"""
Copyright 2015-2025 Stephane De Mita, Mathieu Siol
This file is part of EggLib.
EggLib is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
EggLib is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with EggLib. If not, see <http://www.gnu.org/licenses/>.
"""
from ._ms import to_ms
from ._fasta import fasta_iter, from_fasta, from_fasta_string
from ._gff3 import GFF3, Gff3Feature
from ._vcf import VcfParser, VcfStringParser, VcfVariant, make_vcf_index, VcfSlidingWindow, VcfWindow, BED
from ._genbank import GenBank, GenBankFeature, GenBankFeatureLocation
from ._legacy import from_clustal, from_staden, from_genalys, get_fgenesh
from ._genepop import from_genepop
from .. import config
from .. import _site
from .. import alphabets
#: First available position of a contig.
FIRST = _vcf.FIRST
#: Last available position of a contig.
LAST = _vcf.LAST
try:
from ._vcfparser import VCF, index_vcf
from ._vcfslider import VcfSlider
config.htslib = 1
class VCF(VCF):
[docs]
def as_site(self):
"""
Extract current variant. Return the current genotype values
as a :class:`.Site` object. The alphabet is DNA if the site
is a SNP, or a string-type alphabet with ad hoc alleles
otherwise.
.. versionadded:: 3.4
"""
site = _site.Site()
genotypes = self.get_genotypes()
if genotypes is None:
raise TypeError('genotype field not available for this variant')
match self.get_allele_type():
case 0: alphabet = alphabets.DNA
case 1: alphabet = alphabets.Alphabet('string', self.get_alleles(), ['?'])
case 2: alphabet = alphabets.Alphabet('custom', self.get_alleles(), ['?'])
case None: return None
case _: raise RuntimeError('unexpected return code of VCF.get_allele_type()')
site.from_list([j if j is not None else '?' for i in genotypes for j in i], alphabet = alphabet)
site.position = self.get_pos()
site.chrom = self.get_chrom()
return site
[docs]
def iter_sites(self, *args, **kwargs):
"""iter_sites([chrom[, start][, stop]][, max_missing][, only_snp])
Return an iterator over sites. Each variant found in the VCF
file is returned as a :class:`.Site` instance.
By default, process sites from the current position up to
the end of the file. To control the region used for
iteration, use the *chrom*, *start*, and *stop* argument.
:param chrom: name of the chromosome to process. If *None*,
process all chromosomes. By default (if *start* and
*stop* are not specified) process the whole chromosome,
going back to the first position if needed. Only
available if the VCF is indexed.
:param start: start position. Only allowed if *chrom* is
specified. The first site returned will be at the
smallest available position starting from *start*. By
default, start at the beginning of the chromosome.
:param stop: stop position. Only allowed if *chrom* is
specified. The position of the last site returned will
be a most the one before the *stop* position. By
default, stop at the last site of the chromosome.
:param max_missing: maximum number of missing data to
consider a variant. By default, all sites with at least
one missing data are ignored.
:param mode: 0: include only SNP variants (variants with at
least two alleles, all corresponding to a single
nucleotide, although those alleles are not required to
be called in genotypes); 1: include SNP variants and
invariant positions; 2: include all variants from the
VCF.
.. versionadded:: 3.4
"""
return self.site_iterator(self, *args, **kwargs)
class site_iterator:
def __init__(self, vcf, chrom=None, start=None, stop=None, max_missing=0, mode=0):
if start is not None and chrom is None:
raise ValueError('cannot specify `start` without `chrom`')
if stop is not None:
if stop < 0:
raise ValueError('invalid value for `stop`')
if chrom is None:
raise ValueError('cannot specify `stop` without `chrom`')
if max_missing < 0:
raise ValueError('invalid value for `max_missing`')
if mode not in {0, 1, 2}:
raise ValueError('invalid value for `mode`')
if chrom is not None:
if start is None: self.b = vcf.goto(chrom)
else: self.b = vcf.goto(chrom, start, vcf.END)
else: self.b = vcf.read()
self.vcf = vcf
self.chrom = chrom
self.stop = stop
self.max_missing = max_missing
self.mode = mode
def __iter__(self):
return self
def __next__(self):
while True:
if not self.b: raise StopIteration
if self.chrom is not None and self.vcf.get_chrom() != self.chrom: raise StopIteration
if self.stop is not None and self.vcf.get_pos() >= self.stop: raise StopIteration
if ( (self.mode == 0 and self.vcf.is_snp()) or
(self.mode == 1 and self.vcf.is_single()) or
self.mode == 2 ):
site = self.vcf.as_site()
if site.num_missing <= self.max_missing:
self.b = self.vcf.read()
return site
self.b = self.vcf.read()
VCF.__doc__ = _vcfparser.VCF.__doc__
except ImportError:
config.htslib = 0
[docs]
def VCF(*args, **kwargs):
raise NotImplementedError('EggLib was compiled without htslib. Please refer to the installation instructions on https://egglib.org/install.html for more information.')
def index_vcf(*args, **kwargs):
raise NotImplementedError('EggLib was compiled without htslib. Please refer to the installation instructions on https://egglib.org/install.html for more information.')
def VcfSlider(*args, **kwargs):
raise NotImplementedError('EggLib was compiled without htslib. Please refer to the installation instructions on https://egglib.org/install.html for more information.')
