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... | @@ -502,7 +502,7 @@ class BiorseoInstance: | ... | @@ -502,7 +502,7 @@ class BiorseoInstance: |
502 | cmd = ["java", "-jar", jar3dexec, filename, ILmotifDir+"/all.txt", | 502 | cmd = ["java", "-jar", jar3dexec, filename, ILmotifDir+"/all.txt", |
503 | loop.header[1:]+".ILloop.csv", loop.header[1:]+".ILseq.csv"] | 503 | loop.header[1:]+".ILloop.csv", loop.header[1:]+".ILseq.csv"] |
504 | nowhere = open(devnull, 'w') | 504 | nowhere = open(devnull, 'w') |
505 | - logfile = open("log_of_the_run.sh", 'a') | 505 | + logfile = open(biorseoDir + "/log_of_the_run.sh", 'a') |
506 | logfile.write(' '.join(cmd)) | 506 | logfile.write(' '.join(cmd)) |
507 | logfile.write("\n") | 507 | logfile.write("\n") |
508 | logfile.close() | 508 | logfile.close() |
... | @@ -742,7 +742,7 @@ class BiorseoInstance: | ... | @@ -742,7 +742,7 @@ class BiorseoInstance: |
742 | if c == 0: | 742 | if c == 0: |
743 | seq = l[:-1].upper() | 743 | seq = l[:-1].upper() |
744 | if is_canonical_nts(seq): | 744 | if is_canonical_nts(seq): |
745 | - header = header.replace('/', '_').replace('\'','').replace('(','').replace(')','') | 745 | + header = header.replace('/', '_').replace('\'','').replace('(','').replace(')','').replace(' ','_') |
746 | RNAcontainer.append(RNA(header, seq)) | 746 | RNAcontainer.append(RNA(header, seq)) |
747 | if not path.isfile(self.outputf + header + ".fa"): | 747 | if not path.isfile(self.outputf + header + ".fa"): |
748 | rna = open(self.outputf + header + ".fa", "w") | 748 | rna = open(self.outputf + header + ".fa", "w") | ... | ... |
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