phe.variant¶

Submodules¶

Classes and methods to work with _variants and such.

Similarly to Implementing Mapper and Implementing Filter adding your variant caller is easy and sraight forward. Implement VariantCaller class with the following attributes/methods:

VariantCaller.name - Name of your variant caller, used to dynamically load it.
VariantCaller.make_vcf() - Create a VCF from input BAM. See VariantCaller.make_vcf() for input list.
VariantCaller.get_version() - Return the version of this variant caller.
VariantCaller.get_info() - Return information about this caller and included in the VCF header.
VariantCaller.create_aux_files() - Create auxilliary files needed by the caller. Also used in phenix.

Save your new variant caller in the variant directiry and it will be automatically picked up by the system. To verify run:

run_snp_pipeline.py --help

It should appear in the list of available callers.

class VCFTemplate(vcf_reader)[source]¶

Bases: object

This is a small hack class for the Template used in generating VCF file.

class VariantCaller(cmd_options=None)[source]¶

Abstract class used for access to the implemented variant callers.

Methods

`create_aux_files`(ref)	Create needed (if any) auxiliary files.
`get_info`([plain])	Get information about this variant caller.
`get_meta`()	Get the metadata about this variant caller.
`get_version`()	Get the version of the underlying command used.
`make_vcf`(args, *kwargs)	Create a VCF from BAM file.
`validate`()	Check if the command can run.

create_aux_files(ref)[source]¶: Create needed (if any) auxiliary files. These files are required for proper functioning of the variant caller.

get_info(plain=False)[source]¶: Get information about this variant caller.

make_vcf(*args, **kwargs)[source]¶

Create a VCF from BAM file.

Parameters:	ref: str Path to the reference file. bam: str Path to the indexed BAM file for calling _variants. vcf_file: str path to the VCF file where data will be written to. make_aux: bool, optional True/False create auxilliary files (default: False).
Returns:	bool: True if variant calling was successful, False otherwise.

class VariantSet(vcf_in, filters=None, reference=None)[source]¶

Bases: object

A convenient representation of set of _variants. TODO: Implement iterator and generator for the variant set.

Methods

`add_metadata`(info)	Add metadata to the variant set.
`filter_variants`([keep_only_snps, only_good])	Filter the VCF records.
`variants`([only_good])	Generator over the variant set.
`write_to_json`(vcf_file_name[, verbose])	Write _variants to a json file.
`write_variants`(vcf_out[, only_snps, only_good])	Write _variants to a VCF file.

add_metadata(info)[source]¶

Add metadata to the variant set.

Parameters:	info: dict Dictionary of key value pairs to be inserted into metadata.

filter_variants(keep_only_snps=False, only_good=False)[source]¶

Filter the VCF records.

Parameters:	keep_only_snps: bool, optional Retain only SNP variants (default: False). only_good: bool, optional True/False if only SNPs that PASS should output.
Returns:	list of records is returned.

variants(only_good=False)[source]¶

Generator over the variant set.

Parameters:	only_good: bool, optional Iff True good and bad variants are returned, otherwise only good are returned (default: False).

write_to_json(vcf_file_name, verbose=False)[source]¶: Write _variants to a json file.

write_variants(vcf_out, only_snps=False, only_good=False)[source]¶

Write _variants to a VCF file.

Parameters:	vcf_out: str Path to the file where VCF data is written. only_snps: bool, optional True is only SNP are to be written to the output (default: False). only_good: bool, optional True if only those records that PASS all filters should be written (default: False). Returns: int: Number of records written.