import math usage = 'compare-inspect.py <inspect output file1> <inspect output file2>' usage += ' <png file>(optional)' if(len(sys.argv) != 3 and len(sys.argv) != 4): print usage sys.exit(1) file1 = sys.argv[1] file2 = sys.argv[2] file_png = '' if( len(sys.argv) == 4 ): file_png = sys.argv[3] inspect1 = inspect.read_inspect_out(file1) inspect2 = inspect.read_inspect_out(file2) sample_name1 = file1 sample_name2 = file2 re_sample_name = re.compile('([A-z0-9\_]+)\.inspect') if( re_sample_name.search(sample_name1) ): rv = re_sample_name.search(sample_name1) sample_name1 = rv.group(1) if( re_sample_name.search(sample_name2) ): rv = re_sample_name.search(sample_name2) sample_name2 = rv.group(1) proteins = dict() peptides = dict() for ms2 in inspect1.values():
import math usage = 'compare-inspect.py <inspect output file1> <inspect output file2>' usage += ' <png file>(optional)' if (len(sys.argv) != 3 and len(sys.argv) != 4): print usage sys.exit(1) file1 = sys.argv[1] file2 = sys.argv[2] file_png = '' if (len(sys.argv) == 4): file_png = sys.argv[3] inspect1 = inspect.read_inspect_out(file1) inspect2 = inspect.read_inspect_out(file2) sample_name1 = file1 sample_name2 = file2 re_sample_name = re.compile('([A-z0-9\_]+)\.inspect') if (re_sample_name.search(sample_name1)): rv = re_sample_name.search(sample_name1) sample_name1 = rv.group(1) if (re_sample_name.search(sample_name2)): rv = re_sample_name.search(sample_name2) sample_name2 = rv.group(1) proteins = dict() peptides = dict() for ms2 in inspect1.values():
#!/usr/bin/python2.5 import marcottelab.inspect as inspect import marcottelab.pepxml as pepxml import sys file_inspect_out = sys.argv[1] for rv in inspect.read_inspect_out(file_inspect_out).values(): print rv.start_scan_id