[med-svn] [Git][med-team/cat-bat][upstream] New upstream version 5.2.3

[Nilesh Patra]

Nilesh Patra pushed to branch upstream at Debian Med / cat-bat


Commits:
9eb95c03 by Nilesh Patra at 2021-02-11T19:05:36+05:30
New upstream version 5.2.3
- - - - -


4 changed files:

- CAT_pack/about.py
- CAT_pack/add_names.py
- CAT_pack/prepare.py
- CHANGELOG.md


Changes:

=====================================
CAT_pack/about.py
=====================================
@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
 
 __author__ = 'F. A. Bastiaan von Meijenfeldt'
-__version__ = '5.2.2'
-__date__ = '15 January, 2021'
+__version__ = '5.2.3'
+__date__ = '10 February, 2021'


=====================================
CAT_pack/add_names.py
=====================================
@@ -127,8 +127,7 @@ def run():
 
                 continue
 
-            if (line[1].startswith('no taxid found') or
-                    line[2].startswith('no taxid found')):
+            if any([c.startswith('no taxid found') for c in line[2:4]]):
                 # ORF has database hits but the accession number is not found
                 # in the taxonomy files.
                 outf1.write('{0}\n'.format('\t'.join(line)))


=====================================
CAT_pack/prepare.py
=====================================
@@ -106,7 +106,7 @@ def download_taxonomy_files(taxonomy_folder, date, log_file, quiet):
             'taxonomy folder.'.format(url))
     shared.give_user_feedback(message, log_file, quiet)
 
-    url = 'ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz'
+    url = '{0}taxdump.tar.gz'.format(url)
     tmp_taxonomy_file = '{0}{1}.taxdump.tar.gz'.format(taxonomy_folder, date)
     try:
         urllib.request.urlretrieve(url, tmp_taxonomy_file)
@@ -153,8 +153,7 @@ def download_prot_accession2taxid_file(
             url)
     shared.give_user_feedback(message, log_file, quiet)
 
-    url = ('ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/'
-            'prot.accession2taxid.FULL.gz')
+    url = '{0}prot.accession2taxid.FULL.gz'.format(url)
     try:
         urllib.request.urlretrieve(url, prot_accession2taxid_file)
     except:
@@ -187,7 +186,7 @@ def download_nr(nr_file, log_file, quiet):
             url)
     shared.give_user_feedback(message, log_file, quiet)
 
-    url = 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz'
+    url = '{0}nr.gz'.format(url)
     try:
         urllib.request.urlretrieve(url, nr_file)
     except:


=====================================
CHANGELOG.md
=====================================
@@ -1,5 +1,8 @@
 # Changelog
 
+## 5.2.3
+Minor bug fix for `CAT add_names`.
+
 ## 5.2.2
 We have added the DIAMOND specific `--no_self_hits` flag. We have also added some extra checks and removed redundancy from the parser code. Databases constructed by `CAT prepare` now have a slightly different naming scheme.
 



View it on GitLab: https://salsa.debian.org/med-team/cat-bat/-/commit/9eb95c036fab37ced872b11389dfad262df3564b

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View it on GitLab: https://salsa.debian.org/med-team/cat-bat/-/commit/9eb95c036fab37ced872b11389dfad262df3564b
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