CrossMapper.py

import urllib.request
import os
from Modules import CrossMap


class CrossMapper:

    """

    Class to download chain_files for chrossmapping hg38 or mm10 to older assembly versions.
    Utilizes CrossMap.py. see wiki for more information.

    """

    def __init__(self, org, wd, out, is_dir):
        self.org = org
        if is_dir:
            self.infile = os.path.join( wd + "/temp/" + org + ".gtf")
        else:
            self.infile = os.path.join(wd+"/data/temp/"+org+".gtf")
        self.outfile = os.path.join(out+"/" + org + "_mapped.gtf")
        self.chainfile = self.get_chain_file(org, wd, is_dir)
        # Execute Crossmapper for gff/gtf files
        (mapTree, targetChromSizes, sourceChromSizes) = CrossMap.read_chain_file(self.chainfile)
        CrossMap.crossmap_gff_file(mapTree, self.infile, self.outfile)

    def get_chain_file(self, org, wd, isdir):

        # Defines the Chain files for different conversions.

        if org == "hg19":
            if isdir:
                file_link = os.path.join(wd+"temp/hg38tohg19.over.chain.gz")
            else:
                file_link = os.path.join(wd + "/data/temp/hg38tohg19.over.chain.gz" )
            urllib.request.urlretrieve("http://hgdownload.soe.ucsc.edu/goldenPath/hg38/"
                                       "liftOver/hg38ToHg19.over.chain.gz",
                                       file_link)
            return file_link

        elif org == "mm9":
            if isdir:
                file_link = os.path.join(wd+"temp/mm10ToMm9.over.chain.gz")
            else:
                file_link = os.path.join(wd + "/data/temp/hg38tohg19.over.chain.gz" )
            urllib.request.urlretrieve("http://hgdownload.soe.ucsc.edu/goldenPath/mm10/"
                                       "liftOver/mm10ToMm9.over.chain.gz",
                                       file_link)
            return file_link