| Previous changeset 0:2d6315e241e4 (2017-05-10) Next changeset 2:0ea254c514b7 (2017-05-24) |
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Commit message:
Uploaded |
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added:
fseq_wrapper.py |
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| diff -r 2d6315e241e4 -r 29760e9a840b fseq_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fseq_wrapper.py Wed May 24 00:35:08 2017 -0400 |
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| @@ -0,0 +1,57 @@ +#/usr/bin/python + +import optparse, sys, subprocess, tempfile +import shutil, os + +CHUNK_SIZE = 2**20 #1mbi + +def cleanup_before_exit( tmp_dir ): + if tmp_dir and os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + +def __main__(): + parser = optparse.OptionParser() + parser.add_option( '-p', '--pass_through', dest='pass_through_options', action='append', type="string", help='These options are passed through directly to GATK, without any modification.' ) + parser.add_option('', '--of', dest='output_format', action='store', type="string", help='output format') + parser.add_option('-i', '--input-files', dest='input_files', action='store', type="string", help='input files') + parser.add_option( '-o', '--output-file', dest='output_file', action='store', type="string", default=None, help='bed output' ) + + (options, args) = parser.parse_args() + pass_through = "" + if options.pass_through_options: + pass_through = ' '.join( options.pass_through_options ) + + cmd = "fseq %s -of %s %s" % (pass_through, options.output_format, options.input_files) + print cmd + tmp_dir = tempfile.mkdtemp( prefix='tmp-tool-' ) + + stdout = tempfile.NamedTemporaryFile( prefix="fseq-stdout-", dir=tmp_dir ) + stderr = tempfile.NamedTemporaryFile( prefix="fseq-stderr-", dir=tmp_dir ) + proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir ) + return_code = proc.wait() + + if return_code: + stderr_target = sys.stderr + else: + stderr_target = sys.stdout + stderr.flush() + stderr.seek(0) + + while True: + chunk = stderr.read( CHUNK_SIZE ) + if chunk: + stderr_target.write( chunk ) + else: + break + stderr.close() + stdout.close() + if options.output_format == 'bed': + os.system("cat %s/*.bed > %s/output.bed" % (tmp_dir, tmp_dir)) + shutil.copy("%s/output.bed" % tmp_dir, options.output_file) + else: + os.system("cat %s/*.wig > %s/output.wig" % (tmp_dir, tmp_dir)) + shutil.copy("%s/output.wig" % tmp_dir, options.output_file) + + cleanup_before_exit( tmp_dir ) + +if __name__ == "__main__": __main__() |