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source: trunk/grails-app/services/nl/tno/metagenomics/FastaService.groovy @ 13

Last change on this file since 13 was 13, checked in by robert@…, 9 years ago
Improved user interface and implemented basic export functionality
File size: 24.3 KB

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1	package nl.tno.metagenomics
2
3	import java.io.BufferedWriter;
4	import java.io.File;
5	import java.io.Writer;
6	import java.util.ArrayList;
7	import java.util.zip.ZipEntry
8	import java.util.zip.ZipOutputStream
9	import org.codehaus.groovy.grails.commons.ConfigurationHolder
10
11	class FastaService {
12	def fileService
13	def fuzzySearchService
14	def sampleExcelService
15
16	static transactional = true
17
18	/**
19	* Parses uploaded files and checks them for FASTA and QUAL files
20	* @param filenames List of filenames currently existing in the upload directory
21	* @param onProgress Closure to execute when progress indicators should be updated.
22	* Has 4 parameters: numFilesProcessed, numBytesProcessed that indicate the number
23	* of files and bytes that have been processed in total. totalFiles, totalBytes indicate the change
24	* in total number of files and bytes (e.g. should take 1 if a new file is added to the list)
25	* @param directory Directory to move the files to
26	* @return Structure with information about the parsed files. The 'success' files are
27	* moved to the given directory
28	*
29	* [
30	* success: [
31	* [filename: 'abc.fasta', type: FASTA, numSequences: 190]
32	* [filename: 'cde.fasta', type: FASTA, numSequences: 140]
33	* [filename: 'abc.qual', type: QUAL, numSequences: 190, avgQuality: 38]
34	* [filename: 'cde.qual', type: QUAL, numSequences: 140, avgQuality: 29]
35	* ],
36	* failure: [
37	* [filename: 'testing.xls', type: 'unknown', message: 'Type not recognized']
38	* ]
39	* ]
40	*
41	*/
42	def parseFiles( ArrayList filenames, Closure onProgress, File directory = null ) {
43	if( filenames.size() == 0 ) {
44	return [ success: [], failure: [] ];
45	}
46
47	if( !directory ) {
48	directory = fileService.absolutePath( ConfigurationHolder.config.metagenomics.fileDir )
49	}
50
51	def success = [];
52	def failure = [];
53
54	long filesProcessed = 0;
55	long bytesProcessed = 0;
56
57	// Loop through all filenames
58	for( int i = 0; i < filenames.size(); i++ ) {
59	def filename = filenames[ i ];
60
61	if( fileService.isZipFile( filename ) ) {
62	// ZIP files are extracted and appended to the filenames list.
63	def newfiles = fileService.extractZipFile( filename, { files, bytes, totalFiles, totalBytes ->
64	filesProcessed += files;
65	bytesProcessed += bytes;
66
67	onProgress( filesProcessed, bytesProcessed, totalFiles, totalBytes );
68	} );
69	if( newfiles ) {
70	newfiles.each {
71	filenames.add( it );
72	}
73	}
74	} else {
75	def file = fileService.get( filename );
76	String filetype = fileService.determineFileType( file );
77
78	if( !fileTypeValid( filetype ) ) {
79	// If files are not valid for parsing, delete them and return a message to the user
80	fileService.delete(filename);
81	failure << [ filename: filename, originalfilename: fileService.originalFilename( filename ), type: filetype, message: 'File type not accepted' ];
82	} else {
83	try {
84	def contents = parseFile( file, filetype, { files, bytes ->
85	filesProcessed += files;
86	bytesProcessed += bytes;
87
88	onProgress( filesProcessed, bytesProcessed, 0, 0 );
89	} );
90
91	contents.filename = file.getName();
92	contents.originalfilename = fileService.originalFilename( contents.filename )
93
94	if( contents.success ) {
95	success << contents;
96	} else {
97	fileService.delete(filename);
98	failure << contents;
99	}
100	} catch( Exception e ) {
101	// If anything fails during parsing, return an error message
102	fileService.delete(filename);
103	failure << [ filename: filename, originalfilename: fileService.originalFilename( filename ), type: filetype, message: e.getMessage() ];
104	}
105	}
106	}
107	}
108
109	return [ success: success, failure: failure ];
110	}
111
112	/**
113	* Matches uploaded fasta and qual files and combines them with the samples they probably belong to
114	* @param parsedFiles Parsed files
115	* [
116	* [filename: 'abc.fasta', type: FASTA, numSequences: 190]
117	* [filename: 'cde.fasta', type: FASTA, numSequences: 140]
118	* [filename: 'abc.qual', type: QUAL, numSequences: 190, avgQuality: 38]
119	* [filename: 'cde.qual', type: QUAL, numSequences: 140, avgQuality: 29]
120	* ]
121	* @param samples AssaySample objects to which the files should be matched.
122	* @return Structure with information about the matching.
123	* [
124	* [
125	* fasta: [filename: 'abc.fasta', type: FASTA, numSequences: 190],
126	* qual: [filename: 'abc.qual', type: QUAL, numSequences: 190, avgQuality: 38],
127	* feasibleQuals: [
128	* [filename: 'abc.qual', type: QUAL, numSequences: 190, avgQuality: 38],
129	* [filename: 'def.qual', type: QUAL, numSequences: 190, avgQuality: 21]
130	* ]
131	* sample: AssaySample object
132	*/
133	def matchFiles( def parsedFiles, def samples ) {
134	def fastas = parsedFiles.findAll { it.type == "fasta" }
135	def quals = parsedFiles.findAll { it.type == "qual" }
136	samples = samples.toList()
137
138	def files = [];
139
140	fastas.each { fastaFile ->
141	// Remove extension
142	def matchWith = fastaFile.originalfilename.substring( 0, fastaFile.originalfilename.lastIndexOf( '.' ) )
143
144	// Determine feasible quals (based on number of sequences )
145	def feasibleQuals = quals.findAll { it.numSequences == fastaFile.numSequences }
146
147	// Best matching qual file
148	def qualIdx = fuzzySearchService.mostSimilarWithIndex( matchWith + '.qual', feasibleQuals.originalfilename );
149
150	def qual = null
151	if( qualIdx != null )
152	qual = feasibleQuals[ qualIdx ];
153
154	// Best matching sample
155	// TODO: Implement method to search for sample matches in a provided excel sheet
156	def sampleIdx = fuzzySearchService.mostSimilarWithIndex( matchWith, samples.sample.name );
157	def assaySample = null
158	if( sampleIdx != null ) {
159	assaySample = samples[ sampleIdx ];
160	}
161
162	files << [
163	fasta: fastaFile,
164	feasibleQuals: feasibleQuals,
165	qual: qual,
166	assaySample: assaySample
167	]
168	}
169
170	return files;
171
172
173	}
174
175	/**
176	* Determines whether a file can be processed.
177	* @param filetype Filetype of the file
178	* @see determineFileType()
179	* @return
180	*/
181	protected boolean fileTypeValid( String filetype ) {
182	switch( filetype ) {
183	case "fasta":
184	case "qual":
185	return true;
186	default:
187	return false;
188	}
189	}
190
191	/**
192	* Parses the given file
193	* @param file File to parse
194	* @param filetype Type of the given file
195	* @param onProgress Closure to execute when progress indicators should be updated.
196	* Has 2 parameters: numFilesProcessed and numBytesProcessed that indicate the number
197	* of files and bytes that have been processed in this file (so the first parameter should
198	* only be 1 when the file is finished)
199	*
200	* @return List structure. Examples:
201	*
202	* [ success: true, filename: 'abc.fasta', type: 'fasta', numSequences: 200 ]
203	* [ success: true, filename: 'abc.qual', type: 'qual', numSequences: 200, avgQuality: 36 ]
204	* [ success: false, filename: 'abc.txt', type: 'txt', message: 'Filetype could not be parsed.' ]
205	*/
206	protected def parseFile( File file, String filetype, Closure onProgress ) {
207	switch( filetype ) {
208	case "fasta":
209	return parseFasta( file, onProgress );
210	case "qual":
211	return parseQual( file, onProgress );
212	default:
213	onProgress( 1, file.length() );
214	return [ success: false, type: filetype, message: 'Filetype could not be parsed.' ]
215	}
216	}
217
218	/**
219	* Parses the given FASTA file
220	* @param file File to parse
221	* @param onProgress Closure to execute when progress indicators should be updated.
222	* Has 2 parameters: numFilesProcessed and numBytesProcessed that indicate the number
223	* of files and bytes that have been processed in this file (so the first parameter should
224	* only be 1 when the file is finished)
225	* @return List structure. Examples:
226	*
227	* [ success: true, filename: 'abc.fasta', type: 'fasta', numSequences: 200 ]
228	* [ success: false, filename: 'def.fasta', type: 'fasta', message: 'File is not a valid FASTA file' ]
229	*/
230	protected def parseFasta( File file, Closure onProgress ) {
231
232	long startTime = System.nanoTime();
233	log.trace "Start parsing FASTA " + file.getName()
234
235	// Count the number of lines, starting with '>' (and where the following line contains a character other than '>')
236	long numSequences = 0;
237	long bytesProcessed = 0;
238	boolean lookingForSequence = false;
239
240	file.eachLine { line ->
241	if( line ) {
242	if( !lookingForSequence && line[0] == '>' ) {
243	lookingForSequence = true;
244	} else if( lookingForSequence ) {
245	if( line[0] != '>' ) {
246	numSequences++;
247	lookingForSequence = false;
248	}
249	}
250
251
252	// Update progress every time 1MB is processed
253	bytesProcessed += line.size();
254	if( bytesProcessed > 1000000 ) {
255	onProgress( 0, bytesProcessed );
256	bytesProcessed = 0;
257	}
258	}
259
260	}
261
262	// Update progress and say we're finished
263	onProgress( 1, bytesProcessed );
264
265	log.trace "Finished parsing FASTA " + file.getName() + ": " + ( System.nanoTime() - startTime ) / 1000000L
266
267	return [ success: true, type: "fasta", numSequences: numSequences ];
268	}
269
270	/**
271	* Parses the given QUAL file
272	* @param file File to parse
273	* @param onProgress Closure to execute when progress indicators should be updated.
274	* Has 2 parameters: numFilesProcessed and numBytesProcessed that indicate the number
275	* of files and bytes that have been processed in this file (so the first parameter should
276	* only be 1 when the file is finished)
277	* @return List structure. Examples:
278	*
279	* [ success: true, filename: 'abc.qual', type: 'qual', numSequences: 200, avgQuality: 31 ]
280	* [ success: false, filename: 'def.qual', type: 'qual', message: 'File is not a valid QUAL file' ]
281	*/
282	protected def parseQual( File file, Closure onProgress ) {
283	long startTime = System.nanoTime();
284	log.trace "Start parsing QUAL " + file.getName()
285
286	// Count the number of lines, starting with '>'. After we've found such a character, we continue looking for
287	// quality scores
288	long numSequences = 0;
289	long bytesProcessed = 0;
290	def quality = [ quality: 0.0, number: 0L ]
291
292	boolean lookingForFirstQualityScores = false;
293	file.eachLine { line ->
294	if( line ) {
295	if( !lookingForFirstQualityScores && line[0] == '>' ) {
296	lookingForFirstQualityScores = true;
297	} else if( lookingForFirstQualityScores ) {
298	if( line[0] != '>' ) {
299	numSequences++;
300	lookingForFirstQualityScores = false;
301
302	// Don't compute average quality because it takes too much time
303	//quality = updateQuality( quality, line );
304	}
305	} else {
306	// Don't compute average quality because it takes too much time
307	//quality = updateQuality( quality, line );
308	}
309
310	// Update progress every time 1MB is processed
311	bytesProcessed += line.size();
312	if( bytesProcessed > 1000000 ) {
313	onProgress( 0, bytesProcessed );
314	bytesProcessed = 0;
315	}
316	}
317
318	}
319
320	// Update progress and say we're finished
321	onProgress( 1, bytesProcessed );
322
323	log.trace "Finished parsing QUAL " + file.getName() + ": " + ( System.nanoTime() - startTime ) / 1000000L
324
325	return [ success: true, type: "qual", numSequences: numSequences, avgQuality: quality.quality ];
326	}
327
328	/**
329	* Parses the given line and updates the average quality based on the scores
330	* @param quality [quality: 0.0f, number: 0L]
331	* @param line String of integer quality scores, separated by a whitespace
332	* @return [quality: 0.0f, number: 0L]
333	*/
334	protected def updateQuality( def quality, String line ) {
335	// Determine current average
336	List tokens = line.tokenize();
337	Long total = 0;
338
339	tokens.each {
340	total += Integer.parseInt( it );
341	}
342
343	int numTokens = tokens.size();
344
345	// Update the given average
346	if( numTokens > 0 ) {
347	quality.number += numTokens;
348	quality.quality = quality.quality + ( ( total / numTokens as double ) - quality.quality ) / quality.number * numTokens;
349	}
350
351	return quality
352	}
353
354	/**
355	* Moves a fasta and qual file to their permanent location, and returns information about these files
356	*
357	* @param fastaFile Filename of the fasta file in the temporary directory
358	* @param qualFile Filename of the fasta file in the temporary directory
359	* @param processedFiles Structure with data about uploaded files and matches
360	* @return [ fasta: <fasta filename>, qual: <qual filename>, numSequences: <number of sequences>, avgQuality: <average quality> ]
361	*/
362	public def savePermanent( String fastaFile, String qualFile, def processedFiles ) {
363	File permanentDirectory = fileService.absolutePath( ConfigurationHolder.config.metagenomics.fileDir );
364	def returnStructure = [:];
365
366	if( fileService.fileExists( fastaFile ) ) {
367	// Lookup the original filename
368	def fastaData = processedFiles.parsed.success.find { it.filename == fastaFile };
369	if( fastaData ) {
370	returnStructure.fasta = fileService.moveFileToUploadDir( fileService.get( fastaFile ), fastaData.originalfilename, permanentDirectory );
371	returnStructure.numSequences = fastaData.numSequences;
372	} else {
373	throw new Exception( "Fasta file wasn't uploaded the right way. Maybe the session has expired/" );
374	}
375	} else {
376	// If the file doesn't exist, we can't save anything to the database.
377	throw new Exception( "Fasta file to save doesn't exist on disk" );
378	}
379
380	if( qualFile && fileService.fileExists( qualFile ) ) {
381	// Lookup the original filename
382	def qualData = processedFiles.parsed.success.find { it.filename == qualFile };
383
384	if( qualData ) {
385	returnStructure.qual = fileService.moveFileToUploadDir( fileService.get(qualFile ), qualData.originalfilename, permanentDirectory );
386	returnStructure.avgQuality = qualData.avgQuality
387	} else {
388	// Delete the uploaded fasta file, since this is a serious error
389	fileService.delete( returnStructure.fasta, permanentDirectory );
390	throw new Exception( "Qual file wasn't uploaded the right way. Maybe the session has expired" );
391	}
392	} else {
393	// If the file doesn't exist, we don't save any quality information
394	returnStructure.qual = null
395	returnStructure.avgQuality = 0;
396	}
397
398	return returnStructure;
399	}
400
401	/**
402	* Exports the fasta data of a list of assaysamples
403	* @param assaySamples Assaysamples to export
404	* @param outStream Outputstream to send the data to
405	* @return
406	*/
407	public def export( List assaySamples, OutputStream outStream, String name ) {
408	if( !assaySamples \|\| assaySamples.size() == 0 )
409	return false;
410
411	// Determine the directory the uploaded files are stored in
412	File permanentDirectory = fileService.absolutePath( ConfigurationHolder.config.metagenomics.fileDir );
413
414	// First check whether qual files should be exported or not
415	// It is only exported if qual scores are available for all sequences
416	def exportQual = ( assaySamples.numSequences().sum() == assaySamples.numQualScores().sum() );
417
418	// First create tags for every sample
419	def tags = [];
420
421	// Determine new tag length. Since we can use 4 characters per
422	// tag position, we only have to use 4log( #samples)
423	int tagLength = Math.ceil( Math.log( assaySamples.size() ) / Math.log( 4 ) )
424	int tagNumber = 0;
425
426	assaySamples.each { assaySample ->
427	if( assaySample.numSequences() > 0 ) {
428	// Create a new tag for this assaysample
429	def tag = createTag( tagLength, tagNumber++);
430
431	// Save the tag for exporting
432	tags << [assaySampleId: assaySample.id, sampleName: assaySample.sample.name, assayName: assaySample.assay.name, studyName: assaySample.assay.study.name, tag: tag]
433	}
434	}
435
436	// Now create zip file for fasta and qual files
437	ZipOutputStream zipFile = new ZipOutputStream( new BufferedOutputStream( outStream ) );
438	BufferedWriter zipWriter = new BufferedWriter( new OutputStreamWriter( zipFile ) );
439
440	// We have to loop twice through the sequenceData, since we can't write part of the sequence
441	// file and part of the qual files mixed. We have to write the full sequence file first.
442	try {
443	zipFile.putNextEntry( new ZipEntry( name + ".fasta" ) );
444
445	assaySamples.each { assaySample ->
446	if( assaySample.numSequences() > 0 ) {
447	def currentTag = tags.find { it.assaySampleId == assaySample.id };
448
449	assaySample.sequenceData.each { sequenceData ->
450	copyFastaFileForExport( fileService.get( sequenceData.sequenceFile, permanentDirectory ), currentTag.tag, zipWriter)
451	}
452	}
453	}
454	zipWriter.flush();
455	zipFile.closeEntry();
456
457	if( exportQual ) {
458	zipFile.putNextEntry( new ZipEntry( name + ".qual" ) );
459
460	assaySamples.each { assaySample ->
461	if( assaySample.numSequences() > 0 ) {
462	def currentTag = tags.find { it.assaySampleId == assaySample.id };
463
464	assaySample.sequenceData.each { sequenceData ->
465	copyQualFileForExport( fileService.get( sequenceData.qualityFile, permanentDirectory ), currentTag.tag, zipWriter)
466	}
467	}
468	}
469
470	zipWriter.flush();
471	zipFile.closeEntry();
472	}
473
474	} catch( Exception e ) {
475	log.error "Error while writing to fastafile or qualfile: " + e.getMessage();
476	} finally {
477	// Always close zip entry
478	try {
479	zipFile.closeEntry();
480	} catch( Exception e ) {
481	log.error "Error while closing zip entry for fasta and qual: " + e.getMessage();
482	}
483	}
484
485	// Export a tab delimited file with tags
486	zipFile.putNextEntry( new ZipEntry( name + "_sample-tag.tab" ) );
487	exportSampleTagFile( tags, zipWriter );
488	zipWriter.flush();
489	zipFile.closeEntry();
490
491	// Export an excel file with information about the samples
492	zipFile.putNextEntry( new ZipEntry( name + ".xls" ) );
493	sampleExcelService.exportExcelSampleData( assaySamples, tags, zipFile );
494	zipFile.closeEntry();
495
496	zipFile.close();
497	}
498
499	/**
500	* Creates a tab delimited file with two columns and column headers "Sequence" and "Samplename"
501	* @param tags Map with newly created tags
502	* @param zipWriter Writer to write the data to
503	*/
504	protected void exportSampleTagFile( List tags, Writer zipWriter ) {
505	zipWriter.write( "Sequence" + "\t" + "Samplename" + "\n" );
506
507	// Check whether the sample names are unique. If they aren't, the assay and study names
508	// are appended to the sample name
509	def sampleNames = tags*.sampleNames;
510	if( sampleNames.unique().size() < sampleNames.size() ) {
511	tags.each {
512	it.uniqueName = it.sampleName + " (" + it.assayName + " / " + it.studyName + ")";
513	}
514	} else {
515	tags.each {
516	it.uniqueName = it.sampleName;
517	}
518	}
519
520	tags.each {
521	zipWriter.write( it.tag + "\t" + it.uniqueName + "\n" );
522	}
523	}
524
525	/**
526	* Creates a unique tag for the given number
527	* @param length
528	* @param tagNumber
529	* @return
530	*/
531	public String createTag( int length, int tagNumber ) {
532	def chars = ["C", "A", "G", "T"];
533	def numChars = chars.size();
534
535	if( tagNumber > numChars ** length )
536	throw new Exception( "Given tag number (" + tagNumber + ") is too large for the specified length (" + length + ")")
537
538	String tag = "";
539
540	for( def i = 0; i < length; i++ ) {
541	int currentChar = tagNumber % numChars
542
543	tag = chars[ currentChar ] + tag;
544
545	tagNumber = Math.floor( tagNumber / numChars );
546	}
547
548	return tag
549	}
550
551	/**
552	* Copies the contents of the given sequence file to the output file and prepends the tag to every sequences
553	* @param inFile Filename of the file to be read
554	* @param tag
555	* @param outWriter
556	* @return
557	*/
558	protected boolean copyFastaFileForExport( File inFile, String tag, BufferedWriter outWriter ) {
559	// Walk through the lines in the file, starting with '>'
560	// (and where the following line contains a character other than '>')
561
562	try {
563	BufferedReader inReader = new BufferedReader( new FileReader( inFile ) );
564
565	String line = null
566	String newLine = null
567	String sequence = "";
568
569	def lengthPattern = ~/length=(\d+)/
570	def lengthMatches
571	int length = 0;
572	int tagLength = tag.size();
573
574	while( ( line = inReader.readLine()) != null) {
575	if( line.size() == 0 ) {
576	// Print the sequence we collected, before writing the empty line
577	printSequence( outWriter, sequence, tag );
578	sequence = "";
579
580	// Empty line
581	outWriter.newLine();
582	} else if( line[ 0 ] == '>' ) {
583	// Print the sequence we collected, before writing the new comments tag
584	printSequence( outWriter, sequence, tag );
585	sequence = "";
586
587	// Comments line: replace length=### with the
588	// updated length, and put the line in the
589	lengthMatches = ( line =~ lengthPattern );
590	if( lengthMatches ) {
591	length = Integer.valueOf( lengthMatches[0][1] ) + tagLength;
592	newLine = lengthMatches.replaceAll( "length=" + length );
593	}
594
595	outWriter.write(newLine);
596	outWriter.newLine();
597	} else {
598	// This is part of the sequence. We collect the whole sequence and
599	// determine in the end how to write it to the file
600	sequence += line;
601	}
602	}
603
604	// Print the sequence we collected, before ending the file
605	printSequence( outWriter, sequence, tag );
606	sequence = "";
607
608	} catch( Exception e ) {
609	log.error( "An error occurred while copying contents from " + inFile.getName() + ": " + e.getMessage() );
610	return false;
611	}
612	}
613
614	/**
615	* Prints a sequence to the output file
616	* @param outWriter
617	* @param sequence
618	* @param tag
619	*/
620	private void printSequence( BufferedWriter outWriter, String sequence, String tag, int maxWidth = 60 ) {
621	// If no sequence is given, also don't prepend it with the tag
622	if( sequence.size() == 0 )
623	return
624
625	// Prepend the tag to the sequence
626	sequence = tag + sequence;
627
628	// Write the sequence with a width of maxWidth characters per line
629	while( sequence ) {
630	if( sequence.size() > maxWidth ) {
631	outWriter.write( sequence[0..maxWidth-1] );
632	sequence = sequence[maxWidth..-1]
633	} else {
634	outWriter.write( sequence );
635	sequence = null;
636	}
637	outWriter.newLine();
638	}
639	}
640
641	/**
642	* Copies the contents of the given qual file to the output file and prepends the tag quality score to every sequence.
643	* For every tag character '40' is prepended to the qual scores
644	*
645	* @param inFile Filename of the file to be read
646	* @param tag
647	* @param outWriter
648	* @return
649	*/
650	protected boolean copyQualFileForExport( File inFile, String tag, BufferedWriter outWriter ) {
651	// Walk through the lines in the file, starting with '>'
652	// (and where the following line contains a character other than '>')
653	try {
654	BufferedReader inReader = new BufferedReader( new FileReader( inFile ) );
655
656	String line = null
657	String newLine = null
658	List<Integer> qualScores = []
659
660	def lengthPattern = ~/length=(\d+)/
661	def lengthMatches
662	int length = 0;
663	int tagLength = tag.size();
664
665	while( ( line = inReader.readLine()) != null) {
666	if( line.size() == 0 ) {
667	// Print the quality scores we collected, before writing the empty line
668	printQualScore( outWriter, qualScores, tagLength );
669	qualScores = [];
670
671	// Empty line
672	outWriter.newLine();
673	} else if( line[ 0 ] == '>' ) {
674	// Print the quality scores we collected, before writing the empty line
675	printQualScore( outWriter, qualScores, tagLength );
676	qualScores = [];
677
678	// Comments line: replace length=### with the
679	// updated length, and put the line in the
680	lengthMatches = ( line =~ lengthPattern );
681	if( lengthMatches ) {
682	length = Integer.valueOf( lengthMatches[0][1] ) + tagLength;
683	newLine = lengthMatches.replaceAll( "length=" + length );
684	}
685
686	outWriter.write(newLine);
687	outWriter.newLine();
688	} else {
689	// This is part of the quality score. We collect the whole set of quality
690	// scores and determine in the end how to write it to the file
691	qualScores += line.split( " " ).collect {
692	if( !it.isInteger() )
693	return 0;
694	else
695	return Integer.parseInt( it );
696	};
697	}
698	}
699
700	// Print the quality scores we collected, before ending the file
701	printQualScore( outWriter, qualScores, tagLength );
702	qualScores = [];
703
704	} catch( Exception e ) {
705	log.error( "An error occurred while copying contents from " + inFile.getName() + ": " + e.getMessage() );
706	return false;
707	}
708	}
709
710	/**
711	* Prints a sequence to the output file
712	* @param outWriter
713	* @param sequence
714	* @param tag
715	*/
716	private void printQualScore( BufferedWriter outWriter, List<Integer> qualScores, int tagLength, int maxWidth = 60 ) {
717	// If no qualScores are given, also don't prepend it with the tag
718	if( qualScores.size() == 0 )
719	return
720
721	// Prepend the tag to the sequence
722	qualScores = Collections.nCopies( tagLength, 40 ) + qualScores;
723
724	// Write the sequence with a width of maxWidth characters per line
725	while( qualScores ) {
726	if( qualScores.size() > maxWidth ) {
727	outWriter.write( qualScores[0..maxWidth-1].join( " " ) );
728	qualScores = qualScores[maxWidth..-1]
729	} else {
730	outWriter.write( qualScores.join( " " ) );
731	qualScores = null;
732	}
733	outWriter.newLine();
734	}
735	}
736
737	}

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