Mercurial > repos > jackcurragh > ribogalaxy_umi_extraction

comparison UMI_riboseq_tool/UMI.py @ 1:4605a1af1f3d draft default tip

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Uploaded
author triasteran
date Fri, 30 Sep 2022 09:07:04 +0000
parents 393b73b2eb5f
children
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0:393b73b2eb5f 1:4605a1af1f3d
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