Python parse_fastx_file Examples

Example #1

File: test_python.py Project: natir/needletail

 def get_fasta_reader(self):
     return parse_fastx_file(FASTA_FILE)

Example #2

#!/usr/bin/env python

if __name__ == "__main__":
    import sys
    from needletail import parse_fastx_file
    if len(sys.argv) == 1:
        print("Usage: fqcnt.py <in.fq.gz>")
        sys.exit(0)
    n, slen, qlen = 0, 0, 0
    for record in parse_fastx_file(sys.argv[1]):
        n += 1
        slen += len(record.seq)
        qlen += len(record.qual) if record.qual else 0
    print('{}\t{}\t{}'.format(n, slen, qlen))

Example #3

 def test_file_not_found(self):
     with self.assertRaises(NeedletailError):
         parse_fastx_file("hey")