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Commit 920c097e authored by sauloal's avatar sauloal
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gff output

parent 7df8b089
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public/converter/bionano_parser.js
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......@@ -681,10 +681,13 @@ bionano_parser.prototype.report_xmap = function(self, clbk) {
var outdata_wig_g = [];
var outdata_wig = [];
var outdata_gff_g = ["##gff-version 3"];
var outdata_gff = [];
for ( var RefContigName in chrom_names ) {
var RefContigSize = chrom_sizes[RefContigName];
var RefContigID = chrom_names[RefContigName];
var RefContigSize = chrom_sizes[RefContigName];
var RefContigID = chrom_names[RefContigName];
var donePos = {};
var doneRangeStart = [];
......@@ -703,6 +706,7 @@ bionano_parser.prototype.report_xmap = function(self, clbk) {
var contig_order = {};
for ( QryContigID in RefData ) {
var QryData = RefData[QryContigID];
for ( var rowid in QryData ) {
var cols = QryData[rowid];
var RefStart = get_val('RefStartPos' , cols);
......@@ -719,6 +723,8 @@ bionano_parser.prototype.report_xmap = function(self, clbk) {
}
}
var sorted_contig_ids = [];
for (var QryContigID in contig_order) {
sorted_contig_ids.push([QryContigID, contig_order[QryContigID]])
......@@ -728,6 +734,7 @@ bionano_parser.prototype.report_xmap = function(self, clbk) {
console.log('report_xmap :: sorted_contig_ids', sorted_contig_ids);
for ( QryContigNum in sorted_contig_ids ) {
var QryContigID = sorted_contig_ids[QryContigNum][0];
var QryData = RefData[QryContigID];
......@@ -751,10 +758,15 @@ bionano_parser.prototype.report_xmap = function(self, clbk) {
[] // 11 starts
];
var out_row_gff = [];
var out_row_gff_e = [];
var lastPos = -1;
var lastFeatSize = -1;
var lastStrand = '+';
var num_valids = 0;
for ( var rowid in QryData ) {
var cols = QryData[rowid];
......@@ -801,6 +813,7 @@ bionano_parser.prototype.report_xmap = function(self, clbk) {
23 222 4 5234942.7 4030155.6 19604658.0 20802360.0 - 88.75 3M1D1M 5244212.9 70787664.0 1 (1188,384)(1189,383)(1190,382)(1192,381)
*/
var XmapEntryID = get_val('XmapEntryID' , cols);
var RefId = get_val('RefContigID' , cols);
var RefStart = get_val('RefStartPos' , cols);
var RefEnd = get_val('RefEndPos' , cols);
......@@ -813,8 +826,10 @@ bionano_parser.prototype.report_xmap = function(self, clbk) {
var Orientation = get_val('Orientation' , cols);
var Confidence = get_val('Confidence' , cols);
var Alignment = get_val('Alignment' , cols);
var featSize = nick_sites[LabelChannel][1];
lastFeatSize = featSize;
lastStrand = Orientation;
if (RefStart > RefEnd) {
......@@ -914,6 +929,25 @@ bionano_parser.prototype.report_xmap = function(self, clbk) {
out_row_bed[10].push(featSize);
out_row_bed[11].push(refPos );
var uid = QryContigID+'.'+(rowid+1)+'.'+p;
var row_gff = [
RefContigName , // seqid
'.' , // source
'CDS' , // type
refPos , // start
refPos + featSize , // end
Confidence , // score
Orientation , // strand
'.' , // phase
'ID=' +uid +';'+ // attributes
'Name=' +uid +';'+
'Parent=' +QryContigID+'.g;'+
'qryContigID='+QryContigID+';'+
'xMapEntryID='+XmapEntryID
];
out_row_gff_e.push(row_gff.join("\t"));
if (refPos <= RefStartW) {
......@@ -925,6 +959,7 @@ bionano_parser.prototype.report_xmap = function(self, clbk) {
}
while (refPos in donePos) {
refPos += 1;
}
......@@ -936,13 +971,14 @@ bionano_parser.prototype.report_xmap = function(self, clbk) {
}
if (refPos in donePos) {
continue;
}
donePos[refPos] = 1;
lastPos = refPos;
lastPos = refPos;
outdata_wig.push( refPos + " 1" );
} else {
......@@ -968,6 +1004,32 @@ bionano_parser.prototype.report_xmap = function(self, clbk) {
out_row_bed[ 2] += lastFeatSize;
out_row_bed[ 7] += lastFeatSize;
var row_gff_g = [
RefContigName , // seqid
'.' , // source
'gene' , // type
out_row_bed[1] , // start
out_row_bed[2] , // end
'.' , // score
'.' , // strand
'.' , // phase
'ID=' +QryContigID+';' + // attributes
'Name=' +QryContigID
];
var row_gff_m = [
RefContigName , // seqid
'.' , // source
'mRNA' , // type
out_row_bed[1] , // start
out_row_bed[2] , // end
'.' , // score
'.' , // strand
'.' , // phase
'ID=' +QryContigID+'.g;'+ // attributes
'Name=' +QryContigID
];
for (var rp = 0; rp < out_row_bed[11].length; rp++) {
out_row_bed[11][rp] -= out_row_bed[1];
}
......@@ -977,25 +1039,40 @@ bionano_parser.prototype.report_xmap = function(self, clbk) {
out_row_bed[11] = out_row_bed[11].join(',');
out_row_bed = out_row_bed.join("\t");
outdata_bed.push(out_row_bed);
outdata_gff.push(row_gff_g.join("\t"));
outdata_gff.push(row_gff_m.join("\t"));
outdata_gff.push.apply(outdata_gff, out_row_gff_e);
} // QryContigID
//console.log('report_xmap :: outdata_wig', outdata_wig);
//clbk(filename, RefContigName+'.wig', outdata_wig.join("\n"));
//clbk(filename, RefContigName+'.wig' , outdata_wig.join("\n"));
outdata_wig_g.push.apply(outdata_wig_g, outdata_wig);
outdata_wig = [];
outdata_wig = [];
//clbk(filename, RefContigName+'.bed', outdata_bed.join("\n"));
//clbk(filename, RefContigName+'.bed' , outdata_bed.join("\n"));
outdata_bed_g.push.apply(outdata_bed_g, outdata_bed);
outdata_bed = [];
outdata_bed = [];
//clbk(filename, RefContigName+'.gff3', "##gff-version 3\n"+outdata_gff.join("\n"));
outdata_gff_g.push.apply(outdata_gff_g, outdata_gff);
outdata_gff = [];
} // RefContigID
clbk(filename, 'wig', outdata_wig_g.join("\n"));
//console.log('report_xmap :: outdata_bed', outdata_bed);
clbk(filename, 'bed', outdata_bed_g.join("\n"));
clbk(filename, 'wig' , outdata_wig_g.join("\n"));
clbk(filename, 'bed' , outdata_bed_g.join("\n"));
clbk(filename, 'gff3', outdata_gff_g.join("\n"));
}
......
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