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How to read vcf file in python?

When I try to do simply like this:

import vcf
vcf_reader = vcf.Reader(filename="in.vcf.gz")

there is an error:

AttributeError: partially initialized module 'vcf' has no attribute 'Reader' (most likely due to a circular import)

But vcf module has that attribute .. Kindly help.

vcf reader python
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updated by BCArg BCArg • written by ja4123 • ja4123

I always read it by pandas (after removing the heads).

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written by shoujun.gu shoujun.gu

personally, I just use GATK VariantsToTable to convert it to a .tsv first. Its much easier to parse this way. Unless you wanted something from the header? Another option might to be convert to another tabular format such as .maf

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written by steve steve

3 answers

Try Pysam . You can easily pip install it (pip install pysam)

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written by onestop_data onestop_data

I like to use Pandas. I find the line that starts with '#CHROM', split that row to make a list of names for names=<list of names>, and read in chunks with comment='#'

import pandas as pd
import gzip

def get_vcf_names(vcf_path):
    with gzip.open(vcf_path, "rt") as ifile:
          for line in ifile:
            if line.startswith("#CHROM"):
                  vcf_names = [x for x in line.split('\t')]
                  break
    ifile.close()
    return vcf_names


names = get_vcf_names('file.vcf.gz')
vcf = pd.read_csv('file.vcf.gz', compression='gzip', comment='#', chunksize=10000, delim_whitespace=True, header=None, names=names)
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written by d.vitale199 • d.vitale199

I have zip file instead of gzip so how can I change my code?

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written by anasjamshed anasjamshed

The line under if statement could be improved to:

vcf_names = line.strip('#\n').split('\t')
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written by vladimir.yu.kiselev • vladimir.yu.kiselev

I actually ind pyvcf useful to parse vcf files, it contains a lot of useful attributes.

Below is the code I use to get attributes from each entry in the vcf:

import vcf
vcf_fullPath = '/path/to/file.vcf'

records = vcf.Reader(open(vcf_fullPath, 'r'))

# records is an iterable, from which you can get attributes such as REF, ALT, POS etc.

for row in records:
    chr = row.CHROM
    pos = row.POS
    id = row.ID
    ref = row.REF
    alt = row.ALT

print(f"chr is {chr}, pos is {pos}, alternate allele is {alt}")
chr is 1, pos is 781258, alternate allele is [T]
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written by BCArg BCArg

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