Python pyvcf file processing VCF file format example details

introduction

PyVCF The installation of the library

PyVCF Library import

PyVCF Library details

Using examples ：

_Record object ------ Storage form of location information

Reader object ------ Handle vcf file , Building structured information

Comprehensive use ：

vcf The full name of the document is variant call file, The mutation identification file , It's a document produced in the genome workflow , What's preserved is information about mutations in the genome . Through to vcf Document analysis , We can get individual variation information . Um. , All in all , This is a very important document , So how to deal with it is also very important . Its file information is as follows ：

The beginning of the file is a pile of “##” Comment line at the beginning , Contains the basic information of the file . And then with “#” The first line , common 9+n Parts of , The first nine parts are marked with the information represented by each part in the following line , Equivalent to header . The following part is the sample name , There can be multiple . After the end of the comment line is the specific mutation information , Each line is divided into 9+n Parts of , Use tabs between each part （‘\t’） Separate .

Usually deal with vcf When you file , In the reading , There is always a lot of repetitive code written in the processing stage , The core task code is very few . Of course , If it's just looking for sites CHROM,POS,ID,REF,ALT,QUAL These parameters , You can do that . because vcf Format specification , The structure of these parameters is relatively simple . But if you deal with header information , Or deal with INFO,FORMAT When parameters are , To write more complex regular expressions , This is not only cumbersome , And it's easy to make mistakes .

Python Of PyVCF Library solves this problem , It uses regular expressions to put vcf File information is transformed into structured information , To simplify the vcf File processing , Facilitate the subsequent extraction of relevant parameters and processing .

cmd Interface

Or from https://github.com/jamescasbon/PyVCF Download the installation package from the website , Its installation .

PyVCF The name of the library is vcf, After importing, you can use its method to vcf File processing .

call vcf.Reader Class processing vcf file ,vcf The file information is saved to vcf_reader It's in . It's an iterative object , Its iteration element is a _Record Instance of object , Save a line of information that is not a comment line , That is, the specific information of the heterotopic point . Through it , We can easily get the details of the site .

_Record yes vcf.model One of the objects in , Besides it, there are _Call,_AltRecord Objects such as . Its basic attribute is CHROM,POS,ID,REF,ALT,QUAL,FILTER,INFO,FORMAT, That is to say vcf A line of site information in . Next, we will explain these attributes one by one ：

CHROM： Chromosome name , The type is str.

POS： The position of the locus on the chromosome , The type is int.

ID： Usually mutated rs Number , The type is str. If it is ‘.’, Then for None.

REF： The base of the reference genome at this site , The type is str.

ALT： Sequencing results at this site . yes _AltRecord A list of subclass instances of the class . The type is list._AltRecord Like 4 A subclass , Represents several types of mutations ： Such as snp,indel,structual variants etc. . All examples can be compared （ Limited to equal comparisons , There is no greater than less than ）, Some subclasses do not implement str Method , In other words, it cannot be converted into a string .

QUAL： The sequencing quality of this site , The type is int or float.

FILTER： Filtering information . take FILTER A list of strings separated by semicolons , The type is list. If no parameters are given, it is None.

INFO： Some test indicators of this locus . take ‘=’ The previous parameter is used as the key , The following parameters are used as values , Build into a dictionary . The type is dict.

FORMAT： Genotype information . preservation vcf Of FORMAT Original form of column , The type is str.

In addition to these basic attributes ,_Record Objects have some other properties ：

samples： hold FORMAT Information as a key , The following corresponding information is taken as the value , Build into a dictionary （CallData object ）, as well as sample name , These two values form a Call object , Co constitute samples An element of . This way sample And genotype information , Press the subscript to access each Call object .samples The type is list.

start： Where the mutation started

end： Where the mutation ends

alleles： All possible conditions of this site , from REF and ALT A list of parameters （REF The type is str,ALT Parameter is _AltRecord Subclass instances of objects ）, The type is list.

_Record Object methods ：

Compare size methods between objects ： Compare according to chromosome name and location information .Python3 only ‘=’ and ‘<’ Comparison .

Iterative method ： Yes samples Iterate over the elements in .

String method ： Only return CHROM,POS,REF,ALT Four columns of information .

genotype(name) Method , and samples Press subscript to access different , This method provides by sample Name the function to access .

add_format(fmt), add_filter(flt), add_info(info, value=True)： Add elements to the corresponding attributes .

get_hom_refs()： Get samples All that are not mutated at this site sample, Returns a list of .

get_hom_alts()： Get samples At this site 100% All of the mutations sample, Returns a list of .

get_hets()： Get samples All genotypes at this locus are heterozygous sample, Returns a list of .

get_unknown()： Get samples In all cases where the genotype of this locus is unknown sample, Returns a list of .

_Record Objects also have many useful method properties ：

num_called： The site has been identified sample number .

call_rate： Identified sample Number accounting for sample The proportion of the total .

num_hom_ref,num_hom_alt,num_het,num_unknown： The number of four genotypes

aaf： all sample Allele frequency （ Except REF）, Returns a list of .

heterozygosity： Heterozygosity of this site ,0.5 Heterozygous mutation ,0 Homozygous mutation .

var_type： Mutation types , Include ‘snp’,‘indel’,‘sv’（structural variant）,‘unknown’.

var_subtype： More refined mutation types , Such as ‘indel’ Include ‘del’,‘ins’,‘unknown’.

is_snp,is_indel,is_sv,is_transition,is_deletion： Judge whether the mutation is snp,indel,sv,transition,deletion wait .

reading vcf When you file , There are a total of six parameters to choose from , As shown in the figure above .

fsock： The file object of the target file , It can be used open( file name ) Get this file object .

filename： file name , When fsock and filename Simultaneous existence , Give priority to fsock.

compressed： Do you want to decompress , If no parameters are provided, the program will judge by itself （ Whether the file name is .gz At the end, judge whether you need to decompress ）.
prepend_chr： When saving chromosome names , Prefix or not ‘chr’, The default without , If vcf The chromosome name of the file does not have a prefix ‘chr’, Can be set to True, Automatically add .

strict_whitespace： Is it strictly tab ‘\t’ Separate data .True Then it means strictly according to tab ,False Indicates that spaces can be mixed .

encoding： File encoding .

Header information is mainly stored in Reader In the properties of the object , Include alts,contigs,filters,formats,infos,metadata.

alts Using examples ：

The usage of other attributes is similar .

Reader Object implements two methods ：

next()： Get the data of the next row , That is to return to the next _Record object . Can be explicitly called next() Get the next row of data , You can also iterate directly Reader object , It will automatically call next() Function to get the next row of data .

fetch(chrom,start=None,end=None)： return chrom Chromosomes from start+1 To end All mutation sites of coordinates . Do not give end, Just go back to chrom Chromosomes from start+1 All mutation sites to the end ;

start and end Not even , Just go back to chrom All mutation sites on chromosome . This method requires another third party Python modular pysam To index files , If this module is not installed , Can cause errors .

in addition , After using this method , It will change the iteratable range of the object to fetch() The obtained mutation site , So use this method , The original iteration schedule is invalid .

This library has another Writer object , I won't go into details here , Because most of them are right vcf The processing of documents can be done with the knowledge of the above two objects .

All the functions implemented by this library , Can write their own code to achieve , And the implementation method is relatively simple . The reason why we use this library to deal with vcf file , Because this library may consider more things than we know ourselves , Its implementation may also be more complete and reasonable than our own code .

also , It's always bad to build cars repeatedly .

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