clustal-js

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

Changelog

v1.0.3

• Add generated typescript declarations to output