--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/subtools.py	Wed Dec 21 12:13:04 2016 -0500
@@ -0,0 +1,245 @@
+#!/usr/bin/python
+# -*- coding: utf8 -*-
+
+"""
+This class handles the subprocess calls of the different tools used
+in HubArchiveCreator
+"""
+
+import logging
+import os
+import subprocess
+import sys
+
+class PopenError(Exception):
+    def __init__(self, cmd, error, return_code):
+        self.cmd = cmd
+        self.error = error
+        self.return_code = return_code
+
+    def __str__(self):
+        message = "The subprocess {0} has returned the error: {1}.".format(self.cmd, self.return_code)
+        message = ','.join((message, "Its error message is: {0}".format(self.error)))
+        return repr(message)
+
+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
+    """
+    stdout = kwargs.get('stdout', subprocess.PIPE)
+    stderr = kwargs.get('stderr', subprocess.PIPE)
+    shell = kwargs.get('shell', False)
+
+    cmd = array_call[0]
+
+    output = None
+    error = None
+
+    # TODO: Check the value of array_call and <=[0]
+    logging.debug("Calling {0}:".format(cmd))
+
+    logging.debug("---------")
+
+    # TODO: Use universal_newlines option from Popen?
+    try:
+        p = subprocess.Popen(array_call, stdout=stdout, stderr=stderr, shell=shell)
+
+        # TODO: Change this because of possible memory issues => https://docs.python.org/2/library/subprocess.html#subprocess.Popen.communicate
+
+        output, error = p.communicate()
+
+        if stdout == subprocess.PIPE:
+            logging.debug("\t{0}".format(output))
+        else:
+            logging.debug("\tOutput in file {0}".format(stdout.name))
+        # If we detect an error from the subprocess, then we raise an exception
+        # TODO: Manage if we raise an exception for everything, or use CRITICAL etc... but not stop process
+        # TODO: The responsability of returning a sys.exit() should not be there, but up in the app.
+        if p.returncode:
+            if stderr == subprocess.PIPE:
+                raise PopenError(cmd, error, p.returncode)
+            else:
+                # TODO: To Handle properly with a design behind, if we received a option as a file for the error
+                raise Exception("Error when calling {0}. Error as been logged in your file {1}. Error code: {2}"\
+                                .format(cmd, stderr.name, p.returncode))
+
+    except OSError as e:
+        message = "The subprocess {0} has encountered an OSError: {1}".format(cmd, e.strerror)
+        if e.filename:
+            message = '\n'.join((message, ", against this file: {0}".format(e.filename)))
+        logging.error(message)
+        sys.exit(-1)
+    except PopenError as p:
+        message = "The subprocess {0} has returned the error: {1}.".format(p.cmd, p.return_code)
+        message = '\n'.join((message, "Its error message is: {0}".format(p.error)))
+
+        logging.exception(message)
+
+        sys.exit(p.return_code)
+    except Exception as e:
+        message = "The subprocess {0} has encountered an unknown error: {1}".format(cmd, e)
+        logging.exception(message)
+
+        sys.exit(-1)
+    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, twoBitFile):
+    """
+    This function call faToTwoBit UCSC tool, and return the twoBitFile
+    :param fasta_file_name:
+    :param mySpecieFolder:
+    :return:
+    """
+
+    array_call = ['faToTwoBit', fasta_file_name, twoBitFile]
+    _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 genePredToBigGenePred(gene_pred_file_name, unsorted_bigGenePred_file_name):
+    """
+    Call genePredToBigGenePred and write the result into unsorted_bigGenePred_file_name
+    :param gene_pred_file_name:
+    :param unsorted_bigGenePred_file_name:
+    :return:
+    """
+    array_call = ['genePredToBigGenePred',
+                  gene_pred_file_name,
+                  unsorted_bigGenePred_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, tab=False):
+    """
+    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:
+    """
+
+    # TODO: Move this into the _handleExceptionAndCheckCall function
+    # Parse the array
+    logging.debug("sorted_bed_file_name: {0}".format(sorted_bed_file_name))
+    logging.debug("chrom_sizes_file_name: {0}".format(chrom_sizes_file_name))
+    logging.debug("big_bed_file_name: {0}".format(big_bed_file_name))
+    logging.debug("typeOption: {0}".format(typeOption))
+    logging.debug("autoSql: {0}".format(autoSql))
+    logging.debug("tab option: {0}".format(tab))
+
+    array_call = ['bedToBigBed', sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name]
+    if typeOption:
+        typeOption = ''.join(['-type=', typeOption])
+        array_call.append(typeOption)
+    if autoSql:
+        autoSql = ''.join(['-as=', autoSql])
+        array_call.append(autoSql)
+    if tab:
+        array_call.append('-tab')
+
+    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
+
+def pslToBigPsl(input_psl_file_name, output_bed12_file_name):
+    """
+    Call `pslToBigPsl` on input_psl_file_name and output the result in output_bed12_file_name
+    :param input_psl_file_name: Name of the psl input file
+    :param output_bed12_file_name: Name of the output file where to store the result of the cmd
+    :return:
+    """
+    # The command to send
+    array_call = ['pslToBigPsl', input_psl_file_name, output_bed12_file_name]
+
+    p = _handleExceptionAndCheckCall(array_call)
+    return p