mmagnus /
rna-tools
| @@ 440-454 (lines=15) @@ | ||
| 437 | """ |
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| 438 | global ref_seq, ref_ss, verbose, methods, lock, c |
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| 439 | ||
| 440 | if opt.seq_ss_filename: |
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| 441 | pdb_id, ref_seq, ref_ss = [x.strip() for x in open(opt.seq_ss_filename).read().strip().split('\n')] |
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| 442 | #sg.phr_text('FASTA SEQ/SS') |
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| 443 | sg.poptions({'AnalyzeGeometry': True, 'SSAgreement' : True}) |
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| 444 | sg.poption('pdb_id', pdb_id) |
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| 445 | sg.poption('ref_seq', ref_seq) |
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| 446 | sg.poption('ref_ss', ref_ss) |
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| 447 | else: |
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| 448 | pdb_id, ref_seq, ref_ss = ['', '', ''] |
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| 449 | sg.poptions({'SSAgreement' : True}) |
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| 450 | # hack |
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| 451 | try: # if it's not on the list |
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| 452 | methods.remove('SSAgreement') |
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| 453 | except ValueError: |
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| 454 | pass |
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| 455 | ||
| 456 | verbose = opt.verbose |
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| 457 | ||
| @@ 417-431 (lines=15) @@ | ||
| 414 | """ |
|
| 415 | global ref_seq, ref_ss, verbose, methods, lock, c |
|
| 416 | ||
| 417 | if opt.seq_ss_filename: |
|
| 418 | pdb_id, ref_seq, ref_ss = [x.strip() for x in open(opt.seq_ss_filename).read().strip().split('\n')] |
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| 419 | #sg.phr_text('FASTA SEQ/SS') |
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| 420 | sg.poptions({'AnalyzeGeometry': True, 'SSAgreement' : True}) |
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| 421 | sg.poption('pdb_id', pdb_id) |
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| 422 | sg.poption('ref_seq', ref_seq) |
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| 423 | sg.poption('ref_ss', ref_ss) |
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| 424 | else: |
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| 425 | pdb_id, ref_seq, ref_ss = ['', '', ''] |
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| 426 | sg.poptions({'SSAgreement' : True}) |
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| 427 | # hack |
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| 428 | try: # if it's not on the list |
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| 429 | methods.remove('SSAgreement') |
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| 430 | except ValueError: |
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| 431 | pass |
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| 432 | ||
| 433 | verbose = opt.verbose |
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| 434 | ||
