Mercurial > repos > modencode-dcc > spp_package
comparison spp_wrapper.py @ 10:c57381059179 draft
Uploaded
| author | modencode-dcc |
|---|---|
| date | Thu, 07 Feb 2013 23:06:21 -0500 |
| parents | dfdaa943f855 |
| children | d063cc917090 |
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| 9:dfdaa943f855 | 10:c57381059179 |
|---|---|
| 45 cmdline = "%s -s=%s %s -x=%s -fdr=%s -npeak=%s %s %s" % ( cmdline, options['s'], options['speak'], options['x'], options['fdr'], options['npeak'], options['filtchr'], options['rf'] ) | 45 cmdline = "%s -s=%s %s -x=%s -fdr=%s -npeak=%s %s %s" % ( cmdline, options['s'], options['speak'], options['x'], options['fdr'], options['npeak'], options['filtchr'], options['rf'] ) |
| 46 cmdline = "%s %s %s %s %s %s > default_output.txt" % ( cmdline, options['out'], options['savn'], options['savr'], options['savp'], options['savd'] ) | 46 cmdline = "%s %s %s %s %s %s > default_output.txt" % ( cmdline, options['out'], options['savn'], options['savr'], options['savp'], options['savd'] ) |
| 47 | 47 |
| 48 #run cmdline | 48 #run cmdline |
| 49 #======================================================================================== | 49 #======================================================================================== |
| 50 tmp_dir = tempfile.mkdtemp() | 50 #tmp_dir = tempfile.mkdtemp() |
| 51 tmp_dir = os.path.dirname(options['chip_file']) | |
| 51 stderr_name = tempfile.NamedTemporaryFile().name | 52 stderr_name = tempfile.NamedTemporaryFile().name |
| 52 proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) ) | 53 proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) ) |
| 53 proc.wait() | 54 proc.wait() |
| 54 | 55 |
| 55 #Do not terminate if error code, allow dataset (e.g. log) creation and cleanup | 56 #Do not terminate if error code, allow dataset (e.g. log) creation and cleanup |
| 64 sys.stderr.write( chunk ) | 65 sys.stderr.write( chunk ) |
| 65 | 66 |
| 66 | 67 |
| 67 #determine if the outputs are there, copy them to the appropriate dir and filename | 68 #determine if the outputs are there, copy them to the appropriate dir and filename |
| 68 #======================================================================================== | 69 #======================================================================================== |
| 70 chip_name = os.path.basename(options['chip_file']) | |
| 71 input_name = os.path.basename(options['input_file']) | |
| 72 | |
| 69 created_default_file = os.path.join( tmp_dir, "default_output.txt" ) | 73 created_default_file = os.path.join( tmp_dir, "default_output.txt" ) |
| 70 if os.path.exists( created_default_file ): | 74 if os.path.exists( created_default_file ): |
| 71 shutil.move( created_default_file, output_default_file ) | 75 shutil.move( created_default_file, output_default_file ) |
| 72 | 76 |
| 73 chip_name = os.path.basename(options['chip_file']) | 77 created_narrow_peak = os.path.join( tmp_dir, "%s_VS_%s.narrowPeak" % (chip_name, input_name) ) |
| 74 input_name = os.path.basename(options['input_file']) | |
| 75 created_narrow_peak = os.path.join( tmp_dir, "%s_VS_%s.narrowPeak.gz" % (chip_name, input_name) ) | |
| 76 if os.path.exists( created_narrow_peak ): | 78 if os.path.exists( created_narrow_peak ): |
| 77 shutil.move( created_narrow_peak, output_narrow_peak ) | 79 shutil.move( created_narrow_peak, output_narrow_peak ) |
| 78 | 80 |
| 79 created_region_peak = os.path.join( tmp_dir, "%s_VS_%s.regionPeak.gz" % (chip_name, input_name) ) | 81 created_region_peak = os.path.join( tmp_dir, "%s_VS_%s.regionPeak" % (chip_name, input_name) ) |
| 80 if os.path.exists( created_region_peak ): | 82 if os.path.exists( created_region_peak ): |
| 81 shutil.move( created_region_peak, output_region_peak ) | 83 shutil.move( created_region_peak, output_region_peak ) |
| 82 | 84 |
| 83 created_peakshift_file = os.path.join( tmp_dir, "peakshift.txt" ) | 85 created_peakshift_file = os.path.join( tmp_dir, "peakshift.txt" ) |
| 84 if os.path.exists( created_peakshift_file ): | 86 if os.path.exists( created_peakshift_file ): |
| 85 shutil.move( created_peakshift_file, output_peakshift_file ) | 87 shutil.move( created_peakshift_file, output_peakshift_file ) |
| 86 | 88 |
| 87 created_rdata_file = os.path.join( tmp_dir, "%s.Rdata" % options['chip_file'] ) | 89 created_rdata_file = os.path.join( tmp_dir, "%s.Rdata" % chip_name ) |
| 88 if os.path.exists( created_rdata_file ): | 90 if os.path.exists( created_rdata_file ): |
| 89 shutil.move( created_rdata_file, output_rdata_file ) | 91 shutil.move( created_rdata_file, output_rdata_file ) |
| 90 | 92 |
| 91 created_plot_file = os.path.join( tmp_dir, "%s.pdf" % options['chip_file'] ) | 93 created_plot_file = os.path.join( tmp_dir, "%s.pdf" % chip_name ) |
| 92 if os.path.exists( created_plot_file ): | 94 if os.path.exists( created_plot_file ): |
| 93 shutil.move( created_plot_file, output_plot_file ) | 95 shutil.move( created_plot_file, output_plot_file ) |
| 94 | 96 |
| 95 | 97 |
| 96 os.unlink( stderr_name ) | 98 os.unlink( stderr_name ) |