Python 3 VCF library with good support for both reading and writing
INFO and FORMAT fields is based on OrderedDict allows for easier modification than PyVCF (also I find this more pythonic)vcfpyI've been using PyVCF with quite some success in the past. However, the main bottleneck of PyVCF is when you want to modify the per-sample genotype information. There are some issues in the tracker of PyVCF but none of them can really be considered solved. I tried several hours to solve these problems within PyVCF but this never got far or towards a complete rewrite...
For this reason, VCFPy was born and here it is!
VCFPy is the result of two full days of development plus some maintenance work later now (right now). I'm using it in several projects but it is not as battle-tested as PyVCF.
As I'm only using Python 3 code, I see no advantage in carrying around support for legacy Python 2 and maintaining it. At a later point when VCFPy is known to be stable, Python 2 support might be added if someone contributes a pull request.
setup.py that prevented pysam dependency to be loaded (#150)..bgz files the same as .gz (#145, #149)Record.update_calls.Record.{format,calls} use list when emptyCall.set_genotype().Call.ploidy.Call.is_variant.GT describes only one allele.INFO and FORMAT.GT describes only one allele.PASS filter if not defined in header.black formatting.FORMAT or any sample
column.FORMAT and
any sample columns.pip module from setup.py which is not recommended
anyway.FORMAT
fields (#127). Writing out . instead of keeping trailing empty
records empty.FORMAT/FT is now expected to be a semicolon-separated
string. Internally, we will handle it as a list.warnings
module.str in case of problems with parsing value.names list in the SamplesInfos for the Writer).Writer constructionsamples attribute from Header in Reader and Writer
instead of passing explicitelyGT fieldsrequirements*.txt files now from setup.pyHeader.has_header_line for querying existence of header
lineHeader.add_*_line return a bool no indicating any conflicts__eq__, __neq__ and __hash__ to data types (where
applicable)record.SV_CODESINFO and FORMAT fields on reading (#8)INFO and FORMAT fields to pyvcf.header (#32)HOM_REF, HOM_ALT, HETCall.is_phased, Call.is_het, Call.is_variant,
Call.is_phased, Call.is_hom_ref, Call.is_hom_altCall.phased (breaks API, next release is 0.4.0)CallFORMAT/FT being a string; this is done so in the Delly
outputReader and Writer can now be used as context manager (with
with)example-4.1-bnd.vcf example file because v4.1 tumor
derival lacks ID fieldAltAlleleHeaderLine, MetaHeaderLine,
PedigreeHeaderLine, and SampleHeaderLineSimpleHeaderFile to SimpleHeaderLineFILTER entries on parsingfrom_stream and from_file (#18)from_file to from_stream (#18)Reader.jump_to to Reader.fetchheader_without_lines functionFAQs
Python 3 VCF library with good support for both reading and writing
We found that vcfpy demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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