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bam2fq.py
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bam2fq.py
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import sys
import pysam
from Bio import SeqIO
from Bio import SeqRecord
from Bio import Seq
open(sys.argv[2], "w").close()
handle = open(sys.argv[2], "a")
buffer = []
processed_ids = set()
for a in pysam.AlignmentFile(sys.argv[1], "r", check_sq=False):
seq = a.get_forward_sequence()
if not seq:
continue
read_id = a.query_name
if read_id in processed_ids:
continue
processed_ids.add(read_id)
qual = a.get_forward_qualities()
buffer.append(SeqRecord.SeqRecord(seq=Seq.Seq(seq), id=read_id, description="", letter_annotations={'phred_quality':qual}))
if len(buffer) > 100000:
SeqIO.write(buffer, handle, "fastq")
buffer = []
SeqIO.write(buffer, handle, "fastq")
handle.close()