clustal-js
This parses clustal output format
Usage
import {parse} from '@gmod/clustal'
const file = fs.readFileSync('test.aln', 'utf8')
const ret = parse(file)
Example
Input
CLUSTAL O(1.2.4) multiple sequence alignment
sp|P69905|HBA_HUMAN MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG 60
sp|P01942|HBA_MOUSE MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHG 60
sp|P13786|HBAZ_CAPHI MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHSGSAQLRAHG 60
* *: ::: : : *.*:. :. *:*:***:* .:* :********: ****::.**
sp|P69905|HBA_HUMAN KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP 120
sp|P01942|HBA_MOUSE KKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTP 120
sp|P13786|HBAZ_CAPHI SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHFPADFTA 120
.**. *: .*. :*:: .*** **:***: *********:**********:* **:**
sp|P69905|HBA_HUMAN AVHASLDKFLASVSTVLTSKYR 142
sp|P01942|HBA_MOUSE AVHASLDKFLASVSTVLTSKYR 142
sp|P13786|HBAZ_CAPHI DAHAAWDKFLSIVSGVLTEKYR 142
.**: ****: ** ***.***
Output
{ consensus:
'* *: ::: : : *.*:. :. *:*:***:* .:* :********: ****::.**.**. *: .*. :*:: .*** **:***: *********:**********:* **:** .**: ****: ** ***.***',
alns:
[ { id: 'sp|P69905|HBA_HUMAN',
seq:
'MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR' },
{ id: 'sp|P01942|HBA_MOUSE',
seq:
'MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHGKKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTPAVHASLDKFLASVSTVLTSKYR' },
{ id: 'sp|P13786|HBAZ_CAPHI',
seq:
'MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHSGSAQLRAHGSKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHFPADFTADAHAAWDKFLSIVSGVLTEKYR' } ],
header:
{ info: 'CLUSTAL O(1.2.4) multiple sequence alignment',
version: '1.2.4' } }
Notes
See tests for example files