Python pysam.faidx() Examples

The following are 4 code examples of pysam.faidx(). You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may also want to check out all available functions/classes of the module pysam , or try the search function .
Example #1
Source File: samtools_variants.py    From ariba with GNU General Public License v3.0 6 votes vote down vote up 
def _make_vcf_and_read_depths_files(self):
        if not os.path.exists(self.ref_fa + '.fai'):
            pysam.faidx(self.ref_fa)

        tmp_vcf = self.vcf_file + '.tmp'
        with open(tmp_vcf, 'w') as f:
            print(pysam.mpileup(
                '-t', 'INFO/AD,INFO/ADF,INFO/ADR',
                '-L', '99999999',
                '-A',
                '-f', self.ref_fa,
                '-u',
                '-v',
                self.bam,
            ), end='', file=f)

        got = vcfcall_ariba.vcfcall_ariba(tmp_vcf, self.outprefix, self.min_var_read_depth, self.min_second_var_read_depth, self.max_allele_freq)
        if got != 0:
            raise Error('Error parsing vcf file. Cannot contine')

        pysam.tabix_compress(self.outprefix + '.read_depths', self.read_depths_file)
        pysam.tabix_index(self.read_depths_file, seq_col=0, start_col=1, end_col=1)
        os.unlink(self.outprefix + '.read_depths')
        os.unlink(tmp_vcf)
Example #2
Source File: pipeline_variants.py    From CGATPipelines with MIT License 6 votes vote down vote up 
def indexGenome(infile, outfile):
    '''index the genome for samtools.

    Samtools does not like long lines, so create a new file
    with split lines (what a waste).
    '''

    # statement = '''fold %(infile)s | perl -p -e "s/chr//" > %(outfile)s'''
    statement = '''fold %(infile)s > %(outfile)s'''
    P.run()

    pysam.faidx(outfile)

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Example #3
Source File: kmer_repeat_counter.py    From MANTIS with GNU General Public License v3.0 5 votes vote down vote up 
def get_sequence(self, locus):
        if self.genome_path is None:
            tprint('MSILocusLoader error: Can not use .get_sequence() without' 
                + ' specifying the path to the reference genome!')
            exit(1)
    
        sequence = []
        for subseq in pysam.faidx(self.genome_path, locus)[1:]:
            sequence.append(subseq.strip())
        return ''.join(sequence).upper()
        # end .get_sequence()    

    # end MSILocusLoader class definition.
Example #4
Source File: faidx.py    From ariba with GNU General Public License v3.0 5 votes vote down vote up 
def write_fa_subset(seq_names, infile, outfile):
    if not os.path.exists(infile + '.fai'):
        pysam.faidx(infile)

    f = pyfastaq.utils.open_file_write(outfile)
    for name in seq_names:
        print(pysam.faidx(infile, name), end='', file=f)
    pyfastaq.utils.close(f)