Sha256: 23b8946ca241d40b227585be1514e722bf1c14d95efd7a58a52f57321afe8513
Contents?: true
Size: 1.42 KB
Versions: 11
Compression:
Stored size: 1.42 KB
Contents
import * as Exporter from './exporter';
import _ from 'underscore';
export default class AlignmentExporter {
constructor() {}
wrap_string(str, width) {
var idx = 0;
var wrapped = '';
while(true) {
wrapped += str.substring(idx, idx + width);
idx += width;
if(idx < str.length) {
wrapped += '\n';
} else {
break;
}
}
return wrapped;
}
generate_fasta(hsps) {
var fasta = "";
_.each(hsps, _.bind(function (hsp) {
fasta += ">"+hsp.query_id+":"+hsp.qstart+"-"+hsp.qend+"\n";
fasta += hsp.qseq+"\n";
fasta += ">"+hsp.query_id+":"+hsp.qstart+"-"+hsp.qend+"_alignment_"+hsp.hit_id+":"+hsp.sstart+"-"+hsp.send+"\n";
fasta += hsp.midline+"\n";
fasta += ">"+hsp.hit_id+":"+hsp.sstart+"-"+hsp.send+"\n";
fasta += hsp.sseq+"\n";
}, this));
return fasta;
}
export_alignments(hsps, filename_prefix) {
var fasta = this.generate_fasta(hsps);
var blob = new Blob([fasta], { type: 'text/fasta' });
// var filename_prefix = query_def + '_' + subject_def;
// var filename_prefix = query_id + '_' + subject_id;
var filename = Exporter.sanitize_filename(filename_prefix) + '.txt';
Exporter.download_blob(blob, filename);
}
export_alignments_of_all(hsps, name) {
}
}
Version data entries
11 entries across 11 versions & 1 rubygems