biopython

1MRR_A.gp

Test case for GenPept files with bond features

2013-12-10 10:22:50 +00:00

addgene-plasmid-11664-sequence-180430.gbk

Improve GenBank parsing for origin-spanning features (#3881 )

2022-03-22 09:54:28 +00:00

addgene-plasmid-39296-sequence-49545.gbk

Improve GenBank parsing for origin-spanning features (#3881 )

2022-03-22 09:54:28 +00:00

arab1.gb

Updated GenBank tests to check the ability to write out GenBank records.

2001-05-19 17:13:16 +00:00

bad_loc_wrap.gb

Edited version of first 6000bp from arab1.gb

2015-06-03 09:23:10 +01:00

bad_origin_wrap_CDS.gb

Automatically fix implicit origin wrapping in GenBank/EMBL (#1770 )

2018-08-27 10:48:22 +01:00

bad_origin_wrap_fuzzy.gb

Automatically fix malformed origin wrapping for fuzzy location in GenBank (#2162 )

2019-07-06 18:03:43 +01:00

bad_origin_wrap_linear.gb

Automatically fix implicit origin wrapping in GenBank/EMBL (#1770 )

2018-08-27 10:48:22 +01:00

bad_origin_wrap.gb

Fix origin wrapping inside join()

2019-09-05 17:04:51 +01:00

blank_seq.gb

Fix for GenBank problem reported by Leighton Pritchard. If you had a value-less

2004-05-05 17:48:26 +00:00

cor6_6.gb

Tests for GenBank and Location Parsers

2001-01-20 21:08:33 +00:00

cor6_6.gb.bgz

Include multi-record GenBank BGZF test case

2012-06-21 16:48:33 +01:00

dbsource_wrap.gb

Fixes and Tests for another RefSeq-style file. This one had a block DBSOURCE line, and extra Bond-related tags in the feature table.

2002-04-16 15:45:26 +00:00

DS830848.gb

Matching EMBL and GenBank example with PR project line

2015-12-03 14:17:11 +00:00

empty_accession.gbk

SeqIO: Don't crash when indexing empty VERSION and ACCESSION lines

2017-07-31 15:51:58 +01:00

empty_feature_qualifier.gb

SeqIO.GenBank: survive empty feature qualifiers

2013-06-25 01:22:23 +01:00

empty_version.gbk

SeqIO: Don't crash when indexing empty VERSION and ACCESSION lines

2017-07-31 15:51:58 +01:00

EU851978_output.gbk

Fix empty structured comment parser (#4492 )

2023-12-19 14:11:23 +00:00

EU851978.gbk

Fix empty structured comment parser (#4492 )

2023-12-19 14:11:23 +00:00

extra_keywords.gb

Cope with odd GenBank features from ApE (Bug 3176)

2011-02-09 10:45:53 +00:00

EZ116220.gb

Add test GenBank file and unit test

2024-12-31 18:13:30 +00:00

gbvrl1_start.seq

GenBank test case with an NCBI header

2007-03-12 16:47:44 +00:00

GU949562.1.gb

Parse multiline structured comments in GenBank files

2019-12-04 13:16:19 +00:00

HM138502_output.gbk

Write structured GenBank comments; robust parsing

2016-12-22 14:39:52 +09:00

HM138502.gbk

Parse GenBank structured comments.

2016-01-04 19:01:41 +09:00

invalid_locus_line_spacing.gb

Adding test case from Kai Blin; Fixed some warnings.

2013-06-17 12:22:11 +01:00

invalid_misc_feature.gb

GenBank: Don't die parsing files with too short feature qualifiers

2013-06-25 01:24:23 +01:00

invalid_product.gb

GenBank: Give better error output on invalid qualifiers

2013-08-26 14:55:35 +01:00

invalid_structured_comment.gb

Handle malformed structured comment (#2851 )

2020-04-28 12:55:25 +01:00

iro.gb

Updated GenBank tests to check the ability to write out GenBank records.

2001-05-19 17:13:16 +00:00

KF527485_output.gbk

Write structured GenBank comments; robust parsing

2016-12-22 14:39:52 +09:00

KF527485.gbk

Parse GenBank structured comments.

2016-01-04 19:01:41 +09:00

NC_000932.faa

Using Arabidopsis thaliana chloroplast for testing, downloaded from NCBI using Entrez

2009-05-06 10:58:09 +00:00

NC_000932.gb

Using Arabidopsis thaliana chloroplast for testing, downloaded from NCBI using Entrez

2009-05-06 10:58:09 +00:00

NC_000932.gb.bgz

BGZF compressed GenBank file as test case

2012-06-21 16:48:30 +01:00

NC_005816.faa

FASTA files to go with the existing GenBank file NC_005816

2009-04-22 13:19:22 +00:00

NC_005816.ffn

Update NC_005816 GenBank example files, note slight change to DBLINK line formatting

2011-08-29 07:34:01 +01:00

NC_005816.fna

FASTA files to go with the existing GenBank file NC_005816

2009-04-22 13:19:22 +00:00

NC_005816.gb

Update NC_005816 GenBank example files, note slight change to DBLINK line formatting

2011-08-29 07:34:01 +01:00

NC_005816.tsv

Include a simple tabbed file in the Bio.SeqIO.index() tests

2010-05-06 17:28:06 +01:00

negative_location.gb

GenBank: Explicitly check for current behaviour on negative location coordinates

2015-07-17 14:05:51 +02:00

no_end_marker.gb

GenBank: Cope with records that miss an end-of-record marker at the end of the file

2013-01-08 17:05:37 +00:00

no_origin_no_end.gb

GenBank: Avoid infinite loop while parsing

2015-04-08 11:53:18 +02:00

noref_date_warning.gb

4775: raise warnings instead of errors if dashes are not in the expected places for dates

2024-12-31 18:44:31 +00:00

noref.gb

Added test to make sure GenBank parser handles records with no REFERENCE section, from Bug Report 30.

2001-05-04 16:56:41 +00:00

NP_416719.gbwithparts

GenPept file with CONTIG and ORIGIN lines

2013-07-12 15:31:28 +01:00

NT_019265.gb

Updated GenBank tests to handle RefSeq and other non-handled records found while working through GenBank downloads.

2001-11-07 16:59:15 +00:00

one_of.gb

Updated GenBank tests to handle RefSeq and other non-handled records found while working through GenBank downloads.

2001-11-07 16:59:15 +00:00

origin_line.gb

Check the LOCUS line sequence length matches the actual length of the sequence found at the end of the record. Fixed origin_line.gb example to obey this.

2009-03-28 22:52:07 +00:00

pBAD30.gb

Adding test GenBank file from VectorNTI without date in LOCUS line (bug 2872)

2009-07-08 10:15:27 +00:00

pri1.gb

Updated GenBank tests to check the ability to write out GenBank records.

2001-05-19 17:13:16 +00:00

protein_refseq2.gb

Resolved problem with db_xref in GenBank/protein_refseq.gb, the NCBI have replaced an 'odd' entry - thus the additional test GenBank file for NP_034640

2007-11-20 22:17:59 +00:00

protein_refseq.gb

GenBank tests to check protein REFSEQ records.

2001-09-19 01:14:35 +00:00

qualifier_escaping_read.gb

Escaping double quotes in EMBL/GenBank feature qualifiers (#1689 )

2018-10-04 10:43:04 +01:00

qualifier_escaping_write.gb

Escaping double quotes in EMBL/GenBank feature qualifiers (#1689 )

2018-10-04 10:43:04 +01:00

tls_KDHP01000000.gb

Fix newline

2020-02-11 12:46:29 +00:00

tsa_acropora.gb

Minimal support for GenBank TSA files (#2269 )

2019-09-17 11:49:26 +01:00

wrong_sequence_indent.gb

GenBank: Survive input with sequence indented one space too many

2013-01-08 17:05:37 +00:00