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 -- View it on GitLab: https://salsa.debian.org/med-team/cat-bat/-/commit/9eb95c036fab37ced872b11389dfad262df3564b You're receiving this email because of your account on salsa.debian.org.
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