https://github.com/brentp/ksw2-nim
nim wrapper for lhs/ksw2 for fast smith-waterman
https://github.com/brentp/ksw2-nim
Last synced: 3 months ago
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nim wrapper for lhs/ksw2 for fast smith-waterman
- Host: GitHub
- URL: https://github.com/brentp/ksw2-nim
- Owner: brentp
- License: mit
- Created: 2019-08-19T15:28:49.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2019-08-19T19:38:05.000Z (almost 6 years ago)
- Last Synced: 2025-01-17T20:46:20.331Z (5 months ago)
- Language: C
- Size: 17.6 KB
- Stars: 3
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
```Nim
import ksw2
import sequtils
var tgt = "CGAAACTGGGCTACTCCATGACCAGGGGCAAAATAGGCTTTTAGCCGCTGCGTTCTGGGAGCTCCTCCCCCTTCTGGGAGCTCCTCCCCCTCCCCAGAAGGCCAAGGGATGTGGGGGCTGGGGGACTGGGAGGCCTGGCAGTCTT"
var qry = "CGAAACTGGGCTACTCCATGACCAGGGGCAAAATAGGCTTTTAGCCGCTGCGTTCTGGGAGCTCCTCCCCCTCCCCAGAAGGCCAAGGGATGTTGGGG"
var tenc = new_seq[uint8](tgt.len)
var tqry = new_seq[uint8](qry.len)
# encode the strings into uint8s
tgt.encode(tenc)
qry.encode(tqry)
var ez = new_ez(match=int8(1), mismatch=int8(-2), gap_open=3'i8, gap_ext=1'i8)
tqry.align_to(tenc, ez, flag=KSW_EZ_EXTZ_ONLY or KSW_EZ_RIGHT)
var cig = toSeq(ez.cigar)
echo cig
echo ez.draw(qry, tgt)
```