unmapped reads with pysam

Question

[grant.hovhannisyan]

I have a bam file produces by BWA-MEM. It has some unmapped reads, e.g.

D00733:389:CD1T7ANXX:3:1101:1572:2235   77  *   0   0   *   *   0   0   CAGTTTCACTGTATAAATTGCTTATACTTAGACATGCATGGCTTAATCTT  AAB=AFGDGCFFGGGGGGGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGF  AS:i:0  XS:i:0
D00733:389:CD1T7ANXX:3:1101:1572:2235   141 *   0   0   *   *   0   0   GTATCTTCTAGAGAGAGGGAATGGGCGAGAGAAAAAGAGATTTCGGTTTC  BBB@BGGGGGGGGFGGGGGGGGEGGGGGGDGFGGGGGGGGEGGGGGFGGG  AS:i:0  XS:i:0
D00733:389:CD1T7ANXX:3:1101:6797:2243   77  *   0   0   *   *   0   0   TGTCTGGACCTGGTGAGTTTCCCCGTGTTGAGTCAAATTAAGCCGCAGGC  3A<0BDGGGGGGGGGGGGGFGGGGGFGGGGGGGGGGGGGGGGGGGGGGGG  AS:i:0  XS:i:0

I use pysam to count some stats on the bam file, but for some reason pysam does not find these unmapped reads.

bam=pysam.AlignmentFile(file,"rb")
for line in bam.fetch():
    line=line.tostring(bam)
    line=line.split("\t")
    if  line[2]=="*":
        print(line)

The code does not return anything

Any ideas how to fix this?

Thanks

Answer 1

[Asaf]

you should add until_eof=True in the fetch()

[grant.hovhannisyan]

Accepted :) Thank you!