Question: unmapped reads with pysam
1
gravatar for grant.hovhannisyan
8 months ago by
grant.hovhannisyan1.7k wrote:

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

pysam • 382 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by grant.hovhannisyan1.7k
2
gravatar for Asaf
8 months ago by
Asaf6.3k
Israel
Asaf6.3k wrote:

you should add until_eof=True in the fetch()

ADD COMMENTlink written 8 months ago by Asaf6.3k

Accepted :) Thank you!

ADD REPLYlink written 8 months ago by grant.hovhannisyan1.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2373 users visited in the last hour