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: [email protected] -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 You're receiving this email because of your account on salsa.debian.org.
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