Steffen Möller pushed to branch upstream 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 - - - - - 3 changed files: - PKG-INFO - cgecore/__init__.py - cgecore/blaster/blaster.py 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 View it on GitLab: https://salsa.debian.org/med-team/python-cgecore/-/commit/34790c462a60216d558e72645abad74b8f49a627 -- View it on GitLab: https://salsa.debian.org/med-team/python-cgecore/-/commit/34790c462a60216d558e72645abad74b8f49a627 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
