hubarchivecreator: util/subtools.py comparison

comparison util/subtools.py @ 16:3233451a3bd6 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c

author	rmarenco
date	Sun, 25 Sep 2016 11:25:38 -0400
parents	25809f699cb3
children	884ee2a71680

comparison

equal deleted inserted replaced

-:2a45cd656e8e
+:3233451a3bd6
 """
 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', subprocess.PIPE)
-stdout = kwargs.get('stdout')
+stderr = kwargs.get('stderr', subprocess.PIPE)
-stderr = kwargs.get('stderr')
+shell = kwargs.get('shell', False)
-shell = kwargs.get('shell')
 cmd = array_call[0]
 output = None
 error = None
 logging.debug("---------")
 # TODO: Use universal_newlines option from Popen?
 try:
-p = subprocess.Popen(array_call, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=shell)
+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()
-logging.debug("\t{0}".format(output))
+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:
-raise PopenError(cmd, error, 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.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:
 """
 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:
 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:
 """
 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:
 """
 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
 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:
 """
 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

Mercurial > repos > rmarenco > hubarchivecreator

comparison util/subtools.py @ 16:3233451a3bd6 draft