Mercurial > repos > mheinzl > variant_analyzer2
diff mut2read.py @ 84:e46d5e377760 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
| author | mheinzl |
|---|---|
| date | Fri, 19 Aug 2022 11:23:37 +0000 |
| parents | fdfe9a919ff7 |
| children |
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--- a/mut2read.py Fri Aug 05 08:23:34 2022 +0000 +++ b/mut2read.py Fri Aug 19 11:23:37 2022 +0000 @@ -40,6 +40,8 @@ help='Output FASTQ file of reads with mutations.') parser.add_argument('--outputJson', help='Output JSON file to store collected data.') + parser.add_argument('--refalttiers', action="store_true", + help='Store also information about the reference allele.') return parser @@ -52,6 +54,7 @@ file3 = args.familiesFile outfile = args.outputFastq json_file = args.outputJson + refalttiers = args.refalttiers if os.path.isfile(file1) is False: sys.exit("Error: Could not find '{}'".format(file1)) @@ -189,16 +192,26 @@ line = line.rstrip('\n') splits = line.split('\t') tag = splits[0] - - if tag in tag_dict or tag in tag_dict_ref: - str1 = splits[4] - curr_seq = str1.replace("-", "") - str2 = splits[5] - curr_qual = str2.replace(" ", "") - out.write("@" + splits[0] + "." + splits[1] + "." + splits[2] + "\n") - out.write(curr_seq + "\n") - out.write("+" + "\n") - out.write(curr_qual + "\n") + if refalttiers is True: + if tag in tag_dict or tag in tag_dict_ref: + str1 = splits[4] + curr_seq = str1.replace("-", "") + str2 = splits[5] + curr_qual = str2.replace(" ", "") + out.write("@" + splits[0] + "." + splits[1] + "." + splits[2] + "\n") + out.write(curr_seq + "\n") + out.write("+" + "\n") + out.write(curr_qual + "\n") + else: + if tag in tag_dict: + str1 = splits[4] + curr_seq = str1.replace("-", "") + str2 = splits[5] + curr_qual = str2.replace(" ", "") + out.write("@" + splits[0] + "." + splits[1] + "." + splits[2] + "\n") + out.write(curr_seq + "\n") + out.write("+" + "\n") + out.write(curr_qual + "\n") if __name__ == '__main__':