[med-svn] [Git][med-team/python-cgecore][upstream] 2 commits: New upstream version 1.5.3
Steffen Möller
gitlab at salsa.debian.org
Tue Mar 17 12:36:28 GMT 2020
Steffen Möller pushed to branch upstream at Debian Med / python-cgecore
Commits:
3b828448 by Steffen Moeller at 2020-03-17T13:15:13+01:00
New upstream version 1.5.3
- - - - -
918eda8f by Steffen Moeller at 2020-03-17T13:23:57+01:00
New upstream version 1.5.3+ds
- - - - -
7 changed files:
- PKG-INFO
- − cgecore.egg-info/PKG-INFO
- − cgecore.egg-info/SOURCES.txt
- − cgecore.egg-info/dependency_links.txt
- − cgecore.egg-info/top_level.txt
- cgecore/__init__.py
- cgecore/blaster/blaster.py
Changes:
=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 1.0
Name: cgecore
-Version: 1.5.2
+Version: 1.5.3
Summary: Center for Genomic Epidemiology Core Module
Home-page: https://bitbucket.org/genomicepidemiology/cge_core_module
Author: Center for Genomic Epidemiology
=====================================
cgecore.egg-info/PKG-INFO deleted
=====================================
@@ -1,38 +0,0 @@
-Metadata-Version: 1.0
-Name: cgecore
-Version: 1.5.2
-Summary: Center for Genomic Epidemiology Core Module
-Home-page: https://bitbucket.org/genomicepidemiology/cge_core_module
-Author: Center for Genomic Epidemiology
-Author-email: cgehelp at cbs.dtu.dk
-License: Apache License, Version 2.0
-Description: # cge_core_module
-
- Core module for the Center for Genomic Epidemiology
-
- This module contains classes and functions needed to run the service wrappers and pipeline scripts
-
- The pypi project can be found here:
- https://pypi.org/project/cgecore/
-
- # How to update:
- 1. Make changes to the modules
- 2. Bump the version number accordingly in cgecore/__init__.py
- 3. Install package locally
- 4. Test the changes locally (for both python2 and python3)
- 5. Distribute to Pypi
-
- # Install package locally
- python2 setup.py install
-
- python3 setup.py install
-
- # Distribute to PyPi
- python3 setup.py sdist bdist_wheel
-
- twine upload dist/*
-
- *deprecated:*
- ~~python setup.py sdist upload -r pypi~~
-
-Platform: UNKNOWN
=====================================
cgecore.egg-info/SOURCES.txt deleted
=====================================
@@ -1,20 +0,0 @@
-README.md
-setup.py
-cgecore/__init__.py
-cgecore/alignment.py
-cgecore/argumentparsing.py
-cgecore/cgefinder.py
-cgecore/cmdline.py
-cgecore/utility.py
-cgecore.egg-info/PKG-INFO
-cgecore.egg-info/SOURCES.txt
-cgecore.egg-info/dependency_links.txt
-cgecore.egg-info/top_level.txt
-cgecore/blaster/__init__.py
-cgecore/blaster/blaster.py
-cgecore/blaster/run_blaster.py
-cgecore/organisminfo/__init__.py
-cgecore/organisminfo/gram_neg.txt
-cgecore/organisminfo/gram_pos.txt
-cgecore/organisminfo/gramstain.py
-cgecore/organisminfo/species.py
\ No newline at end of file
=====================================
cgecore.egg-info/dependency_links.txt deleted
=====================================
@@ -1 +0,0 @@
-
=====================================
cgecore.egg-info/top_level.txt deleted
=====================================
@@ -1 +0,0 @@
-cgecore
=====================================
cgecore/__init__.py
=====================================
@@ -13,7 +13,7 @@ from .argumentparsing import (check_file_type, get_arguments, get_string,
)
#####################
-__version__ = "1.5.2"
+__version__ = "1.5.3"
__all__ = [
"argumentparsing",
"cmdline",
=====================================
cgecore/blaster/blaster.py
=====================================
@@ -194,31 +194,32 @@ class Blaster():
'strand': strand,
'perc_coverage': perc_coverage
}
-
-
-
- # 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
+ 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
result_handle.close()
@@ -463,7 +464,7 @@ 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 keept.
+ # which gene should be chosen?? Now they are both kept.
# Save a split if the new hit creats one - both
# hits are saved
View it on GitLab: https://salsa.debian.org/med-team/python-cgecore/-/compare/422e7b5eb5e98a546ffa7d7c6c19f145a39b3ac8...918eda8f21120c7b534a3d24024eee7c2cb23bf2
--
View it on GitLab: https://salsa.debian.org/med-team/python-cgecore/-/compare/422e7b5eb5e98a546ffa7d7c6c19f145a39b3ac8...918eda8f21120c7b534a3d24024eee7c2cb23bf2
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