[med-svn] [Git][med-team/python-cgecore][upstream] New upstream version 1.5.4+ds

[Steffen Möller]

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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200505/44289ac3/attachment-0001.html>