTGGT GCAACTCCAA
TAACAGCTAT CCCTTGGTCT TAGGATCCAA AAATTTTGGT GCAACTCCAA
TAACAGCTAT CCATTGGTCT TAGGACCCAA AAATTTTGGT GCAACTCCAA
TAACAGCTAT CCATTGACCT TAGGAGTCAA AAACATTGGT GCAACTCCAA
TAACAGCTAT CCATTGACCT TAGGAGTCAA AAATATTGGT GCAACTCCAA
TAACAGCTAT CCATTGACCT TAGGAGTCAA AAACATTGGT GCAACTCCAA
TAACAGCTAT CCATTGGCCT TAGGAGTCAA AAATATTGGT GCAACTCCAA
TAGTAGTTAT CCATTGGTCT TAGGAGCCAA AAACATTGGT GCAACTCCAA
ATAAAAGTAA TAAATTTATT TTCATCCTCC ATTTTACTAT CACTTACACT
ATAAAAGTAA TAAATCTATT ATCCTCTTTC ACCCTTGTCA CACTGATTAT
ATAAAAGTAA TAACCATGCA CACTACTATA ACCACCCTAA CCCTGACTTC
ATAAAAGTAA TAACCATGTA TACTACCATA ACCACCTTAA CCCTAACTCC
ATAAAAGTAA TAACTATGTA CGCTACCATA ACCACCTTAG CCCTAACTTC
ATAAAAGTAA CAGCCATGTT TACCACCATA ACTGCCCTCA CCTTAACTTC
ATAAAAGTAA TAGCAATGTA CACCACCATA GCCATTCTAA CGCTAACCTC
ATAAAAGTAA TAATCATGCA CACCCCCATC ATTATAACAA CCCTTATCTC
ATAAAAGTAA TAATCATGCA CACCCCTATC ATAATAACAA CCCTTATCTC
ATAAAAGTAA TAATCATGCA CACCCCCATC ATAATAACAA CCCTCATCTC
ATAAAAGTAA TAATCATGTA TACCCCCATC ATAATAACAA CTCTCATCTC
ATAAAAGTAA TA---ATACA CTTCTCCATC ACTCTAATAA CACTAATTAG
CTTAATTACC CCATTTATTA TTACAACAAC TAAAAAATAT GAAACACATG
CCTAACTTTA CCTATCATTA TAAACGTTAC AAACATATAC AAAAACTACC
CCTAATTCCC CCCATCCTTA CCACCCTCGT TAACCCTAAC AAAAAAAACT
CTTAATTCTC CCCATCCTCA CCACCCTCAT TAACCCTAAC AAAAAAAACT
CTTAATTCCC CCTATCCTTA CCACCTTCAT CAATCCTAAC AAAAAAAGCT
CCTAATCCCC CCCATTACCG CTACCCTCAT TAACCCCAAC AAAAAAAACC
CCTAATTCCC CCCATTACAG CCACCCTTAT TAACCCCAAT AAAAAGAACT
CCTAACTCTC CCAATTTTTG CCACCCTCAT CAACCCTTAC AAAAAACGTC
CCTAACTCTC CCAATTTTTG CCACCCTCAT CAACCCTTAC AAAAAACGTC
CCTGACCCTT CCAATTTTTG CCACCCTCAC CAACCCCTAT AAAAAACGTT
CCTAACTCTT CCAATTTTCG CTACCCTTAT CAACCCCAAC AAAAAACACC
CCTACTAGCG CCAATCCTAG CTACCCTCAT TAACCCTAAC AAAAGCACAC
CATACCCTTA CTACGTAAAA AACTCTATCG CCTGCGCATT TATAACAAGC
CCTATGCACC ATACGTAAAA TCTTCTATTG CATGTGCCTT CATCACTAGC
CATACCCCCA TTATGTAAAA TCCATTGTCG CATCCACCTT TATTATCAGT
CATATCCCCA TTATGTGAAA TCCATTATCG CGTCCACCTT TATCATTAGC
CATACCCCCA TTACGTAAAA TCTATCGTCG CATCCACCTT TATCATCAGC
CATACCCCCA CTATGTAAAA ACGGCCATCG CATCCGCCTT TACTATCAGC
TATACCCGCA CTACGTAAAA ATGACCATTG CCTCTACCTT TATAATCAGC
CATACCCAGA TTACGTAAAA ACAACCGTAA TATATGCTTT CATCATCAGC
CATACCCAGA TTACGTAAAA ACAACCGTAA TATATGCTTT CATCATCAGC
CATACCCAGA CTACGTAAAA ACAACCGTAA TATATGCTTT TATTACCAGT
TATATCCAAA CTACGTAAAA ACAGCCGTAA TATATGCTTT CATTACCAGC
TATACCCGTA CTACGTAAAA CTAGCCATCA TCTACGCCCT CATTACCAGT
CTAGTCCCAA TGCTCATATT TCTATACACA AATCAAGAAA TAATCATTTC
CTCATCCCAA CTATATTATT TATCTCCTCA GGACAAGAAA CAATCATTTC
CTCTTCCCCA CAACAATATT CATGTGCCTA GACCAAGAAG TTATTATCTC
CTTTTCCCCA CAACAATATT CATATGCCTA GACCAAGAAG CTATTATCTC
CTCTTCCCCA CAACAATATT TCTATGCCTA GACCAAGAAG CTATTATCTC
CTTATCCCAA CAACAATATT TATCTGCCTA GGACAAGAAA CCATCGTCAC
CTATTTCCCA CAATAATATT CATGTGCACA GACCAAGAAA CCATTATTTC
CTCCCCTCAA CAACTTTATT CATCTTCTCA AACCAAGAAA CAACCATTTG
CTCCCCTCAA CAACTTTATT CATCTTCTCA AACCAAGAAA CAACCATTTG
CTCCCCTCAA CAACCCTATT CATCCTCTCA AACCAAGAAA CAACCATTTG
CTCTCTTCAA CAACTTTATA TATATTCTTA AACCAAGAAA CAATCATCTG
ACCTTATCTA TAATATTCTT TATCCTTACA GGCCAAGAAT CAATAATTTC
CAACTGACAT TGAATAACGA TTCATACTAT CAAATTATGC CTAAGCTT
CAACTGACAT TGAATAACAA TCCAAACCCT AAAACTATCT ATTAGCTT
GAACTGACAC TGAGCCACAA CCCAAACAAC CCAGCTCTCC CTAAGCTT
AAACTGGCAC TGAGCAACAA CCCAAACAAC CCAGCTCTCC CTAAGCTT
AAGCTGACAC TGAGCAACAA CCCAAACAAT TCAACTCTCC CTAAGCTT
AAACTGATGC TGAACAACCA CCCAGACACT ACAACTCTCA CTAAGCTT
AAACTGACAC TGAACTGCAA CCCAAACGCT AGAACTCTCC CTAAGCTT
GAGCTGACAT TGAATAATGA CCCAAACACT AGACCTAACG CTAAGCTT
AAGCTGACAT TGAATAATAA CCCAAACACT AGACCTAACA CTAAGCTT
GAGTTGACAT TGAATAACAA CCCAAACATT AGACCTAACA CTAAGCTT
AAGCTGGCAC TGAATAATAA CCCAAACACT AAGCCTAACA TTAAGCTT
AAACTGACAC TGAATAACTA TCCAAACCAT CAAACTATCC CTAAGCTT

57
Tests/output/test_AlignIO
View File

@ -7,6 +7,7 @@ Testing reading clustal format file Clustalw/cw02.aln with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -23,6 +24,7 @@ Testing reading clustal format file Clustalw/opuntia.aln with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -39,6 +41,7 @@ Testing reading clustal format file Clustalw/hedgehog.aln with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -51,6 +54,7 @@ Testing reading clustal format file Clustalw/odd_consensus.aln with 1 alignments
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Failed: Repeated name 'AT3G20900.' (originally 'AT3G20900.1-SEQ'), possibly due to truncation
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -68,6 +72,7 @@ Testing reading clustal format file Clustalw/protein.aln with 1 alignments
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Failed: Repeated name 'gi|1377497' (originally 'gi|13774975|gb|AAK39115.1|AF35'), possibly due to truncation
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -85,6 +90,7 @@ Testing reading clustal format file Clustalw/promals3d.aln with 1 alignments
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Failed: Repeated name 'gi_1393639' (originally 'gi_13936397_dbj_BAB47195.'), possibly due to truncation
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -97,6 +103,7 @@ Testing reading fasta format file GFF/multi.fna with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -112,6 +119,8 @@ Testing reading nexus format file Nexus/test_Nexus_input.nex with 1 alignments
Checking can write/read as 'clustal' format
Checking can write/read as 'nexus' format
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Failed: Whitespace not allowed in identifier: t2 the name
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -123,6 +132,7 @@ Testing reading stockholm format file Stockholm/simple.sth with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -139,6 +149,7 @@ Testing reading stockholm format file Stockholm/funny.sth with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -155,6 +166,8 @@ Testing reading phylip format file Phylip/reference_dna.phy with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Failed: Whitespace not allowed in identifier: B. virgini
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -171,6 +184,8 @@ Testing reading phylip format file Phylip/reference_dna2.phy with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Failed: Whitespace not allowed in identifier: B. virgini
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -187,6 +202,7 @@ Testing reading phylip format file Phylip/hennigian.phy with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -203,6 +219,8 @@ Testing reading phylip format file Phylip/horses.phy with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Failed: Whitespace not allowed in identifier: M. secundu
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -219,6 +237,7 @@ Testing reading phylip format file Phylip/random.phy with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -231,6 +250,7 @@ Testing reading phylip format file Phylip/interlaced.phy with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -244,6 +264,24 @@ Testing reading phylip format file Phylip/interlaced2.phy with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
Testing reading phylip-extended format file ExtendedPhylip/primates.phyx with 1 alignments
Alignment 0, with 12 sequences of length 898
AAAAAAAAAAAA alignment column 0
AAAAAAAAAAAA alignment column 1
GGGGGGGGGGGG alignment column 2
TCCCCCCCCCCC alignment column 3
TTTTTTTTTTTT alignment column 4
|||||||||||| ...
TTTTTTTTTTTT alignment column 897
Checking can write/read as 'clustal' format
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -257,6 +295,7 @@ Testing reading emboss format file Emboss/alignret.txt with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -278,6 +317,7 @@ Testing reading emboss format file Emboss/needle.txt with 5 alignments
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -290,6 +330,8 @@ Testing reading emboss format file Emboss/needle_asis.txt with 1 alignments
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
Checking can write/read as 'phylip-extended' format
Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
Checking can write/read as 'stockholm' format
Failed: Duplicate record identifier: asis
Checking can write/read as 'fasta' format
@ -302,6 +344,7 @@ Testing reading emboss format file Emboss/water.txt with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -314,6 +357,8 @@ Testing reading emboss format file Emboss/water2.txt with 1 alignments
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
Checking can write/read as 'phylip-extended' format
Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
Checking can write/read as 'stockholm' format
Failed: Duplicate record identifier: asis
Checking can write/read as 'fasta' format
@ -326,6 +371,7 @@ Testing reading emboss format file Emboss/matcher_simple.txt with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -347,6 +393,7 @@ Testing reading emboss format file Emboss/matcher_pair.txt with 5 alignments
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -367,6 +414,7 @@ Testing reading fasta-m10 format file Fasta/output001.m10 with 4 alignments
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -388,6 +436,7 @@ Testing reading fasta-m10 format file Fasta/output002.m10 with 6 alignments
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -405,6 +454,7 @@ Testing reading fasta-m10 format file Fasta/output003.m10 with 3 alignments
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -417,6 +467,7 @@ Testing reading fasta-m10 format file Fasta/output004.m10 with 1 alignments
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Failed: Repeated name 'ref|NC_002' (originally 'ref|NC_002695.1|:1970775-1971404'), possibly due to truncation
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -428,6 +479,7 @@ Testing reading fasta-m10 format file Fasta/output005.m10 with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -439,6 +491,7 @@ Testing reading fasta-m10 format file Fasta/output006.m10 with 1 alignments
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -460,6 +513,7 @@ Testing reading fasta-m10 format file Fasta/output007.m10 with 9 alignments
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -481,6 +535,7 @@ Testing reading fasta-m10 format file Fasta/output008.m10 with 12 alignments
Checking can write/read as 'nexus' format
Failed: We can only write one Alignment to a Nexus file.
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -497,6 +552,7 @@ Testing reading ig format file IntelliGenetics/VIF_mase-pro.txt with 1 alignment
Checking can write/read as 'nexus' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format
@ -507,6 +563,7 @@ Testing reading pir format file NBRF/clustalw.pir with 1 alignments
Checking can write/read as 'clustal' format
Checking can write/read as 'nexus' format
Checking can write/read as 'phylip' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'fasta' format
Checking can write/read as 'tab' format

137
Tests/output/test_SeqIO
View File

@ -16,6 +16,8 @@ Testing reading sff format file Roche/E3MFGYR02_random_10_reads.sff
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Checking can write/read as 'fastq-illumina' format
@ -45,6 +47,7 @@ Testing reading clustal format file Clustalw/cw02.aln as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -88,6 +91,7 @@ Testing reading clustal format file Clustalw/opuntia.aln as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -131,6 +135,7 @@ Testing reading clustal format file Clustalw/hedgehog.aln as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -170,6 +175,7 @@ Testing reading clustal format file Clustalw/odd_consensus.aln as an alignment
Checking can write/read as 'phylip' format
Failed: Repeated name 'AT3G20900.' (originally 'AT3G20900.1-CDS'), possibly due to truncation
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -198,6 +204,7 @@ Testing reading fasta format file Fasta/lupine.nu
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -226,6 +233,7 @@ Testing reading fasta format file Fasta/elderberry.nu
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -254,6 +262,7 @@ Testing reading fasta format file Fasta/phlox.nu
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -282,6 +291,7 @@ Testing reading fasta format file Fasta/centaurea.nu
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -310,6 +320,7 @@ Testing reading fasta format file Fasta/wisteria.nu
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -338,6 +349,7 @@ Testing reading fasta format file Fasta/sweetpea.nu
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -366,6 +378,7 @@ Testing reading fasta format file Fasta/lavender.nu
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -394,6 +407,7 @@ Testing reading fasta format file Fasta/aster.pro
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -422,6 +436,7 @@ Testing reading fasta format file Fasta/loveliesbleeding.pro
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -450,6 +465,7 @@ Testing reading fasta format file Fasta/rose.pro
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -478,6 +494,7 @@ Testing reading fasta format file Fasta/rosemary.pro
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -506,6 +523,7 @@ Testing reading fasta format file Fasta/f001
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -541,6 +559,8 @@ Testing reading fasta format file Fasta/f002
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -574,6 +594,8 @@ Testing reading fasta format file Fasta/fa01
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -602,6 +624,7 @@ Testing reading fasta format file GenBank/NC_005816.fna
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -640,6 +663,8 @@ Testing reading fasta format file GenBank/NC_005816.ffn
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -678,6 +703,8 @@ Testing reading fasta format file GenBank/NC_005816.faa
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -716,6 +743,8 @@ Testing reading fasta format file GenBank/NC_000932.faa
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -754,6 +783,8 @@ Testing reading tab format file GenBank/NC_005816.tsv
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -782,6 +813,7 @@ Testing reading fasta format file GFF/NC_001802.fna
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -810,6 +842,7 @@ Testing reading fasta format file GFF/NC_001802lc.fna
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -850,6 +883,7 @@ Testing reading fasta format file GFF/multi.fna as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -883,6 +917,8 @@ Testing reading fasta format file Registry/seqs.fasta
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -926,6 +962,8 @@ Testing reading nexus format file Nexus/test_Nexus_input.nex as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Failed: Whitespace not allowed in identifier: one should be punished, for (that)!
Checking can write/read as 'embl' format
Failed: Cannot have spaces in EMBL accession, 'one should be punished, for (that)!'
Checking can write/read as 'fastq' format
@ -953,6 +991,7 @@ Testing reading swiss format file SwissProt/sp001
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13454).
@ -977,6 +1016,7 @@ Testing reading swiss format file SwissProt/sp002
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P54101).
@ -1001,6 +1041,7 @@ Testing reading swiss format file SwissProt/sp003
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P42655).
@ -1025,6 +1066,7 @@ Testing reading swiss format file SwissProt/sp004
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P23082).
@ -1049,6 +1091,7 @@ Testing reading swiss format file SwissProt/sp005
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P24973).
@ -1073,6 +1116,7 @@ Testing reading swiss format file SwissProt/sp006
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P39896).
@ -1097,6 +1141,7 @@ Testing reading swiss format file SwissProt/sp007
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O95832).
@ -1121,6 +1166,7 @@ Testing reading swiss format file SwissProt/sp008
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01892).
@ -1145,6 +1191,7 @@ Testing reading swiss format file SwissProt/sp009
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=O23729).
@ -1169,6 +1216,7 @@ Testing reading swiss format file SwissProt/sp010
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
@ -1193,6 +1241,7 @@ Testing reading swiss format file SwissProt/sp011
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P16235).
@ -1217,6 +1266,7 @@ Testing reading swiss format file SwissProt/sp012
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q9Y736).
@ -1241,6 +1291,7 @@ Testing reading swiss format file SwissProt/sp013
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P82909).
@ -1265,6 +1316,7 @@ Testing reading swiss format file SwissProt/sp014
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P12166).
@ -1289,6 +1341,7 @@ Testing reading swiss format file SwissProt/sp015
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=IPI00383150).
@ -1313,6 +1366,7 @@ Testing reading swiss format file SwissProt/sp016
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01100).
@ -1337,6 +1391,7 @@ Testing reading swiss format file Registry/EDD_RAT.dat
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q62671).
@ -1361,6 +1416,7 @@ Testing reading uniprot-xml format file SwissProt/uni001
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q91G55).
@ -1392,6 +1448,8 @@ Testing reading uniprot-xml format file SwissProt/uni002
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P0C9J6).
@ -1417,6 +1475,7 @@ Testing reading uniprot-xml format file SwissProt/Q13639.xml
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
@ -1441,6 +1500,7 @@ Testing reading swiss format file SwissProt/Q13639.txt
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=Q13639).
@ -1465,6 +1525,7 @@ Testing reading genbank format file GenBank/noref.gb
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NM_006141.1).
@ -1499,6 +1560,8 @@ Testing reading genbank format file GenBank/cor6_6.gb
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AF297471.1).
@ -1524,6 +1587,7 @@ Testing reading genbank format file GenBank/iro.gb
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL109817.1).
@ -1548,6 +1612,7 @@ Testing reading genbank format file GenBank/pri1.gb
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U05344.1).
@ -1572,6 +1637,7 @@ Testing reading genbank format file GenBank/arab1.gb
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AC007323.5).
@ -1596,6 +1662,7 @@ Testing reading genbank format file GenBank/protein_refseq.gb
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1).
@ -1620,6 +1687,7 @@ Testing reading genbank format file GenBank/protein_refseq2.gb
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_034640.1).
@ -1644,6 +1712,7 @@ Testing reading genbank format file GenBank/extra_keywords.gb
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL138972.1).
@ -1668,6 +1737,7 @@ Testing reading genbank format file GenBank/one_of.gb
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U18266.1).
@ -1700,6 +1770,7 @@ Testing reading genbank format file GenBank/origin_line.gb
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_002678.1).
@ -1724,6 +1795,7 @@ Testing reading genbank format file GenBank/blank_seq.gb
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NP_001832.1).
@ -1748,6 +1820,7 @@ Testing reading genbank format file GenBank/dbsource_wrap.gb
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=P01485).
@ -1772,6 +1845,7 @@ Testing reading genbank format file GenBank/NC_005816.gb
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_005816.1).
@ -1796,6 +1870,7 @@ Testing reading genbank format file GenBank/NC_000932.gb
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_000932.1).
@ -1820,6 +1895,7 @@ Testing reading genbank format file GenBank/pBAD30.gb
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=pBAD30).
@ -1851,6 +1927,8 @@ Testing reading genbank format file GenBank/gbvrl1_start.seq
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AB000050.1).
@ -1876,6 +1954,7 @@ Testing reading genbank format file GFF/NC_001422.gbk
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=NC_001422.1).
@ -1910,6 +1989,8 @@ Testing reading embl format file EMBL/epo_prt_selection.embl
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CQ797900.1).
@ -1936,6 +2017,7 @@ Testing reading embl format file EMBL/TRBG361.embl
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=X56734.1).
@ -1960,6 +2042,7 @@ Testing reading embl format file EMBL/DD231055_edited.embl
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=DD231055.1).
@ -1984,6 +2067,7 @@ Testing reading embl format file EMBL/SC10H5.embl
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AL031232).
@ -2008,6 +2092,7 @@ Testing reading embl format file EMBL/U87107.embl
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=U87107.1).
@ -2032,6 +2117,7 @@ Testing reading embl format file EMBL/AAA03323.embl
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AAA03323.1).
@ -2056,6 +2142,7 @@ Testing reading embl format file EMBL/AE017046.embl
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=AE017046.1).
@ -2090,6 +2177,7 @@ Testing reading embl format file EMBL/A04195.imgt
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
@ -2114,6 +2202,7 @@ Testing reading imgt format file EMBL/A04195.imgt
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A04195).
@ -2148,6 +2237,7 @@ Testing reading stockholm format file Stockholm/simple.sth as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2191,6 +2281,7 @@ Testing reading stockholm format file Stockholm/funny.sth as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2234,6 +2325,8 @@ Testing reading phylip format file Phylip/reference_dna.phy as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Failed: Whitespace not allowed in identifier: B. virgini
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2277,6 +2370,8 @@ Testing reading phylip format file Phylip/reference_dna2.phy as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Failed: Whitespace not allowed in identifier: B. virgini
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2320,6 +2415,7 @@ Testing reading phylip format file Phylip/hennigian.phy as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2363,6 +2459,8 @@ Testing reading phylip format file Phylip/horses.phy as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Failed: Whitespace not allowed in identifier: M. secundu
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2406,6 +2504,7 @@ Testing reading phylip format file Phylip/random.phy as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2446,6 +2545,7 @@ Testing reading phylip format file Phylip/interlaced.phy as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2488,6 +2588,7 @@ Testing reading phylip format file Phylip/interlaced2.phy as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2530,6 +2631,7 @@ Testing reading emboss format file Emboss/alignret.txt as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2568,6 +2670,8 @@ Testing reading emboss format file Emboss/needle.txt
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2606,6 +2710,7 @@ Testing reading emboss format file Emboss/water.txt as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2641,6 +2746,8 @@ Testing reading phd format file Phd/phd1
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Checking can write/read as 'fastq-illumina' format
@ -2662,6 +2769,7 @@ Testing reading phd format file Phd/phd2
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Checking can write/read as 'fastq-illumina' format
@ -2684,6 +2792,7 @@ Testing reading phd format file Phd/phd_solexa
Checking can write/read as 'phylip' format
Failed: Repeated name 'HWI-EAS94_' (originally 'HWI-EAS94_4_1_1_537_446'), possibly due to truncation
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Checking can write/read as 'fastq-illumina' format
@ -2704,6 +2813,7 @@ Testing reading phd format file Phd/phd_454
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Checking can write/read as 'fastq-illumina' format
@ -2729,6 +2839,8 @@ Testing reading ace format file Ace/contig1.ace
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Checking can write/read as 'fastq-illumina' format
@ -2749,6 +2861,7 @@ Testing reading ace format file Ace/consed_sample.ace
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Checking can write/read as 'fastq-illumina' format
@ -2768,6 +2881,7 @@ Testing reading ace format file Ace/seq.cap.ace
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Checking can write/read as 'fastq-illumina' format
@ -2797,6 +2911,8 @@ Testing reading ig format file IntelliGenetics/TAT_mase_nuc.txt
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2840,6 +2956,7 @@ Testing reading ig format file IntelliGenetics/VIF_mase-pro.txt as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2878,6 +2995,8 @@ Testing reading ig format file IntelliGenetics/vpu_nucaligned.txt
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -2916,6 +3035,8 @@ Testing reading pir format file NBRF/B_nuc.pir
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01135).
@ -2951,6 +3072,8 @@ Testing reading pir format file NBRF/Cw_prot.pir
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00484).
@ -2985,6 +3108,8 @@ Testing reading pir format file NBRF/DMA_nuc.pir
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA00488).
@ -3020,6 +3145,8 @@ Testing reading pir format file NBRF/DMB_prot.pir
Failed: Sequences must all be the same length
Checking can write/read as 'stockholm' format
Failed: Sequences must all be the same length
Checking can write/read as 'phylip-extended' format
Failed: Sequences must all be the same length
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=HLA:HLA01083).
@ -3055,6 +3182,7 @@ Testing reading pir format file NBRF/clustalw.pir as an alignment
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Checking can write/read as 'fastq' format
Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=815Parelaphostrongylus_odocoil).
@ -3093,6 +3221,7 @@ Testing reading fasta format file Quality/example.fasta as an alignment
Checking can write/read as 'phylip' format
Failed: Repeated name 'EAS54_6_R1' (originally 'EAS54_6_R1_2_1_540_792'), possibly due to truncation
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -3126,6 +3255,7 @@ Testing reading qual format file Quality/example.qual
Checking can write/read as 'phylip' format
Failed: Repeated name 'EAS54_6_R1' (originally 'EAS54_6_R1_2_1_540_792'), possibly due to truncation
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -3162,6 +3292,7 @@ Testing reading fastq format file Quality/example.fastq as an alignment
Checking can write/read as 'phylip' format
Failed: Repeated name 'EAS54_6_R1' (originally 'EAS54_6_R1_2_1_540_792'), possibly due to truncation
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -3200,6 +3331,7 @@ Testing reading fastq format file Quality/tricky.fastq as an alignment
Checking can write/read as 'phylip' format
Failed: Repeated name '071113_EAS' (originally '071113_EAS56_0053:1:1:153:10'), possibly due to truncation
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -3223,6 +3355,7 @@ Testing reading fastq format file Quality/sanger_faked.fastq
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -3246,6 +3379,7 @@ Testing reading fastq format file Quality/sanger_93.fastq
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -3269,6 +3403,7 @@ Testing reading fastq-illumina format file Quality/illumina_faked.fastq
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -3292,6 +3427,7 @@ Testing reading fastq-solexa format file Quality/solexa_faked.fastq
Checking can write/read as 'clustal' format
Checking can write/read as 'phylip' format
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format
@ -3331,6 +3467,7 @@ Testing reading fastq-solexa format file Quality/solexa_example.fastq as an alig
Checking can write/read as 'phylip' format
Failed: Repeated name 'SLXA-B3_64' (originally 'SLXA-B3_649_FC8437_R1_1_1_362_549'), possibly due to truncation
Checking can write/read as 'stockholm' format
Checking can write/read as 'phylip-extended' format
Checking can write/read as 'embl' format
Failed: Need a DNA, RNA or Protein alphabet
Checking can write/read as 'fastq' format

4
Tests/test_AlignIO.py
View File

@ -45,6 +45,7 @@ test_files = [
("phylip",10, 1, 'Phylip/random.phy'),
("phylip", 3, 1, 'Phylip/interlaced.phy'),
("phylip", 4, 1, 'Phylip/interlaced2.phy'),
("phylip-extended", 12, 1, 'ExtendedPhylip/primates.phyx'),
("emboss", 4, 1, 'Emboss/alignret.txt'),
("emboss", 2, 5, 'Emboss/needle.txt'),
("emboss", 2, 1, 'Emboss/needle_asis.txt'),
@ -175,6 +176,9 @@ def simple_alignment_comparison(alignments, alignments2, format):
if format=="phylip":
assert r1.id.replace("[","").replace("]","")[:10] == r2.id, \
"'%s' vs '%s'" % (r1.id, r2.id)
elif format=="phylip-extended":
assert r1.id.replace(" ", "").replace(':', '|') == r2.id, \
"'%s' vs '%s'" % (r1.id, r2.id)
elif format=="clustal":
assert r1.id.replace(" ","_")[:30] == r2.id, \
"'%s' vs '%s'" % (r1.id, r2.id)

11
Tests/test_SeqIO.py
View File

@ -33,14 +33,16 @@ dna_alphas = [Alphabet.generic_dna]
rna_alphas = [Alphabet.generic_rna]
nucleotide_alphas = [Alphabet.generic_nucleotide,
Alphabet.Gapped(Alphabet.generic_nucleotide)]
no_alpha_formats = ["fasta","clustal","phylip","tab","ig","stockholm","emboss",
"fastq","fastq-solexa","fastq-illumina","qual"]
no_alpha_formats = ["fasta","clustal","phylip","phylip-extended","tab","ig",
"stockholm","emboss", "fastq","fastq-solexa",
"fastq-illumina","qual"]
possible_unknown_seq_formats = ["qual", "genbank", "gb", "embl", "imgt"]
#List of formats including alignment only file formats we can read AND write.
#The list is initially hard coded to preserve the original order of the unit
#test output, with any new formats added since appended to the end.
test_write_read_alignment_formats = ["fasta","clustal","phylip","stockholm"]
test_write_read_alignment_formats = ["fasta","clustal","phylip","stockholm",
"phylip-extended"]
for format in sorted(SeqIO._FormatToWriter):
if format not in test_write_read_alignment_formats:
test_write_read_alignment_formats.append(format)
@ -352,6 +354,9 @@ def check_simple_write_read(records, indent=" "):
if format=="phylip":
assert r1.id.replace("[","").replace("]","")[:10] == r2.id, \
"'%s' vs '%s'" % (r1.id, r2.id)
elif format=="phylip-extended":
assert r1.id.replace(" ", "").replace(':', '|') == r2.id, \
"'%s' vs '%s'" % (r1.id, r2.id)
elif format=="clustal":
assert r1.id.replace(" ","_")[:30] == r2.id, \
"'%s' vs '%s'" % (r1.id, r2.id)

4
Tests/test_SeqIO_write.py
View File

@ -62,7 +62,7 @@ test_records = [
SeqRecord(Seq("HNGFTALEGEIHHLTHGEKVAF",Alphabet.generic_protein), id="Gamma")],
"alignment with repeated record",
[(["stockholm"],ValueError,"Duplicate record identifier: Beta"),
(["phylip"],ValueError,"Repeated name 'Beta' (originally 'Beta'), possibly due to truncation")]),
(["phylip","phylip-extended"],ValueError,"Repeated name 'Beta' (originally 'Beta'), possibly due to truncation")]),
]
# Meddle with the annotation too:
assert test_records[4][1] == "3 DNA seq alignment with CR/LF in name/descr"
@ -85,7 +85,7 @@ class WriterTests(unittest.TestCase):
"""
#TODO - Check the exception messages?
lengths = len(set(len(r) for r in records))
if not records and format in ["stockholm", "phylip", "nexus", "clustal", "sff"]:
if not records and format in ["stockholm", "phylip", "phylip-extended", "nexus", "clustal", "sff"]:
self.check_write_fails(records, format, ValueError,
"Must have at least one sequence")
elif lengths > 1 and format in AlignIO._FormatToWriter: