User: drkennetz

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drkennetz0
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Posts by drkennetz

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Answer: A: Counting number of reads and bases fastaQ with python
... This should give you what you are looking for: #!/usr/bin/env python import sys fastq = sys.argv[1] with open(fastq, 'r') as f: reads = [] for line in f: if line.startswith("@"): reads.append(line) print("The total number of reads is: ...
written 6 days ago by drkennetz0
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Answer: A: Extract nucleotides from fasta file by a single position
... for this line: chrom = line.strip().split('>')[1] It could be replaced with: chrom = line.strip().strip('>').split()[0] Which would get rid of the '>' and just return the value (for example when running on an actual genome). printing this line for genome hg19 yields: 1 10 11 12 1 ...
written 7 days ago by drkennetz0

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