How do I add/update the FORMAT field and it values in SAMPLE field?
0
1
Entering edit mode
7.6 years ago
kirannbishwa01 ★ 1.6k

I am trying to add a new FORMAT field and it's value in SAMPLE field.

vcf_read = vcf.Reader(open('RNA_seq.test.vcf'))

# adding the description of new field in the header
vcf_read.formats['My|Sp'] = VcfInfo('My|Sp', num=4, type=str,
                                desc='phased genotype state of the population',
                                source=devnull, version=devnull)

 # now opening the file to write the vcf data to
 vcf_write = vcf.Writer(open('RNA_seq.write.vcf', 'w'), vcf_read,
                   lineterminator='\n')


for record in vcf_read:

    # update the FORMAT field id
    record.FORMAT = record.FORMAT+'foo'   # this works

    # select the sample to be updated
    sample_name = record.genotype('2ms01e')

    sample_name.add_field('foo', 'bar')  # this doesn't work

Error message:

Traceback (most recent call last):
  File "/home/everestial007/PycharmProjects/stitcher/pHASE-Stitcher-Markov/markov_final_test/phase_to_vcf.py", line 108, in <module>
    sample_name.add_field('foo', 'bar')
AttributeError: '_Call' object has no attribute 'add_field'

But, according to the documents in pyVCF this is supposed to work. I then checked the module.py file in https://github.com/jamescasbon/PyVCF/blob/master/vcf/model.py to see if add_field exists or not, and it unfortunately doesn't.

I then tried to reinstall the new version of PyVcf but still the same problem.

How do I add/update the FORMAT field and it values in SAMPLE field?

software error vcf pyvcf python add_field • 2.6k views
ADD COMMENT

Login before adding your answer.

Traffic: 1635 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6