mmagnus /
rna-tools
| @@ 357-411 (lines=55) @@ | ||
| 354 | return parser |
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| 355 | ||
| 356 | # main |
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| 357 | if __name__ == '__main__': |
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| 358 | parser = get_parser() |
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| 359 | args = parser.parse_args() |
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| 360 | if not args.debug: |
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| 361 | ic.disable() |
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| 362 | ||
| 363 | target = RNAmodel(args.target) |
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| 364 | ||
| 365 | # a trick to get files be default if there is only a path (so a string ;-)) |
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| 366 | if not isinstance(args.files, str): |
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| 367 | models = args.files |
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| 368 | else: |
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| 369 | import glob |
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| 370 | models = glob.glob(args.files) # opts.input_dir |
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| 371 | ||
| 372 | ## tmp = [] |
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| 373 | ## if args.ignore_files: |
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| 374 | ## for f in args.files: |
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| 375 | ## if args.debug: print(f) |
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| 376 | ## if args.ignore_files in f: |
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| 377 | ## continue |
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| 378 | ## tmp.append(f) |
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| 379 | ## models = tmp |
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| 380 | ||
| 381 | print('# of models:', len(models)) |
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| 382 | ||
| 383 | c = 1 |
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| 384 | t = 'fn,' + args.column_name + '\n' # ,aligned_seq, aligned_fn\n' |
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| 385 | for m in models: |
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| 386 | mrna = RNAmodel(m) |
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| 387 | #print r1.fn, r2.fn, r1.get_rmsd_to(r2)#, 'tmp.pdb') |
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| 388 | # print(m) |
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| 389 | rmsd = target.get_rmsd_to(mrna, args.way, args.triple_mode, args.save, args.tseq) #, 'tmp.pdb') |
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| 390 | #except: |
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| 391 | if 0: |
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| 392 | print(m) |
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| 393 | sys.exit(1) |
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| 394 | #print rmsd |
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| 395 | t += mrna.fn + ',' + str(rmsd) + '\n' |
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| 396 | #break |
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| 397 | ||
| 398 | print(t.strip()) |
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| 399 | ||
| 400 | if args.result: |
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| 401 | with open(args.result, 'w') as f: |
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| 402 | f.write(t) |
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| 403 | ||
| 404 | if args.sort: |
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| 405 | import pandas as pd |
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| 406 | df = pd.read_csv(args.result) |
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| 407 | df = df[df.rmsd != -1] |
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| 408 | df = df.sort_values('rmsd') |
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| 409 | df.to_csv(args.result, index=False) |
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| 410 | print('saved: %s' % args.result) |
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| 411 | print(df.to_string(index=False)) |
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| 412 | ||
| @@ 299-353 (lines=55) @@ | ||
| 296 | return parser |
|
| 297 | ||
| 298 | # main |
|
| 299 | if __name__ == '__main__': |
|
| 300 | parser = get_parser() |
|
| 301 | args = parser.parse_args() |
|
| 302 | if not args.debug: |
|
| 303 | ic.disable() |
|
| 304 | ||
| 305 | target = RNAmodel(args.target) |
|
| 306 | ||
| 307 | # a trick to get files be default if there is only a path (so a string ;-)) |
|
| 308 | if not isinstance(args.files, str): |
|
| 309 | models = args.files |
|
| 310 | else: |
|
| 311 | import glob |
|
| 312 | models = glob.glob(args.files) # opts.input_dir |
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| 313 | ||
| 314 | ## tmp = [] |
|
| 315 | ## if args.ignore_files: |
|
| 316 | ## for f in args.files: |
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| 317 | ## if args.debug: print(f) |
|
| 318 | ## if args.ignore_files in f: |
|
| 319 | ## continue |
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| 320 | ## tmp.append(f) |
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| 321 | ## models = tmp |
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| 322 | ||
| 323 | print('# of models:', len(models)) |
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| 324 | ||
| 325 | c = 1 |
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| 326 | t = 'fn,' + args.column_name + '\n' # ,aligned_seq, aligned_fn\n' |
|
| 327 | for m in models: |
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| 328 | mrna = RNAmodel(m) |
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| 329 | #print r1.fn, r2.fn, r1.get_rmsd_to(r2)#, 'tmp.pdb') |
|
| 330 | # print(m) |
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| 331 | rmsd = target.get_rmsd_to(mrna, args.way, args.triple_mode, args.save, args.tseq) #, 'tmp.pdb') |
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| 332 | #except: |
|
| 333 | if 0: |
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| 334 | print(m) |
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| 335 | sys.exit(1) |
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| 336 | #print rmsd |
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| 337 | t += mrna.fn + ',' + str(rmsd) + '\n' |
|
| 338 | #break |
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| 339 | ||
| 340 | if args.show: |
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| 341 | print(t.strip()) # all the data |
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| 342 | ||
| 343 | if args.result: |
|
| 344 | with open(args.result, 'w') as f: |
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| 345 | f.write(t) |
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| 346 | ||
| 347 | if args.sort: |
|
| 348 | import pandas as pd |
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| 349 | df = pd.read_csv(args.result) |
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| 350 | df = df[df.rmsd != -1] |
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| 351 | df = df.sort_values('rmsd') |
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| 352 | df.to_csv(args.result, index=False) |
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| 353 | print('saved: %s' % args.result) |
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| 354 | # print(df.to_string(index=False)) |
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| 355 | ||
