Metadata-Version: 1.1
Name: pytabix
Version: 0.1
Summary: Python interface for tabix
Home-page: https://github.com/slowkow/pytabix
Author: Hyeshik Chang, Kamil Slowikowski
Author-email: hyeshik@snu.ac.kr, slowikow@broadinstitute.org
License: MIT
Description: April 16, 2014
        
        This module allows fast random access to files compressed with bgzip_ and
        indexed by tabix_. It includes a C extension with code from klib_. The bgzip
        and tabix programs are available here_.
        
        
        Installation
        ------------
        
        ::
        
            pip install --user pytabix
        
        
        Synopsis
        --------
        
        Genomics data is often in a table where each row corresponds to a genomic
        region (start, end) or a position:
        
        
        ::
        
            chrom  pos      snp
            1      1000760  rs75316104
            1      1000894  rs114006445
            1      1000910  rs79750022
            1      1001177  rs4970401
            1      1001256  rs78650406
        
        
        With tabix_, you can quickly retrieve all rows in a genomic region by
        specifying a query with a sequence name, start, and end:
        
        
        ::
        
            import tabix
        
            # Open a remote or local file.
            url = "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/"
            url += "ALL.2of4intersection.20100804.genotypes.vcf.gz"
        
            tb = tabix.open(url)
        
            # These queries are identical. A query returns an iterator over the results.
            records = tb.query("1", 1000000, 1250000)
        
            records = tb.queryi(0, 1000000, 1250000)
        
            records = tb.querys("1:1000000-1250000")
        
            # Each record is a list of strings.
            for record in records:
                print record[:5]
                break
        
        
        ::
        
            ['1', '1000071', '.', 'C', 'T']
        
        
        .. _bgzip: http://samtools.sourceforge.net/tabix.shtml
        .. _tabix: http://samtools.sourceforge.net/tabix.shtml
        .. _klib: https://github.com/jmarshall/klib
        .. _here: http://sourceforge.net/projects/samtools/files/tabix/
        
        
Keywords: tabix,bgzip,bioinformatics,genomics
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: C
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
