Mercurial > repos > fubar > microsatbed
comparison find_str.py @ 16:ee773bbde3c3 draft
planemo upload for repository https://github.com/fubar2/microsatbed commit d952bc313f408735456747c3d33e09a3170c8f59-dirty
| author | fubar |
|---|---|
| date | Wed, 17 Jul 2024 05:08:00 +0000 |
| parents | 1085e094cf5f |
| children | 264d79548d19 |
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| 15:4af0486b8513 | 16:ee773bbde3c3 |
|---|---|
| 25 for name, seq in fa: | 25 for name, seq in fa: |
| 26 if args.specific: | 26 if args.specific: |
| 27 ssrs = pytrf.STRFinder( | 27 ssrs = pytrf.STRFinder( |
| 28 name, | 28 name, |
| 29 seq, | 29 seq, |
| 30 args.minreps, | 30 2, |
| 31 args.minreps, | 31 1, |
| 32 args.minreps, | 32 2, |
| 33 args.minreps, | 33 2, |
| 34 args.minreps, | 34 2, |
| 35 args.minreps, | 35 2, |
| 36 ) | 36 ) |
| 37 else: | 37 else: |
| 38 ssrs = pytrf.STRFinder( | 38 ssrs = pytrf.STRFinder( |
| 39 name, | 39 name, |
| 40 seq, | 40 seq, |
| 53 ssr.motif, | 53 ssr.motif, |
| 54 ssr.repeat, | 54 ssr.repeat, |
| 55 ssr.length, | 55 ssr.length, |
| 56 ) | 56 ) |
| 57 # pytrf reports a 1 based start position so start-1 fixes the bed interval lengths | 57 # pytrf reports a 1 based start position so start-1 fixes the bed interval lengths |
| 58 if args.specific and ssr.motif in specific: | 58 if args.specific and ssr.motif in specific and ssr.repeat >= args.minreps: |
| 59 bed.append(row) | 59 bed.append(row) |
| 60 elif args.mono and len(ssr.motif) == 1: | 60 elif args.mono and len(ssr.motif) == 1: |
| 61 bed.append(row) | 61 bed.append(row) |
| 62 elif args.di and len(ssr.motif) == 2: | 62 elif args.di and len(ssr.motif) == 2: |
| 63 bed.append(row) | 63 bed.append(row) |