Mercurial > repos > mheinzl > variant_analyzer2

comparison mut2read.py @ 84:e46d5e377760 draft

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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
comparison
equal deleted inserted replaced
83:8cec772c0bf1 84:e46d5e377760
38 help='TABULAR file with aligned families.') 38 help='TABULAR file with aligned families.')
39 parser.add_argument('--outputFastq', 39 parser.add_argument('--outputFastq',
40 help='Output FASTQ file of reads with mutations.') 40 help='Output FASTQ file of reads with mutations.')
41 parser.add_argument('--outputJson', 41 parser.add_argument('--outputJson',
42 help='Output JSON file to store collected data.') 42 help='Output JSON file to store collected data.')
43 parser.add_argument('--refalttiers', action="store_true",
44 help='Store also information about the reference allele.')
43 return parser 45 return parser
44 46
45 47
46 def mut2read(argv): 48 def mut2read(argv):
47 parser = make_argparser() 49 parser = make_argparser()
50 file1 = args.mutFile 52 file1 = args.mutFile
51 file2 = args.bamFile 53 file2 = args.bamFile
52 file3 = args.familiesFile 54 file3 = args.familiesFile
53 outfile = args.outputFastq 55 outfile = args.outputFastq
54 json_file = args.outputJson 56 json_file = args.outputJson
57 refalttiers = args.refalttiers
55 58
56 if os.path.isfile(file1) is False: 59 if os.path.isfile(file1) is False:
57 sys.exit("Error: Could not find '{}'".format(file1)) 60 sys.exit("Error: Could not find '{}'".format(file1))
58 61
59 if os.path.isfile(file2) is False: 62 if os.path.isfile(file2) is False:
187 with open(file3, 'r') as families: 190 with open(file3, 'r') as families:
188 for line in families: 191 for line in families:
189 line = line.rstrip('\n') 192 line = line.rstrip('\n')
190 splits = line.split('\t') 193 splits = line.split('\t')
191 tag = splits[0] 194 tag = splits[0]
192 195 if refalttiers is True:
193 if tag in tag_dict or tag in tag_dict_ref: 196 if tag in tag_dict or tag in tag_dict_ref:
194 str1 = splits[4] 197 str1 = splits[4]
195 curr_seq = str1.replace("-", "") 198 curr_seq = str1.replace("-", "")
196 str2 = splits[5] 199 str2 = splits[5]
197 curr_qual = str2.replace(" ", "") 200 curr_qual = str2.replace(" ", "")
198 out.write("@" + splits[0] + "." + splits[1] + "." + splits[2] + "\n") 201 out.write("@" + splits[0] + "." + splits[1] + "." + splits[2] + "\n")
199 out.write(curr_seq + "\n") 202 out.write(curr_seq + "\n")
200 out.write("+" + "\n") 203 out.write("+" + "\n")
201 out.write(curr_qual + "\n") 204 out.write(curr_qual + "\n")
205 else:
206 if tag in tag_dict:
207 str1 = splits[4]
208 curr_seq = str1.replace("-", "")
209 str2 = splits[5]
210 curr_qual = str2.replace(" ", "")
211 out.write("@" + splits[0] + "." + splits[1] + "." + splits[2] + "\n")
212 out.write(curr_seq + "\n")
213 out.write("+" + "\n")
214 out.write(curr_qual + "\n")
202 215
203 216
204 if __name__ == '__main__': 217 if __name__ == '__main__':
205 sys.exit(mut2read(sys.argv)) 218 sys.exit(mut2read(sys.argv))