| Bio::DB::HTS::VCF(3pm) | User Contributed Perl Documentation | Bio::DB::HTS::VCF(3pm) |
Copyright [2015-2018] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Rishi Nag <rishi@ebi.ac.uk>, original author.
Alessandro Vullo "<avullo at cpan.org>", the current developer and maintainer.
Bio::DB::HTS::VCF -- Read VCF/BCF data files
This module provides a Perl interface to the HTSlib library for reading variant calls stored in VCF and BCF file databases.
The functions provided are for opening a VCF/BCF file, reading header values, querying specific chromosome intervals and then reading row values.
A sweep set of methods allows running through rows one by one, either backwards or forwards through the file.
use Bio::DB::HTS::VCF ;
### File Open ###
my $v = Bio::DB::HTS::VCF->new( filename => "/path/to/myfile.vcf.gz" );
# once the file has been opened, various global values can be read from the header
my $h = $v->header();
$h->get_seqnames() ;
$h->version() ; # read the VCF file version
$h->num_samples() ;
$h->get_sample_names() ; #return an array of sample names
$h->num_seqnames() ;
$h->get_seqnames() ; # return an array of sequence names
### Individual rows can be read in and fields accessed ###
my $row = $v->next() ;
# row functions
$row->chromosome($h) ;
$row->position() ;
$row->id() ;
$row->num_filters() ;
$row->quality() ;
# retrieve alleles
my $num_alleles = $row->num_alleles();
my $alleles = $row->get_alleles();
my $allele_index = 1;
for my $a (@$alleles) {
printf( "(%s, %s)\n", $a, $row->get_variant_type($allele_index++) ) ;
}
# query filters
$row->has_filter($h,"DP50");
$row->has_filter($h,"."); # PASS filter check
$row->get_info_type($h, "AF"); # one of "String", "Integer", "Float" or "Flag".
$info_result = $row->get_info($h, "NS"); # [3]
$row->get_format_type($h, "GT") ; # "String"
$row->get_format($h, "DP") ; # [ 1, 8, 5 ]
### free memory associated with the row
Bio::DB::HTS::VCF::Row->destroy($row);
### query specific locations
my $iter = $v->query("20:1000000-1231000");
while (my $result = $iter->next) {
print $result->chromosome($h), $result->position(), $result->id(), $result->num_filters(), $result->quality(), "\n";
}
Opens a VCF/BCF file for reading. If the file is indexed (i.e. tabix for VCF, csi for BCF) the index is opened and used for querying arbitrary locations on the chromosomes.
Returns instance of Bio::DB::HTS::VCF::Header, representing the header of the file.
Returns the number of variants (i.e. rows) of the file.
Close the VCF/BCF file, allocated memory will be released, included the index, if present.
Returns the next row (starting from the first one) read from the file.
If the file is indexed, the file can be queried for variants on a specified region. Regions can be specified using either the "chr", "chr:start" or "chr:start-end" format, with start <= end.
Once an iterator is obtained, individual rows belonging to the result set can be sequentially accessed by iteratively invoking the iterator next method until it returns nothing.
Once the file has been opened, various global values can be read from the header.
Returns the VCF file version, as a string
Returns the number of samples
Returns the list of sample names
Returns the number of sequence names
Returns the list of sequence names
Get header formatted text, as a string
Individual rows can be read in and fields accessed. To read a row use the next function, which returns a Bio::DB::HTS::VCF::Row instance.
Various fields can then be read from the row object. Some of the functions to read these fields will need the header object supplied.
The variant type of an allele can be determined using the index of the allele. The index starts from 1 for the first allele:
Each row object has filters that may or may not have been applied to it.
Each row may have additional info fields associated with each allele in the row.
Alternatively, the get_info() method can be invoked by just passing the header. In this case, the whole info field is returned organised as a hash ref where keys are the info IDs and values are the info fields for the corresponding ID.
Formats are dealt with similarly to info fields.
Alternatively, the get_format() method can be invoked by just passing the header. In this case, it returns the complete format specification as a hash ref of FORMAT_ID => [ FORMAT_ID_VALUE, ... ].
Genotype records are currently returned as a series of integers, across all the samples for the row.
Open the file and process using sweeps. Note that the two methods maintain pointers that are independant of one another. Using the next_row() will start at the first row in the file and go on to the next row in subsequent reads. This is independant of previous_row() calls. Similarly previous_row() will start at the last row and read backwards. However a call to next_row() is needed beforehand as the read fails otherwise.
At the time of writing there are issues which seem to be due to the underlying HTSlib API calls, so using the next() function is preferable to using sweeps.
use Bio::DB::HTS::VCF ; my $sweep = Bio::DB::HTS::VCFSweep->new(filename => "data/test.vcf.gz"); $sweep->header; my $row_forwards = $sweep->next_row(); #returns first row in file my $row_backwards = $sweep->previous_row(); #returns last row in file my $row_forwards = $sweep->next_row(); # returns second row in file my $row_backwards = $sweep->previous_row(); #returns penultimate row in file
| 2024-03-31 | perl v5.38.2 |