Mercurial > repos > triasteran > ribogalaxy_umi_processing

comparison UMI_riboseq_tool/UMI.py @ 16:cf1a0cbe5c34 draft

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author triasteran
date Fri, 30 Sep 2022 09:27:53 +0000
parents 0b5c3e35cddb
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15:b90ecf790d5b 16:cf1a0cbe5c34
48 48
49 if is_gz_file(pathToFastaFile) == True: 49 if is_gz_file(pathToFastaFile) == True:
50 print ('file is gzipped fastq') 50 print ('file is gzipped fastq')
51 with gzip.open(pathToFastaFile, "rt") as handle: 51 with gzip.open(pathToFastaFile, "rt") as handle:
52 for i, record in enumerate(SeqIO.parse(handle, "fastq")): 52 for i, record in enumerate(SeqIO.parse(handle, "fastq")):
53 process_fastq_record(record, output, UMI_5_prime_length=2, UMI_3_prime_length=5) 53 process_fastq_record(record, output, UMI_5_prime_length, UMI_3_prime_length)
54 54
55 else: 55 else:
56 for record in SeqIO.parse(pathToFastaFile, 'fastq'): 56 for record in SeqIO.parse(pathToFastaFile, 'fastq'):
57 process_fastq_record(record, output, UMI_5_prime_length, UMI_3_prime_length) 57 process_fastq_record(record, output, UMI_5_prime_length, UMI_3_prime_length)
58 58