[med-svn] [Git][med-team/python-cgecore][master] 4 commits: New upstream version 1.5.4+ds
Steffen Möller
gitlab at salsa.debian.org
Tue May 5 16:41:17 BST 2020
Steffen Möller pushed to branch master at Debian Med / python-cgecore
Commits:
34790c46 by Steffen Moeller at 2020-05-05T17:40:36+02:00
New upstream version 1.5.4+ds
- - - - -
57172ac2 by Steffen Moeller at 2020-05-05T17:40:36+02:00
routine-update: New upstream version
- - - - -
d989c9ca by Steffen Moeller at 2020-05-05T17:40:36+02:00
Update upstream source from tag 'upstream/1.5.4+ds'
Update to upstream version '1.5.4+ds'
with Debian dir 947a9acb123216bcacaa0866759a485fb0c47b10
- - - - -
47f3267d by Steffen Moeller at 2020-05-05T17:40:47+02:00
routine-update: Ready to upload to unstable
- - - - -
4 changed files:
- PKG-INFO
- cgecore/__init__.py
- cgecore/blaster/blaster.py
- debian/changelog
Changes:
=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 1.0
Name: cgecore
-Version: 1.5.3
+Version: 1.5.4
Summary: Center for Genomic Epidemiology Core Module
Home-page: https://bitbucket.org/genomicepidemiology/cge_core_module
Author: Center for Genomic Epidemiology
=====================================
cgecore/__init__.py
=====================================
@@ -13,7 +13,7 @@ from .argumentparsing import (check_file_type, get_arguments, get_string,
)
#####################
-__version__ = "1.5.3"
+__version__ = "1.5.4"
__all__ = [
"argumentparsing",
"cmdline",
=====================================
cgecore/blaster/blaster.py
=====================================
@@ -194,32 +194,31 @@ class Blaster():
'strand': strand,
'perc_coverage': perc_coverage
}
- else:
- best_hsp={}
- continue
-
- # Saving the result if any
- if best_hsp:
- save = 1
-
- # If there are other gene alignments they are compared
- if gene_results:
- tmp_gene_split = gene_split
- tmp_results = gene_results
- # Compare the hit results
- save, gene_split, gene_results = (
- self.compare_results(save, best_hsp,
- tmp_results,
- tmp_gene_split,
- allowed_overlap)
- )
-
- # If the hit is not overlapping with other hit
- # seqeunces it is kept
- if save == 1:
- # DEBUG
- print("Saving: {}".format(hit_id))
- gene_results[hit_id] = best_hsp
+
+
+
+ # Saving the result if any
+ if best_hsp:
+ save = 1
+
+ # If there are other gene alignments they are compared
+ if gene_results:
+ tmp_gene_split = gene_split
+ tmp_results = gene_results
+ # Compare the hit results
+ save, gene_split, gene_results = (
+ self.compare_results(save, best_hsp,
+ tmp_results,
+ tmp_gene_split,
+ allowed_overlap)
+ )
+
+ # If the hit is not overlapping with other hit
+ # seqeunces it is kept
+ if save == 1:
+ # DEBUG
+ print("Saving: {}".format(hit_id))
+ gene_results[hit_id] = best_hsp
result_handle.close()
@@ -464,7 +463,7 @@ class Blaster():
# TODO
# If new_score == old_score but identity and coverages are not the same.
- # which gene should be chosen?? Now they are both kept.
+ # which gene should be chosen?? Now they are both keept.
# Save a split if the new hit creats one - both
# hits are saved
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+python-cgecore (1.5.4+ds-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 05 May 2020 17:40:39 +0200
+
python-cgecore (1.5.3+ds-1) unstable; urgency=medium
* Team upload.
View it on GitLab: https://salsa.debian.org/med-team/python-cgecore/-/compare/cbf0bdd8cd64faa14babb70bc98ab05a25583572...47f3267dd626b2a83b755db6b4bcf26442ad3908
--
View it on GitLab: https://salsa.debian.org/med-team/python-cgecore/-/compare/cbf0bdd8cd64faa14babb70bc98ab05a25583572...47f3267dd626b2a83b755db6b4bcf26442ad3908
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