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
#!/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
