Merge branch 'master' of https://github.com/persalteas/biominserter
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... | @@ -549,7 +549,7 @@ class BiorseoInstance: | ... | @@ -549,7 +549,7 @@ class BiorseoInstance: |
549 | cmd = ["java", "-jar", jar3dexec, filename, ILmotifDir+"/all.txt", | 549 | cmd = ["java", "-jar", jar3dexec, filename, ILmotifDir+"/all.txt", |
550 | loop.header[1:]+".ILloop.csv", loop.header[1:]+".ILseq.csv"] | 550 | loop.header[1:]+".ILloop.csv", loop.header[1:]+".ILseq.csv"] |
551 | nowhere = open(devnull, 'w') | 551 | nowhere = open(devnull, 'w') |
552 | - logfile = open("log_of_the_run.sh", 'a') | 552 | + logfile = open(biorseoDir + "/log_of_the_run.sh", 'a') |
553 | logfile.write(' '.join(cmd)) | 553 | logfile.write(' '.join(cmd)) |
554 | logfile.write("\n") | 554 | logfile.write("\n") |
555 | logfile.close() | 555 | logfile.close() |
... | @@ -789,7 +789,7 @@ class BiorseoInstance: | ... | @@ -789,7 +789,7 @@ class BiorseoInstance: |
789 | if c == 0: | 789 | if c == 0: |
790 | seq = l[:-1].upper() | 790 | seq = l[:-1].upper() |
791 | if is_canonical_nts(seq): | 791 | if is_canonical_nts(seq): |
792 | - header = header.replace('/', '_').replace('\'','').replace('(','').replace(')','') | 792 | + header = header.replace('/', '_').replace('\'','').replace('(','').replace(')','').replace(' ','_') |
793 | RNAcontainer.append(RNA(header, seq)) | 793 | RNAcontainer.append(RNA(header, seq)) |
794 | if not path.isfile(self.outputf + header + ".fa"): | 794 | if not path.isfile(self.outputf + header + ".fa"): |
795 | rna = open(self.outputf + header + ".fa", "w") | 795 | rna = open(self.outputf + header + ".fa", "w") | ... | ... |
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