Bugs..Bugs...

[fsysy]

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

[fsysy]

//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, $channel_number) = @;
// if ($channel_number == 5) {
// $channel_number = 105;
// }
// if ($channel_number < 1 or
// ($channel_number > 5 and $channel_number != 105)) {
// return ();
// }
// my $k = 'DATA' . $channel_number;
// unless (defined $self->{$k}) {
// my @DaTa = map { ($ < $SHORT_MID) ? $ : $_ - $SHORT_MAX }
// $self->get_data_item('DATA', $channel_number, 'n*');
// $self->{$k} = (@DaTa) ? [ @DaTa ] : [ ];
// }

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

};

Reader.prototype.getRawTrace = function(base){
// sub raw_trace {
// 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]

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();
});