Reading CRAM files in pysam
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0
Entering edit mode
5.3 years ago

I'm new to CRAM format and I am wondering if I can read a CRAM file  in pysam or samtools.

Or generally speaking how do I use a CRAM file like a BAM file?

#!/usr/env python
import pysam
CRAM_FH = '/home/admin/data/HG00096.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram'
cram = pysam.AlignmentFile(CRAM_FH,'rb')
for read in cram.fetch(region='chr1:10000000-10000100'):
        print read
cram.close()

 

Returned:

  File "src/test_cram.py", line 5, in <module>
    for read in cram.fetch(region='chr1:10000000-10000100'):
  File "pysam/calignmentfile.pyx", line 874, in pysam.calignmentfile.AlignmentFile.fetch (pysam/calignmentfile.c:10986)
ValueError: fetch called on bamfile without index

 

 

 

pysam python CRAM samtools htslib • 2.9k views
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1
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5.3 years ago
matted 7.5k

It should. Pysam uses recent versions of htslib, and if you look at the release notes for pysam, you'll see this entry with version 0.8.2 (the latest is 0.8.4):

  • Pysam now wraps htslib 1.2.1 and samtools version 1.2
  • Added CRAM file support to pysam
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If the index is in the same directory why wont the code work then?

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What version of pysam are you using?

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most recent

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5.3 years ago
duxan ▴ 50

It seems that pysam doesn't recognize your file as CRAM. You can check this by: cram.is_bam and cram.is_cram.

From the source you can see a way how you can hack it (since I haven't found this in documentation, it is safe to call it a hack) by setting mode to 'rc' instead of 'rb'. This same issue is reported here. I can confirm that changing mode this way worked in my setup (CRAM built with samtools view -C BAM > CRAM, not with pysam, and also index built with samtools index CRAM).

Hope it helps!

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5.3 years ago
ValueError: fetch called on bamfile without index

Does the input cram file actually have an index?

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yes the .cram.crai is in the same directory

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