view util/subtools.py @ 9:4f9847539a28 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b241bbccfc1b90ce2626dc4f49788bb9e693a80

#!/usr/bin/python
# -*- coding: utf8 -*-

"""
This class handles the subprocess calls of the different tools used
in HubArchiveCreator
"""

import os
import subprocess


def _handleExceptionAndCheckCall(array_call, **kwargs):
    """
    This class handle exceptions and call the tool.
    It maps the signature of subprocess.check_call:
    See https://docs.python.org/2/library/subprocess.html#subprocess.check_call
    """
    stdin = kwargs.get('stdin')
    stdout = kwargs.get('stdout')
    stderr = kwargs.get('stderr')
    shell = kwargs.get('shell')
    try:
        p = subprocess.check_call(array_call, stdin=stdin, stdout=stdout, stderr=stderr, shell=shell)
    except subprocess.CalledProcessError:
        raise
    return p


def twoBitInfo(two_bit_file_name, two_bit_info_file):
    """
    Call twoBitInfo and write the result into twoBit_info_file
    :param two_bit_file_name:
    :param two_bit_info_file:
    :return the subprocess.check_call return object:
    """
    array_call = ['twoBitInfo', two_bit_file_name, two_bit_info_file]
    p = _handleExceptionAndCheckCall(array_call)
    return p


def faToTwoBit(fasta_file_name, mySpecieFolder):
    """
    This function call faToTwoBit UCSC tool, and return the twoBitFile
    :param fasta_file_name:
    :param mySpecieFolder:
    :return:
    """
    baseNameFasta = os.path.basename(fasta_file_name)
    suffixTwoBit, extensionTwoBit = os.path.splitext(baseNameFasta)
    nameTwoBit = suffixTwoBit + '.2bit'

    with open(os.path.join(mySpecieFolder, nameTwoBit), 'w') as twoBitFile:
        array_call = ['faToTwoBit', fasta_file_name, twoBitFile.name]
        _handleExceptionAndCheckCall(array_call)

    return twoBitFile


def gtfToGenePred(input_gtf_file_name, gene_pred_file_name):
    """
    Call gtfToGenePred and write the result into gene_pred_file_name
    :param input_gtf_file_name:
    :param gene_pred_file_name:
    :return:
    """
    array_call = ['gtfToGenePred', input_gtf_file_name, gene_pred_file_name]
    p = _handleExceptionAndCheckCall(array_call)
    return p


def gff3ToGenePred(input_gff3_file_name, gene_pred_file_name):
    """
    Call gff3ToGenePred and write the result into gene_pred_file_name
    :param input_gff3_file_name:
    :param gene_pred_file_name:
    :return:
    """
    array_call = ['gff3ToGenePred', input_gff3_file_name, gene_pred_file_name]
    p = _handleExceptionAndCheckCall(array_call)
    return p


def genePredToBed(gene_pred_file_name, unsorted_bed_file_name):
    """
    Call genePredToBed and write the result into unsorted_bed_file_name
    :param gene_pred_file_name:
    :param unsorted_bed_file_name:
    :return:
    """
    array_call = ['genePredToBed', gene_pred_file_name, unsorted_bed_file_name]
    p = _handleExceptionAndCheckCall(array_call)
    return p


def sort(unsorted_bed_file_name, sorted_bed_file_name):
    """
    Call sort with -k1,1 -k2,2n on unsorted_bed_file_name and write the result into sorted_bed_file_name
    :param unsorted_bed_file_name:
    :param sorted_bed_file_name:
    :return:
    """
    array_call = ['sort', '-k', '1,1', '-k', '2,2n', unsorted_bed_file_name, '-o', sorted_bed_file_name]
    p = _handleExceptionAndCheckCall(array_call)
    return p


def sortChromSizes(two_bit_info_file_name, chrom_sizes_file_name):
    """
    Call sort with -k2rn on two_bit_info_file_name and write the result into chrom_sizes_file_name
    :param two_bit_info_file_name:
    :param chrom_sizes_file_name:
    :return:
    """
    array_call = ['sort', '-k2rn', two_bit_info_file_name, '-o', chrom_sizes_file_name]
    p = _handleExceptionAndCheckCall(array_call)
    return p


def bedToBigBed(sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name, typeOption=None, autoSql=None):
    """
    Call bedToBigBed on sorted_bed_file_name, using chrom_sizes_file_name and write the result into big_bed_file_name
    :param sorted_bed_file_name:
    :param chrom_sizes_file_name:
    :param big_bed_file_name:
    :return:
    """
    array_call = ['bedToBigBed', sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name]
    if typeOption:
        array_call.append(typeOption)
    if autoSql:
        array_call.append(autoSql)

    p = _handleExceptionAndCheckCall(array_call)
    return p


def sortBam(input_bam_file_name, output_sorted_bam_name):
    """
    Call samtools on input_bam_file_name and output the result in output_sorted_bam_name
    :param input_bam_file_name:
    :param output_sorted_bam_name:
    :return:
    """
    array_call = ['samtools', 'sort', input_bam_file_name, '-o', output_sorted_bam_name]
    p = _handleExceptionAndCheckCall(array_call)
    return p


def createBamIndex(input_sorted_bam_file_name, output_name_index_name):
    """
    Call `samtools index` on imput_sorted_bam_file_name and output the result in output_name_index_name
    :param input_sorted_bam_file_name:
    :param output_name_index_name:
    :return:
    """
    array_call = ['samtools', 'index', input_sorted_bam_file_name, output_name_index_name]
    p = _handleExceptionAndCheckCall(array_call)
    return p