[med-svn] [Git][med-team/busco][master] 4 commits: routine-update: New upstream version
Nilesh Patra
gitlab at salsa.debian.org
Thu Oct 8 14:06:15 BST 2020
Nilesh Patra pushed to branch master at Debian Med / busco
Commits:
29d9b6a6 by Nilesh Patra at 2020-10-08T18:31:31+05:30
routine-update: New upstream version
- - - - -
0dba4338 by Nilesh Patra at 2020-10-08T18:31:32+05:30
New upstream version 4.1.4
- - - - -
92226cc8 by Nilesh Patra at 2020-10-08T18:31:36+05:30
Update upstream source from tag 'upstream/4.1.4'
Update to upstream version '4.1.4'
with Debian dir 0a4439f7629c750cf2d4f86d87ae5627c7c0ff8d
- - - - -
b98285ec by Nilesh Patra at 2020-10-08T18:31:52+05:30
routine-update: Ready to upload to unstable
- - - - -
5 changed files:
- CHANGELOG
- README.md
- debian/changelog
- src/busco/BuscoTools.py
- src/busco/_version.py
Changes:
=====================================
CHANGELOG
=====================================
@@ -1,3 +1,6 @@
+4.1.4
+- Fix Augustus parsing bug
+
4.1.3
- Issue #296 fixed
- Issue #305 fixed
=====================================
README.md
=====================================
@@ -1,6 +1,8 @@
**BUSCOv4 - Benchmarking sets of Universal Single-Copy Orthologs.**
-######Note: v4.1.3 is the latest stable release. To access v5.beta clone this repository and checkout the v5 branch with `git checkout v5.beta`
+######Note: v4.1.4 is the latest stable release. To access v5.beta clone this repository and checkout the v5 branch with `git checkout v5.beta`
+
+######Note: A critical bug was discovered to have been introduced in v4.1.3. Any analysis on eukaryote genomes done with this version should be repeated with v4.1.4.
For full documentation please consult the user guide: https://busco.ezlab.org/busco_userguide.html
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+busco (4.1.4-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+
+ -- Nilesh Patra <npatra974 at gmail.com> Thu, 08 Oct 2020 18:31:52 +0530
+
busco (4.1.3-1) unstable; urgency=medium
* Team Upload.
=====================================
src/busco/BuscoTools.py
=====================================
@@ -512,7 +512,8 @@ class HMMERRunner(BaseRunner):
elif isinstance(self.input_sequences, list):
input_files = [f for f in self.input_sequences if os.path.basename(f).startswith(busco_id)]
for seq_filename in input_files:
- output_filename = os.path.basename(seq_filename).rpartition(".faa")[0] + ".out"
+ filename_parts = os.path.basename(seq_filename).rpartition(".faa")
+ output_filename = filename_parts[0] + ".out" + filename_parts[-1]
yield busco_id, seq_filename, output_filename
@property
@@ -1931,38 +1932,50 @@ class AugustusRunner(BaseRunner):
for line in f:
- if aa_sequence_section and (line.startswith("# end gene") or "]" in line):
- aa_sequence_section = False
- completed_record = True
- if gene_id is not None:
- aa_sequence = "".join(aa_sequence_parts)
- nt_sequence = "".join(nt_sequence_parts)
- seq_record_aa = SeqRecord(Seq(aa_sequence.upper()), id=gene_id)
- seq_record_nt = SeqRecord(Seq(nt_sequence.upper()), id=gene_id)
- sequences_aa.append(seq_record_aa)
- sequences_nt.append(seq_record_nt)
- aa_sequence_parts = []
- nt_sequence_parts = []
- gene_id = None
- continue
-
- if aa_sequence_section and line.startswith("# sequence of block"):
- aa_sequence_section = False
- continue
-
if aa_sequence_section:
- line = line.strip().lstrip("# ").rstrip("]")
- aa_sequence_parts.append(line)
- continue
+ if "]" in line:
+ line = line.strip().lstrip("# ").rstrip("]")
+ aa_sequence_parts.append(line)
+ aa_sequence_section = False
+ completed_record = True
+ if gene_id is not None:
+ aa_sequence = "".join(aa_sequence_parts)
+ nt_sequence = "".join(nt_sequence_parts)
+ seq_record_aa = SeqRecord(Seq(aa_sequence.upper()), id=gene_id)
+ seq_record_nt = SeqRecord(Seq(nt_sequence.upper()), id=gene_id)
+ sequences_aa.append(seq_record_aa)
+ sequences_nt.append(seq_record_nt)
+ aa_sequence_parts = []
+ nt_sequence_parts = []
+ gene_id = None
+ continue
+
+ else:
+ line = line.strip().lstrip("# ").rstrip("]")
+ aa_sequence_parts.append(line)
+ continue
if line.startswith("# protein"):
nt_sequence_section = False
aa_sequence_section = True
if "]" in line:
+ line = line.strip().rstrip("]").split("[")
+ aa_sequence_parts.append(line[1])
aa_sequence_section = False
completed_record = True
- line = line.strip().rstrip("]").split("[")
- aa_sequence_parts.append(line[1])
+ if gene_id is not None:
+ aa_sequence = "".join(aa_sequence_parts)
+ nt_sequence = "".join(nt_sequence_parts)
+ seq_record_aa = SeqRecord(Seq(aa_sequence.upper()), id=gene_id)
+ seq_record_nt = SeqRecord(Seq(nt_sequence.upper()), id=gene_id)
+ sequences_aa.append(seq_record_aa)
+ sequences_nt.append(seq_record_nt)
+ aa_sequence_parts = []
+ nt_sequence_parts = []
+ gene_id = None
+ else:
+ line = line.strip().rstrip("]").split("[")
+ aa_sequence_parts.append(line[1])
continue
if nt_sequence_section:
=====================================
src/busco/_version.py
=====================================
@@ -6,4 +6,4 @@ Copyright (c) 2016-2020, Evgeny Zdobnov (ez at ezlab.org)
Licensed under the MIT license. See LICENSE.md file.
"""
-__version__ = "4.1.3"
+__version__ = "4.1.4"
View it on GitLab: https://salsa.debian.org/med-team/busco/-/compare/3edc0c112fc9c02d94ed7f9ab93056902f058a61...b98285ec5e8d1cf4ce5fd954ca481e06a0932da5
--
View it on GitLab: https://salsa.debian.org/med-team/busco/-/compare/3edc0c112fc9c02d94ed7f9ab93056902f058a61...b98285ec5e8d1cf4ce5fd954ca481e06a0932da5
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