PyVCF
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jamescasbon
A Variant Call Format reader for Python.
> import vcf > vcf_reader = vcf.Reader(open('vcf/test/example-4.2.vcf', 'r')) > for record in vcf_reader: > ... print record > File "", line 2 > print record > ^ > IndentationError: Missing...
In `scripts/vcf_sample_filter.py` there is 2 usages of `print` without parenthesis. https://github.com/jamescasbon/PyVCF/blob/476169cd457ba0caa6b998b301a4d91e975251d9/scripts/vcf_sample_filter.py#L37 https://github.com/jamescasbon/PyVCF/blob/476169cd457ba0caa6b998b301a4d91e975251d9/scripts/vcf_sample_filter.py#L39
bug with loConfDeNovo/hiConfDeNovo field In case of more than one sample with de novo mutation (sep by ","), report only the first one. The fields loConfDeNovo/hiConfDeNovo generated by GATK Genotype...
I have 40 vcf files, which I need to convert into a tabular format. But the vcf.reader parser complaints while I am parsing it through each row. The same script...
I try to get the length of REF and ALT[0] using below code, once a while I got the error for some record. vcf_reader = vcf.Reader(open('thousand.vcf', 'r')) for record in...
pyvcf does not like MNPs where the REF and ALT alleles share common bases (ex. `REF=AAA` and `ALT=AAT`).
I have problem reading a vcf file. I thinks its because the items in the FORMAT field are not same in all the lines. Something like this: FORMAT 2ms01e GT:AD:DP:PL:PG:PB:PI:PW:PC...
I needed to parse VCF files that I could only open in byte mode (it was streamed files), therefore I adapted the code in order to do so. The only...
The existing __str__ method defines what is superficially a Python snippet which could recreate the object - and captures the key attributes. This follows the style elsewhere in this file...
https://github.com/jamescasbon/PyVCF/blob/master/docs/HISTORY.rst lists changes in v0.6.7 (21 Feb 2014), but not v0.6.8 (18 March 2016), nor any of the as-yet unreleased changes since. Cross reference https://pypi.org/project/PyVCF/#history and #302 - a more...