Analogy of exifread library in pysam for bam and vcf header files

Question

[aiteteji]

Hi Biostars community,

Is there an analogous way in Pysam to the code below to extract the header information in .bam and .vcf (or .vcf.gz) files? Help with a code snippet will great. The code snippet below uses exifread library to get the meta-info (in key-value pair) in jpeg and tiff files.

import exifread


def acPostProcForPut(rule_args, callback, rei):
    sv = session_vars.get_map(rei)
    phypath = sv['data_object']['file_path']
    objpath = sv['data_object']['object_path']
    exiflist = []
    with open(phypath, 'rb') as f:
        tags = exifread.process_file(f, details=False)
        for (k, v) in tags.iteritems():
            if k not in ('JPEGThumbnail', 'TIFFThumbnail', 'Filename', 'EXIF MakerNote'):
                exifpair = '{0}={1}'.format(k, v)
                exiflist.append(exifpair)
    exifstring = '%'.join(exiflist)
<post>

[Pierre Lindenbaum]

did you read the doc ? https://pysam.readthedocs.io/en/latest/api.html#pysam.AlignmentFile

[aiteteji]

Thanks for posting the link. I read it, but I didn't get how to remove the "@" in .bam and "##" in vcf file. I was hoping that someone who knows better can help. Here is my approach:

import pysam

pysamlist = []

with pysam.AlignmentFile("ex1.bam", "rb") as f:
    tags = pysam.view("-h", f)
    for (k, v) in tags.iteritems():
        pysampair = '{0}={1}'.format(k, v)
        pysamlist.append(pysampair)
    pysamstring = '%'.join(pysamlist)

[finswimmer]

Could you please give an example how your output should look like?