update v1.3

RemiAllio · May 27, 2020 · 0d2ba3b · 0d2ba3b
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Showing 78 changed files with 4 additions and 4 deletions.
diff --git a/Bio/Align/Generic.pyc b/Bio/Align/Generic.pyc
diff --git a/Bio/Align/__init__.pyc b/Bio/Align/__init__.pyc
diff --git a/Bio/AlignIO/ClustalIO.pyc b/Bio/AlignIO/ClustalIO.pyc
diff --git a/Bio/AlignIO/EmbossIO.pyc b/Bio/AlignIO/EmbossIO.pyc
diff --git a/Bio/AlignIO/FastaIO.pyc b/Bio/AlignIO/FastaIO.pyc
diff --git a/Bio/AlignIO/Interfaces.pyc b/Bio/AlignIO/Interfaces.pyc
diff --git a/Bio/AlignIO/NexusIO.pyc b/Bio/AlignIO/NexusIO.pyc
diff --git a/Bio/AlignIO/PhylipIO.pyc b/Bio/AlignIO/PhylipIO.pyc
diff --git a/Bio/AlignIO/StockholmIO.pyc b/Bio/AlignIO/StockholmIO.pyc
diff --git a/Bio/AlignIO/__init__.pyc b/Bio/AlignIO/__init__.pyc
diff --git a/Bio/Alphabet/IUPAC.pyc b/Bio/Alphabet/IUPAC.pyc
diff --git a/Bio/Alphabet/__init__.pyc b/Bio/Alphabet/__init__.pyc
diff --git a/Bio/Application/__init__.pyc b/Bio/Application/__init__.pyc
diff --git a/Bio/Blast/NCBIStandalone.pyc b/Bio/Blast/NCBIStandalone.pyc
diff --git a/Bio/Blast/Record.pyc b/Bio/Blast/Record.pyc
diff --git a/Bio/Blast/__init__.pyc b/Bio/Blast/__init__.pyc
diff --git a/Bio/Data/CodonTable.pyc b/Bio/Data/CodonTable.pyc
diff --git a/Bio/Data/IUPACData.pyc b/Bio/Data/IUPACData.pyc
diff --git a/Bio/Data/SCOPData.pyc b/Bio/Data/SCOPData.pyc
diff --git a/Bio/Data/__init__.pyc b/Bio/Data/__init__.pyc
diff --git a/Bio/File.pyc b/Bio/File.pyc
diff --git a/Bio/GenBank/Scanner.pyc b/Bio/GenBank/Scanner.pyc
diff --git a/Bio/GenBank/__init__.pyc b/Bio/GenBank/__init__.pyc
diff --git a/Bio/GenBank/utils.pyc b/Bio/GenBank/utils.pyc
diff --git a/Bio/Nexus/Nexus.pyc b/Bio/Nexus/Nexus.pyc
diff --git a/Bio/Nexus/Nodes.pyc b/Bio/Nexus/Nodes.pyc
diff --git a/Bio/Nexus/Trees.pyc b/Bio/Nexus/Trees.pyc
diff --git a/Bio/Nexus/__init__.pyc b/Bio/Nexus/__init__.pyc
diff --git a/Bio/ParserSupport.pyc b/Bio/ParserSupport.pyc
diff --git a/Bio/SearchIO/BlastIO/__init__.pyc b/Bio/SearchIO/BlastIO/__init__.pyc
diff --git a/Bio/SearchIO/BlastIO/blast_tab.pyc b/Bio/SearchIO/BlastIO/blast_tab.pyc
diff --git a/Bio/SearchIO/BlastIO/blast_text.pyc b/Bio/SearchIO/BlastIO/blast_text.pyc
diff --git a/Bio/SearchIO/BlastIO/blast_xml.pyc b/Bio/SearchIO/BlastIO/blast_xml.pyc
diff --git a/Bio/SearchIO/__init__.pyc b/Bio/SearchIO/__init__.pyc
diff --git a/Bio/SearchIO/_index.pyc b/Bio/SearchIO/_index.pyc
diff --git a/Bio/SearchIO/_model/__init__.pyc b/Bio/SearchIO/_model/__init__.pyc
diff --git a/Bio/SearchIO/_model/_base.pyc b/Bio/SearchIO/_model/_base.pyc
diff --git a/Bio/SearchIO/_model/hit.pyc b/Bio/SearchIO/_model/hit.pyc
diff --git a/Bio/SearchIO/_model/hsp.pyc b/Bio/SearchIO/_model/hsp.pyc
diff --git a/Bio/SearchIO/_model/query.pyc b/Bio/SearchIO/_model/query.pyc
diff --git a/Bio/SearchIO/_utils.pyc b/Bio/SearchIO/_utils.pyc
diff --git a/Bio/Seq.pyc b/Bio/Seq.pyc
diff --git a/Bio/SeqFeature.pyc b/Bio/SeqFeature.pyc
diff --git a/Bio/SeqIO/AbiIO.pyc b/Bio/SeqIO/AbiIO.pyc
diff --git a/Bio/SeqIO/AceIO.pyc b/Bio/SeqIO/AceIO.pyc
diff --git a/Bio/SeqIO/FastaIO.pyc b/Bio/SeqIO/FastaIO.pyc
diff --git a/Bio/SeqIO/IgIO.pyc b/Bio/SeqIO/IgIO.pyc
diff --git a/Bio/SeqIO/InsdcIO.pyc b/Bio/SeqIO/InsdcIO.pyc
diff --git a/Bio/SeqIO/Interfaces.pyc b/Bio/SeqIO/Interfaces.pyc
diff --git a/Bio/SeqIO/PdbIO.pyc b/Bio/SeqIO/PdbIO.pyc
diff --git a/Bio/SeqIO/PhdIO.pyc b/Bio/SeqIO/PhdIO.pyc
diff --git a/Bio/SeqIO/PirIO.pyc b/Bio/SeqIO/PirIO.pyc
diff --git a/Bio/SeqIO/QualityIO.pyc b/Bio/SeqIO/QualityIO.pyc
diff --git a/Bio/SeqIO/SeqXmlIO.pyc b/Bio/SeqIO/SeqXmlIO.pyc
diff --git a/Bio/SeqIO/SffIO.pyc b/Bio/SeqIO/SffIO.pyc
diff --git a/Bio/SeqIO/SwissIO.pyc b/Bio/SeqIO/SwissIO.pyc
diff --git a/Bio/SeqIO/TabIO.pyc b/Bio/SeqIO/TabIO.pyc
diff --git a/Bio/SeqIO/UniprotIO.pyc b/Bio/SeqIO/UniprotIO.pyc
diff --git a/Bio/SeqIO/__init__.pyc b/Bio/SeqIO/__init__.pyc
diff --git a/Bio/SeqRecord.pyc b/Bio/SeqRecord.pyc
diff --git a/Bio/SeqUtils/__init__.pyc b/Bio/SeqUtils/__init__.pyc
diff --git a/Bio/Sequencing/Ace.pyc b/Bio/Sequencing/Ace.pyc
diff --git a/Bio/Sequencing/Phd.pyc b/Bio/Sequencing/Phd.pyc
diff --git a/Bio/Sequencing/__init__.pyc b/Bio/Sequencing/__init__.pyc
diff --git a/Bio/SwissProt/__init__.pyc b/Bio/SwissProt/__init__.pyc
diff --git a/Bio/__init__.pyc b/Bio/__init__.pyc
diff --git a/Bio/_py3k/__init__.pyc b/Bio/_py3k/__init__.pyc
diff --git a/Bio/_utils.pyc b/Bio/_utils.pyc
diff --git a/Bio/bgzf.pyc b/Bio/bgzf.pyc
diff --git a/FirstBuildChecker.pyc b/FirstBuildChecker.pyc
diff --git a/circularizationCheck.pyc b/circularizationCheck.pyc
diff --git a/genbankOutput.pyc b/genbankOutput.pyc
diff --git a/geneChecker.pyc b/geneChecker.pyc
diff --git a/mitofinder b/mitofinder
@@ -1512,13 +1512,13 @@ if __name__ == "__main__":
 	#sort gff
 	pathlist = glob.glob(pathOfFinalResults+"/*.gb")
 	if len(pathlist) == 1 :
-		for f in glob.glob(pathOfFinalResults+"/*_raw.gff"):
+		for f in sorted(glob.glob(pathOfFinalResults+"/*_raw.gff"), key=os.path.getmtime):
 			command = module_dir+"/sort_gff.py " + f + " " + args.processName +".1 " + str(args.organismType) + " " + str(args.rename)
 			args1 = shlex.split(command)
 			sort_gff = Popen(args1, cwd=pathOfFinalResults, stdout=open('geneChecker.log', 'a'), stderr=open('geneChecker_erreur.log', 'a'))
 			sort_gff.wait()	
 	else:
-		for f in glob.glob(pathOfFinalResults+"/*_raw.gff"):
+		for f in sorted(glob.glob(pathOfFinalResults+"/*_raw.gff"), key=os.path.getmtime):
 			command = module_dir+"/sort_gff.py " + f + " " + args.processName +"."+ f.split("_raw")[0][-1] + " " + str(args.organismType) + " " + str(args.rename)
 			args1 = shlex.split(command)
 			sort_gff = Popen(args1, cwd=pathOfFinalResults, stdout=open('geneChecker.log', 'a'), stderr=open('geneChecker_erreur.log', 'a'))
@@ -1536,7 +1536,7 @@ if __name__ == "__main__":
 			shutil.copy(f+"_AA.fasta",pathOfFinalResults+"/"+args.processName+"_final_genes_AA.fasta")
 			shutil.copy(f+"_NT.fasta",pathOfFinalResults+"/"+args.processName+"_final_genes_NT.fasta")
 	if c > 1 and args.numt == 0:	
-		for f in glob.glob(pathOfFinalResults+"/*_genes_NT.fasta"):
+		for f in sorted(glob.glob(pathOfFinalResults+"/*_genes_NT.fasta"), key=os.path.getmtime):
 			for name, seq in read_fasta(open(f,'r')):
 				gene=name.split("@")[1]
 				if dico_genes.has_key(gene):
@@ -1561,7 +1561,7 @@ if __name__ == "__main__":
 		final_fasta.close()
 
 		dico_genes={}
-		for f in glob.glob(pathOfFinalResults+"/*_genes_AA.fasta"):
+		for f in sorted(glob.glob(pathOfFinalResults+"/*_genes_AA.fasta"), key=os.path.getmtime):
 			for name, seq in read_fasta(open(f,'r')):
 				gene=name.split("@")[1]
 				if dico_genes.has_key(gene):

diff --git a/runIDBA.pyc b/runIDBA.pyc
diff --git a/runMegahit.pyc b/runMegahit.pyc
diff --git a/runMetaspades.pyc b/runMetaspades.pyc
diff --git a/tRNAscanChecker.pyc b/tRNAscanChecker.pyc