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imlucas / node-abif

An ABIF reader for node
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Bugs..Bugs... #1

Open fsysy opened 8 years ago

fsysy commented 8 years ago

I need this module. But i can't use it without debug. Making new module for AB1 file maybe better than debugging.

fsysy commented 8 years ago

//Debug version

"use strict";

var ABIF_TYPES = { 1: 'byte', 2: 'char', 3: 'word', 4: 'short', 5: 'long', 7: 'float', 8: 'double', 10: 'date', 11: 'time', 12: 'thumb', 13: 'bool', 18: 'pString', 19: 'cString' };

module.exports = function(buf){ return new Reader(buf); };

module.exports.Reader = Reader;

function Reader(buf){ this.buf = buf; this.pos = 0; this.type = this.readNextString(4); this.version = this.readNextShort();

var dir = new DirEntry(this);
this.seek(dir.dataoffset);

this.entries = [];
for(var i =0; i<= dir.numelements -1; i++){
    var e = new DirEntry(this);
    this.entries.push(e);
}

} Reader.prototype.showEntries = function(){ this.entries.map(function(entry){ console.log(entry.name); }); };

Reader.prototype.getData = function(name, num){ if(num === undefined){ num = 1; } var entry = this.getEntry(name, num); if(!entry){ // throw new Error('Entry ' + name + ' (' +num + ') not found.'); return undefined; } this.seek(entry.mydataoffset); var data = this.readData(entry.elementtype, entry.numelements); return data.length === 1 ? data[0] : data; };

//modified script to include sequence_quality_value Reader.prototype.getRawSequence_value = function(){ var qual_val=[]; var qual_val_ascii= this.getData('PCON',2); for (var k in qual_val_ascii){ qual_val.push(qual_val_ascii[k].charCodeAt(0)); //charCodeAt(0): ascii to number } return qual_val;
};

Reader.prototype.getRawSequence = function(){ var sequence= this.getData('PBAS',2); return sequence;
};

Reader.prototype.getEntry = function(name, num){ var entry;

this.entries.some(function(e){
    if(e.name === name && e.number === num){
        entry = e;
        return true;
    }
});
return entry;

};

Reader.prototype.readData = function(type, num){ var m = { 1: 'Byte', 3: 'UnsignedInt', 4: 'Short', 5: 'Long', 7: 'Float', 8: 'Double', 10: 'Date', 11: 'Time', 12: 'Thumb', 13: 'Bool' };

if(m[type]){
    return this._loop(m[type], num);
}
else if(type === 2){
    return this.readNextString(num);
}
else if(type === 18){
    return this.readNextpString(num);
}
else if(type === 19){
    return this.readNextcString(num);
}
return this[m[type]](num);

};

Reader.prototype._loop = function(type, num){ var buf = [], method = 'readNext' + type;

for(var i=0; i < num; i++){
    buf.push(this[method]());
}
return buf;

};

Reader.prototype.readNextShort = function(){ var v = this.buf.readInt16BE(this.pos); this.pos += 2; return v; }; Reader.prototype.readNextInt = function(){ var v = this.buf.readInt32BE(this.pos); this.pos += 4; return v; };

Reader.prototype.readNextChar = function(){ var v = this.buf.toString('ascii', this.pos, this.pos+1); this.pos += 1; return v; };

Reader.prototype.readNextByte = function(){ var v = this.buf.readUInt8(this.pos); this.pos += 1; return v; };

Reader.prototype.readNextUnsignedInt = function(){ var v = this.buf.readUInt32BE(this.pos); this.pos += 4; return v; };

Reader.prototype.readNextLong = function(){ var v = this.buf.readInt32BE(this.pos); this.pos += 4; return v; };

Reader.prototype.readNextFloat = function(){ var v = this.buf.readFloatBE(this.pos); this.pos += 4; return v; };

Reader.prototype.readNextDouble = function(){ var v = this.buf.readDoubleBE(this.pos); this.pos += 8; return v; };

Reader.prototype.readNextBool = function(){ return this.readNextByte() === 1; };

Reader.prototype.readNextDate = function(){ var d = new Date(); var y = this.readNextShort(); var m = this.readNextByte(); var day = this.readNextByte();

console.log(y. m, day);
d.setYear(y);
d.setMonth(m);
d.setDate(day);
return d;

};

Reader.prototype.readNextTime = function(){ var d = new Date(); d.setHours(this.readNextByte()); d.setMinutes(this.readNextByte()); d.setSeconds(this.readNextByte()); d.setMilliseconds(this.readNextByte()); return d; };

Reader.prototype.readNextThumb = function(){ return [ this.readNextLong(), this.readNextLong(), this.readNextByte(), this.readNextByte() ]; };

Reader.prototype.readNextString = function(size){ var chars = []; for(var i = 0; i <= size -1; i++){ chars.push(this.readNextChar()); } return chars.join(''); };

Reader.prototype.readNextpString = function(){ return this.readNextString(this.readNextByte()); };

Reader.prototype.readNextcString = function(){ var chars = [], c; while(true){ c = this.readNextChar(); if(c.charAt(0) === 0){ return chars.join(''); } else { chars.push(c); } } };

Reader.prototype.tell = function(){ return this.pos; };

Reader.prototype.seek = function(pos){ this.pos = pos; };

function DirEntry(buf){ this.name = buf.readNextString(4); this.number = buf.readNextInt();

this.elementtype = buf.readNextShort();
this.elementsize = buf.readNextShort();
this.numelements = buf.readNextInt();
this.datasize = buf.readNextInt();
this.dataoffsetpos = buf.tell();
this.dataoffset = buf.readNextInt();
this.datahandle = buf.readNextInt();

this.mydataoffset = (this.datasize <= 4) ? this.dataoffsetpos : this.dataoffset;
this.mytype = (this.elementtype < 1024) ? ABIF_TYPES[this.elementtype] || 'unknown' : 'user';

}

// http://cpansearch.perl.org/src/VITA/Bio-Trace-ABIF-1.05/lib/Bio/Trace/ABIF.pm

Reader.prototype.getAnalyzedDataForChannel = function(channel){ if(channel === 5){ channel = 205; } else { channel += 8; } if (channel < 9 || (channel > 12 && channel!= 205)) { return null; } return this.getEntry('DATA', channel); };

Reader.prototype.getBaseOrder = function(){ return this.getData('FWO_').split(''); };

Reader.prototype.getChannel = function(base){ base = base.toUpperCase(); var order = this.getBaseOrder(); for(var i = 0; i <= order.length; i++){ if(order[i] === base){ return i + 1; } } return undefined; };

Reader.prototype.getPeaks = function(){ // sub peaks { // my ($self, $n) = @_; // my $k = '_PEAK' . $n; // my ($position, $height, $beginPos, $endPos, $beginHI, $endHI, $area, $volume, $fragSize, $isEdited, $label); // my $s = undef; // my @raw_data; // my @peak_array; // my $i;

//     unless (defined $self->{$k}) {
//         @raw_data = $self->get_data_item('PEAK', $n, '(NnNNnnNNB32nZ64)*');
//         for ($i = 0; $i < @raw_data; $i += 11) {
//             ($position, $height, $beginPos, $endPos, $beginHI, $endHI, $area, $volume, $s, $isEdited, $label) = @raw_data[$i .. $i+10];
//             $fragSize = $self->_ieee2decimal($s) if (defined $s);
//             my $peak = {};
//             $peak->{position} = $position;
//             $peak->{height} = $height;
//             $peak->{beginPos} = $beginPos;
//             $peak->{endPos} = $endPos;
//             $peak->{beginHI} = $beginHI;
//             $peak->{endHI} = $endHI;
//             $peak->{area} = $area;
//             $peak->{volume} = $volume;
//             $peak->{fragSize} = $fragSize;
//             $peak->{isEdited} = $isEdited;
//             $peak->{label} = $label;
//             push @peak_array, $peak;
//         }
//     $self->{$k} = (@peak_array) ? [ @peak_array ] : [ ];
//     }
//     return @{$self->{$k}};
// }

};

Reader.prototype.getRawDataForChannel = function(channel){ // sub raw_data_for_channel { // my ($self, $channelnumber) = @; // if ($channel_number == 5) { // $channel_number = 105; // } // if ($channel_number < 1 or // ($channel_number > 5 and $channel_number != 105)) { // return (); // } // my $k = '_DATA' . $channelnumber; // unless (defined $self->{$k}) { // my @data = map { ($ < $SHORTMID) ? $ : $_ - $SHORT_MAX } // $self->get_data_item('DATA', $channel_number, 'n*'); // $self->{$k} = (@data) ? [ @data ] : [ ]; // }

//     return @{$self->{$k}};
// }

};

Reader.prototype.getRawTrace = function(base){ // sub rawtrace { // my ($self, $base) = @; // my %ob = ();

//     $base =~ /^[ACGTacgt]$/ or return ();
//     %ob = $self->order_base();
//     return $self->raw_data_for_channel($ob{uc($base)});
// }

};

Reader.prototype.getTrace = function(base){ // sub trace { // my ($self, $base) = @_; // my %ob = ();

//     $base =~ /^[ACGTacgt]$/ or return ();
//     %ob = $self->order_base();
//     return $self->analyzed_data_for_channel($ob{uc($base)});
// }

};

// These are all just simple tag reads. // Keeping this as a simple map for anyone else's reference. // Don't worry. They'll get all nice and camel cased below. var accessors = { 'analysis_protocol_settings_name': 'APrN', 'analysis_protocol_settings_version': 'APrV', 'analysis_protocol_xml': 'APrX', 'analysis_protocol_xml_schema_version': 'APXV', 'analysis_return_code': 'ARTN', 'average_peak_spacing': 'SPAC', 'basecaller_apsf': 'ASPF', 'basecaller_bcp_dll': ['SPAC', 2], 'basecaller_version': ['SVER', 2], 'basecalling_analysis_timestamp': 'BCTS', 'base_locations': ['PLOC', 2], 'base_locations_edited': 'PLOC', 'base_spacing': ['SPAC', 3], 'buffer_tray_temperature': 'BufT', 'capillary_number': 'LANE', 'chem': 'phCH', 'comment': 'CMNT', 'comment_title': 'CTTL', 'container_identifier': 'CTID', 'container_name': 'CTNM', 'container_owner': 'CTOw', 'current': ['DATA', 6], 'data_collection_module_file': 'MODF', 'data_collection_software_version': 'SVER', 'data_collection_firmware_version': ['SVER', 3], 'data_collection_start_date': ['RUND', 3], 'data_collection_start_time': ['RUNT', 3], 'data_collection_stop_date': ['RUND', 4], 'data_collection_stop_time': ['RUNT', 4], 'detector_heater_temperature': 'DCHT', 'downsampling_factor': 'DSam', 'dye_name': 'DyeN', 'dye_set_name': 'DySN', 'dye_significance': 'DyeB', 'dye_type': 'phDY', 'dye_wavelength': 'DyeW', 'edited_quality_values': 'PCON', 'edited_quality_values_ref': 'PCON', 'edited_sequence': 'PBAS', 'edited_sequence_length': 'PBAS', 'electrophoresis_voltage': 'EPVt', 'gel_type': 'GTyp', 'gene_mapper_analysis_method': 'ANME', 'gene_mapper_panel_name': 'PANL', 'gene_mapper_sample_type': 'STYP', 'gene_scan_sample_name': 'SpNm', 'injection_time': 'InSc', 'injection_voltage': 'InVt', 'instrument_class': 'HCFG', 'instrument_family': ['HCFG', 2], 'instrument_name_and_serial_number': 'MCHN', 'instrument_param': ['HCFG', 4], 'is_capillary_machine': 'CpEP', 'laser_power': 'LsrP', 'length_to_detector': 'LNTD', 'mobility_file': ['PDMF', 2], 'mobility_file_orig': 'PDMF', 'model_number': 'MODL', 'noise': 'NOIS', 'num_capillaries': 'NLNE', 'num_dyes': 'Dye#', 'num_scans': 'SCAN', 'official_instrument_name': ['HCFG', 3], 'offscale_peaks': 'OffS', 'offscale_scans': 'OfSc', 'peak1_location': ['B1Pt', 2], 'peak1_location_orig': 'B1Pt', 'peak_area_ratio': 'phAR', 'pixel_bin_size': 'PXLB', 'pixels_lane': 'NAVG', 'plate_type': 'PTYP', 'plate_size': 'PSZE', 'polymer_expiration_date': 'SMED', 'polymer_lot_number': 'SMLt', 'power': ['DATA', 7], 'quality_levels': 'phQL', 'quality_values': ['PCON', 2], 'quality_values_ref': ['PCON', 2], 'rescaling': 'Scal', 'results_group': 'RGNm', 'results_group_comment': 'RGCm', 'results_group_owner': 'RGOw', 'reverse_complement_flag': 'RevC', 'run_module_name': 'RMdN', 'run_module_version': 'RMdV', 'run_module_xml_schema_version': 'RMXV', 'run_module_xml_string': 'RMdX', 'run_name': 'RunN', 'run_protocol_name': 'RPrN', 'run_protocol_version': 'RPrV', 'run_start_date': 'RUND', 'run_start_time': 'RUNT', 'run_stop_date': ['RUND', 2], 'run_stop_time': ['RUNT', 2], 'run_temperature': 'Tmpr', 'sample_file_format_version': ['SVER', 4], 'sample_name': 'SMPL', 'sample_tracking_id': 'LIMS', 'scanning_rate': 'Rate', 'scan_color_data_values': 'OvrV', 'scan_numbers': 'Satd', 'scan_number_indices': 'OvrI', 'seqscape_project_name': ['PROJ', 4], 'seqscape_project_template': 'PRJT', 'seqscape_specimen_name': 'SPEC', 'sequence': ['PBAS', 2], 'sequence_length': ['PBAS', 2], 'sequencing_analysis_param_filename': ['APFN', 2], 'signal_level': 'S/N%', 'size_standard_filename': 'StdF', 'snp_set_name': 'SnpS', 'start_collection_event': ['EVNT', 3], 'start_point': ['ASPt', 2], 'start_point_orig': 'ASPt', 'start_run_event': 'EVNT', 'stop_collection_event': ['EVNT', 4], 'stop_point': ['AEPt', 2], 'stop_point_orig': 'AEPt', 'stop_run_event': ['EVNT', 2], 'temperature': ['DATA', 8], 'trim_probability_threshold': ['phTR', 2], 'trim_region': 'phTR', 'voltage': ['DATA', 5], 'user': 'User', 'well_id': 'TUBE' };

Object.keys(accessors).map(function(accessor){ var r = /-_/g; var name = accessor.replace(r, function(match, c){ return c.toUpperCase(); }); name = name.charAt(0).toUpperCase() + name.substring(1);

var args = accessors[accessor];
if(!Array.isArray(args)){
    args = [args];
}

Reader.prototype['get' + name] = function(){
    return this.getData.apply(this, args);

};

});

fsysy commented 8 years ago

var fs = require('fs'), abif = require('abif');

fs.readFile('./mitochondrion/chromatogram/JuneBBC-10-LCMtF.ab1', function(err, data){ var reader = abif(data); console.log('Run start date', reader.getRunStartDate()); console.log('Signal to Noise', reader.getData('S/N%', 1)); console.log('original sequence', reader.getRawSequence()); console.log('original quality values', reader.getRawSequence_value()); reader.showEntries(); });