Mercurial > repos > tomnl > metfrag
comparison metfrag.py @ 5:c53ed894d736 draft
planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 826659b9105b635cf240474428122f5a269f5c88
| author | tomnl |
|---|---|
| date | Fri, 02 Aug 2019 11:38:06 -0400 |
| parents | eb581a101672 |
| children | 0b3816a7a14b |
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| 4:eb581a101672 | 5:c53ed894d736 |
|---|---|
| 59 | 59 |
| 60 args = parser.parse_args() | 60 args = parser.parse_args() |
| 61 print(args) | 61 print(args) |
| 62 | 62 |
| 63 if os.stat(args.input_pth).st_size == 0: | 63 if os.stat(args.input_pth).st_size == 0: |
| 64 exit('Input file empty') | 64 print('Input file empty') |
| 65 exit() | |
| 65 | 66 |
| 66 | 67 |
| 67 # Create temporary working directory | 68 # Create temporary working directory |
| 68 if args.temp_dir: | 69 if args.temp_dir: |
| 69 wd = args.temp_dir | 70 wd = args.temp_dir |
| 381 ###################################################################### | 382 ###################################################################### |
| 382 # outputs might have different headers. Need to get a list of all the headers before we start merging the files | 383 # outputs might have different headers. Need to get a list of all the headers before we start merging the files |
| 383 # outfiles = [os.path.join(wd, f) for f in glob.glob(os.path.join(wd, "*_metfrag_result.csv"))] | 384 # outfiles = [os.path.join(wd, f) for f in glob.glob(os.path.join(wd, "*_metfrag_result.csv"))] |
| 384 outfiles = glob.glob(os.path.join(wd, "*_metfrag_result.csv")) | 385 outfiles = glob.glob(os.path.join(wd, "*_metfrag_result.csv")) |
| 385 | 386 |
| 387 if len(outfiles) == 0: | |
| 388 print('No results') | |
| 389 sys.exit() | |
| 390 | |
| 386 headers = [] | 391 headers = [] |
| 387 c = 0 | 392 c = 0 |
| 388 for fn in outfiles: | 393 for fn in outfiles: |
| 389 with open(fn, 'r') as infile: | 394 with open(fn, 'r') as infile: |
| 390 reader = csv.reader(infile) | 395 reader = csv.reader(infile) |
| 398 if i == 1: | 403 if i == 1: |
| 399 break | 404 break |
| 400 | 405 |
| 401 # if no data rows (e.g. matches) then do not save an output and leave the program | 406 # if no data rows (e.g. matches) then do not save an output and leave the program |
| 402 if c == 0: | 407 if c == 0: |
| 408 print('No results') | |
| 403 sys.exit() | 409 sys.exit() |
| 404 | 410 |
| 405 additional_detail_headers = ['sample_name'] | 411 additional_detail_headers = ['sample_name'] |
| 406 for k, paramd in six.iteritems(paramds): | 412 for k, paramd in six.iteritems(paramds): |
| 407 additional_detail_headers = list(set(additional_detail_headers + list(paramd['additional_details'].keys()))) | 413 additional_detail_headers = list(set(additional_detail_headers + list(paramd['additional_details'].keys()))) |