frozenleaves/biopython
1
0
Fork 0
mirror of https://github.com/biopython/biopython.git synced 2025-10-20 13:43:47 +08:00
Code Issues Packages Projects Releases Wiki Activity

Adding 454 and Solexa derived PHD files from the Consed author David Gordon (see also Bug 2865)

Browse Source
This commit is contained in:
peterc
2009-07-02 09:25:20 +00:00
parent 28f8383aa5
commit a520762036
3 changed files with 150 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files

48
Tests/Phd/phd_454 Normal file
View File

@ -0,0 +1,48 @@
BEGIN_SEQUENCE EBE03TV04IHLTF.77-243 1
BEGIN_COMMENT
CHROMAT_FILE: sff:reads.sff:EBE03TV04IHLTF
QUALITY_LEVELS: 99
TIME: Thu Jul 27 12:33:48 2000
TRACE_ARRAY_MIN_INDEX: 0
TRACE_ARRAY_MAX_INDEX: 4723
CHEM: 454
END_COMMENT
BEGIN_DNA
g 37 91
g 37 110
g 37 129
g 37 148
a 37 167
t 37 186
g 37 205
a 37 224
a 37 243
a 37 262
g 37 281
g 37 300
g 37 319
a 26 4385
t 26 4404
c 26 4423
t 30 4442
c 33 4461
g 33 4480
g 33 4499
t 33 4518
g 33 4537
g 36 4556
t 36 4575
a 33 4594
g 33 4613
g 33 4632
t 36 4651
g 26 4670
a 22 4689
END_DNA
END_SEQUENCE

99
Tests/Phd/phd_solexa Normal file
View File

@ -0,0 +1,99 @@
# solexa file ../solexa_dir/solexa_reads.fastq (beginning)
BEGIN_SEQUENCE HWI-EAS94_4_1_1_537_446 1
BEGIN_COMMENT
TIME: Wed Dec 24 11:21:50 2008
CHEM: solexa
END_COMMENT
BEGIN_DNA
g 30
c 30
c 30
a 30
a 30
t 30
c 30
a 30
g 30
g 30
t 30
t 30
t 30
c 30
t 30
c 30
t 30
g 30
c 30
a 30
a 28
g 23
c 30
c 30
c 30
c 30
t 30
t 30
t 28
a 22
g 8
c 22
a 7
g 15
c 15
t 15
g 10
a 10
g 11
c 15
END_DNA
END_SEQUENCE
BEGIN_SEQUENCE HWI-EAS94_4_1_1_602_99 1
BEGIN_COMMENT
TIME: Wed Dec 24 11:21:50 2008
CHEM: solexa
END_COMMENT
BEGIN_DNA
g 30
c 30
c 30
a 30
t 30
g 30
g 30
c 30
a 30
c 30
a 30
t 30
a 30
t 30
a 30
t 30
g 30
a 30
a 30
g 30
g 30
t 30
c 30
a 30
g 30
a 30
g 16
g 30
a 28
c 22
a 22
a 22
c 14
t 15
t 15
g 5
c 10
t 15
g 10
t 5
END_DNA
END_SEQUENCE

4
Tests/test_SeqIO.py
View File

@ -142,7 +142,9 @@ test_files = [ \
#Following PHD (PHRAP) sequencing files are also used in test_Phd.py
("phd", False, 'Phd/phd1', 3),
("phd", False, 'Phd/phd2', 1),
#Following ACE assembly files are also used in test_Phd.py
("phd", False, 'Phd/phd_solexa', 2),
("phd", False, 'Phd/phd_454', 1),
#Following ACE assembly files are also used in test_Ace.py
("ace", False, 'Ace/contig1.ace', 2),
("ace", False, 'Ace/consed_sample.ace', 1),
("ace", False, 'Ace/seq.cap.ace', 1),