details: http://www.bx.psu.edu/hg/galaxy/rev/9dd990a2fa94 changeset: 3429:9dd990a2fa94 user: Dan Blankenberg <dan@bx.psu.edu> date: Tue Feb 23 16:48:07 2010 -0500 description: Add a new FASTQ tool suite. Four FASTQ variants are supported: sanger, illumina, solexa and solid. Tools include: FASTQ Groomer convert between various FASTQ quality formats Combine FASTA and QUAL into FASTQ FASTQ joiner on paired end reads FASTQ splitter on joined paired end reads FASTQ to FASTA converter FASTQ Summary Statistics by column Filter FASTQ reads by quality score and length FASTQ Trimmer by column Manipulate FASTQ reads on various attributes Boxplot of quality statistics (Generic, with outliers) diffstat: datatypes_conf.xml.sample | 7 +- lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py | 2 +- lib/galaxy/datatypes/qualityscore.py | 19 +- lib/galaxy/datatypes/sequence.py | 12 + lib/galaxy_utils/sequence/fastq.py | 702 ++++++++++ lib/galaxy_utils/sequence/sequence.py | 61 + lib/galaxy_utils/sequence/transform.py | 74 + test-data/3.fastqsanger | 1 - test-data/boxplot_summary_statistics_out.png | 0 test-data/combine_phiX_out_1.fastqsolid | 576 ++++++++ test-data/combine_phiX_out_2.fastqsolid | 576 ++++++++ test-data/fastq_combiner_in_1.fasta | 14 + test-data/fastq_combiner_in_1.qual454 | 22 + test-data/fastq_stats_1_out.tabular | 37 + test-data/fastq_to_fasta_python_1.out | 4 + test-data/fastq_to_fasta_python_2.out | 4 + test-data/fastq_trimmer_out1.fastqsanger | 8 + test-data/illumina_full_range_as_sanger.fastqsanger | 8 + test-data/illumina_full_range_as_solexa.fastqsolexa | 8 + test-data/illumina_full_range_as_solid.fastqsolid | 8 + test-data/illumina_full_range_original_illumina.fastqillumina | 8 + test-data/sanger_full_range_as_decimal_sanger.fastqsanger | 8 + test-data/sanger_full_range_as_illumina.fastqillumina | 8 + test-data/sanger_full_range_as_rna.fastqsanger | 8 + test-data/sanger_full_range_as_solexa.fastqsolexa | 8 + test-data/sanger_full_range_as_solid.fastqsolid | 8 + test-data/sanger_full_range_original_sanger.fastqsanger | 8 + test-data/sanger_full_range_rev_comp.fastqsanger | 8 + test-data/sanger_full_range_rev_comp_1_seq.fastqsanger | 8 + test-data/solexa_full_range_as_decimal_solexa.fastqsolexa | 8 + test-data/solexa_full_range_as_illumina.fastqillumina | 8 + test-data/solexa_full_range_as_sanger.fastqsanger | 8 + test-data/solexa_full_range_as_solid.fastqsolid | 8 + test-data/solexa_full_range_original_solexa.fastqsolexa | 8 + test-data/split_pair_reads_1.fastqsanger | 20 + test-data/split_pair_reads_2.fastqsanger | 20 + test-data/split_paired_reads_out_1.fastqsanger | 20 - test-data/split_paired_reads_out_2.fastqsanger | 20 - test-data/wrapping_as_illumina.fastqillumina | 12 + test-data/wrapping_as_sanger.fastqsanger | 12 + test-data/wrapping_as_sanger_decimal.fastqsanger | 12 + test-data/wrapping_as_solexa.fastqsolexa | 12 + test-data/wrapping_original_sanger.fastqsanger | 24 + tool_conf.xml.sample | 13 +- tools/fastq/fastq_combiner.py | 45 + tools/fastq/fastq_combiner.xml | 55 + tools/fastq/fastq_filter.py | 34 + tools/fastq/fastq_filter.xml | 311 ++++ tools/fastq/fastq_groomer.py | 37 + tools/fastq/fastq_groomer.xml | 349 ++++ tools/fastq/fastq_manipulation.py | 37 + tools/fastq/fastq_manipulation.xml | 386 +++++ tools/fastq/fastq_paired_end_joiner.py | 38 + tools/fastq/fastq_paired_end_joiner.xml | 55 + tools/fastq/fastq_paired_end_splitter.py | 33 + tools/fastq/fastq_paired_end_splitter.xml | 56 + tools/fastq/fastq_stats.py | 48 + tools/fastq/fastq_stats.xml | 72 + tools/fastq/fastq_to_fasta.py | 21 + tools/fastq/fastq_to_fasta.xml | 33 + tools/fastq/fastq_trimmer.py | 41 + tools/fastq/fastq_trimmer.xml | 113 + tools/metag_tools/split_paired_reads.xml | 4 +- tools/plotting/boxplot.xml | 72 + 64 files changed, 4210 insertions(+), 50 deletions(-) diffs (truncated from 4591 to 3000 lines): diff -r 03dbef081cf2 -r 9dd990a2fa94 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Tue Feb 23 16:12:20 2010 -0500 +++ b/datatypes_conf.xml.sample Tue Feb 23 16:48:07 2010 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <datatypes> - <registration converters_path="lib/galaxy/datatypes/converters"> + <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/> <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/> <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true"> @@ -34,6 +34,9 @@ </datatype> <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/> <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/> + <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true"/> + <datatype extension="fastqsolid" type="galaxy.datatypes.sequence:FastqSolid" display_in_upload="true"/> + <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"/> <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"> <!-- <display file="genetrack.xml" /> --> </datatype> @@ -60,7 +63,9 @@ </datatype> <datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/> <datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/> + <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /> <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> + <datatype extension="qualillumina" type="galaxy.datatypes.qualityscore:QualityScoreIllumina" display_in_upload="true"/> <datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/> <datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/> <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"/> diff -r 03dbef081cf2 -r 9dd990a2fa94 lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py Tue Feb 23 16:12:20 2010 -0500 +++ b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py Tue Feb 23 16:48:07 2010 -0500 @@ -47,7 +47,7 @@ #does file already conform to bed strict? #if so, we want to keep extended columns, otherwise we'll create a generic 6 column bed file strict_bed = True - if extension == 'bed' and ( chromCol, startCol, endCol, nameCol, strandCol ) == ( 0, 1, 2, 3, 5 ): + if extension in [ 'bed', 'bedstrict' ] and ( chromCol, startCol, endCol, nameCol, strandCol ) == ( 0, 1, 2, 3, 5 ): for count, line in enumerate( open( input_name ) ): line = line.strip() if line == "" or line.startswith("#"): diff -r 03dbef081cf2 -r 9dd990a2fa94 lib/galaxy/datatypes/qualityscore.py --- a/lib/galaxy/datatypes/qualityscore.py Tue Feb 23 16:12:20 2010 -0500 +++ b/lib/galaxy/datatypes/qualityscore.py Tue Feb 23 16:48:07 2010 -0500 @@ -9,7 +9,13 @@ log = logging.getLogger(__name__) -class QualityScoreSOLiD ( data.Text ): +class QualityScore ( data.Text ): + """ + until we know more about quality score formats + """ + file_ext = "qual" + +class QualityScoreSOLiD ( QualityScore ): """ until we know more about quality score formats """ @@ -58,7 +64,7 @@ pass return False -class QualityScore454 ( data.Text ): +class QualityScore454 ( QualityScore ): """ until we know more about quality score formats """ @@ -97,9 +103,14 @@ pass return False -class QualityScoreSolexa ( data.Text ): +class QualityScoreSolexa ( QualityScore ): """ until we know more about quality score formats """ file_ext = "qualsolexa" - \ No newline at end of file + +class QualityScoreIllumina ( QualityScore ): + """ + until we know more about quality score formats + """ + file_ext = "qualillumina" diff -r 03dbef081cf2 -r 9dd990a2fa94 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Tue Feb 23 16:12:20 2010 -0500 +++ b/lib/galaxy/datatypes/sequence.py Tue Feb 23 16:48:07 2010 -0500 @@ -216,6 +216,18 @@ """Class representing a FASTQ sequence ( the Sanger variant )""" file_ext = "fastqsanger" +class FastqSolexa( Fastq ): + """Class representing a FASTQ sequence ( the Solexa variant )""" + file_ext = "fastqsolexa" + +class FastqIllumina( Fastq ): + """Class representing a FASTQ sequence ( the Illumina 1.3+ variant )""" + file_ext = "fastqillumina" + +class FastqSolid( Fastq ): + """Class representing a FASTQ sequence ( the SOLiD (color space) variant )""" + file_ext = "fastqsolid" + try: from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) diff -r 03dbef081cf2 -r 9dd990a2fa94 lib/galaxy_utils/sequence/fastq.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy_utils/sequence/fastq.py Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,702 @@ +#Dan Blankenberg +import math +import string +import transform +from sequence import SequencingRead + +class fastqSequencingRead( SequencingRead ): + format = 'sanger' #sanger is default + ascii_min = 33 + ascii_max = 126 + quality_min = 0 + quality_max = 93 + score_system = 'phred' #phred or solexa + sequence_space = 'base' #base or color + @classmethod + def get_class_by_format( cls, format ): + assert format in FASTQ_FORMATS, 'Unknown format type specified: %s' % format + return FASTQ_FORMATS[ format ] + @classmethod + def convert_score_phred_to_solexa( cls, decimal_score_list ): + def phred_to_solexa( score ): + if score <= 0: #can't take log10( 1 - 1 ); make <= 0 into -5 + return -5 + return int( round( 10.0 * math.log10( math.pow( 10.0, ( float( score ) / 10.0 ) ) - 1.0 ) ) ) + return map( phred_to_solexa, decimal_score_list ) + @classmethod + def convert_score_solexa_to_phred( cls, decimal_score_list ): + def solexa_to_phred( score ): + return int( round( 10.0 * math.log10( math.pow( 10.0, ( float( score ) / 10.0 ) ) + 1.0 ) ) ) + return map( solexa_to_phred, decimal_score_list ) + @classmethod + def restrict_scores_to_valid_range( cls, decimal_score_list ): + def restrict_score( score ): + return max( min( score, cls.quality_max ), cls.quality_min ) + return map( restrict_score, decimal_score_list ) + @classmethod + def convert_base_to_color_space( cls, sequence ): + return cls.color_space_converter.to_color_space( sequence ) + @classmethod + def convert_color_to_base_space( cls, sequence ): + return cls.color_space_converter.to_base_space( sequence ) + def is_ascii_encoded( self ): + return ' ' not in self.quality #as per fastq definition only decimal quality strings can have spaces in them (and must have a trailing space) + def get_ascii_quality_scores( self ): + if self.is_ascii_encoded(): + return list( self.quality ) + else: + quality = self.quality.rstrip() #decimal scores should have a trailing space + if quality: + try: + return [ chr( int( val ) + self.ascii_min - self.quality_min ) for val in quality.split( ' ' ) ] + except ValueError, e: + raise ValueError( 'Error Parsing quality String. ASCII quality strings cannot contain spaces (%s): %s' % ( self.quality, e ) ) + else: + return [] + def get_decimal_quality_scores( self ): + if self.is_ascii_encoded(): + return [ ord( val ) - self.ascii_min + self.quality_min for val in self.quality ] + else: + quality = self.quality.rstrip() #decimal scores should have a trailing space + if quality: + return map( int, quality.split( ' ' ) ) + else: + return [] + def convert_read_to_format( self, format, force_quality_encoding = None ): + assert format in FASTQ_FORMATS, 'Unknown format type specified: %s' % format + assert force_quality_encoding in [ None, 'ascii', 'decimal' ], 'Invalid force_quality_encoding: %s' % force_quality_encoding + new_class = FASTQ_FORMATS[ format ] + new_read = new_class() + new_read.identifier = self.identifier + if self.sequence_space == new_class.sequence_space: + new_read.sequence = self.sequence + else: + if self.sequence_space == 'base': + new_read.sequence = self.convert_base_to_color_space( self.sequence ) + else: + new_read.sequence = self.convert_color_to_base_space( self.sequence ) + new_read.description = self.description + if self.score_system != new_read.score_system: + if self.score_system == 'phred': + score_list = self.convert_score_phred_to_solexa( self.get_decimal_quality_scores() ) + else: + score_list = self.convert_score_solexa_to_phred( self.get_decimal_quality_scores() ) + else: + score_list = self.get_decimal_quality_scores() + new_read.quality = "%s " % " ".join( map( str, new_class.restrict_scores_to_valid_range( score_list ) ) ) #need trailing space to be valid decimal fastq + if force_quality_encoding is None: + if self.is_ascii_encoded(): + new_encoding = 'ascii' + else: + new_encoding = 'decimal' + else: + new_encoding = force_quality_encoding + if new_encoding == 'ascii': + new_read.quality = "".join( new_read.get_ascii_quality_scores() ) + return new_read + def get_sequence( self ): + return self.sequence + def slice( self, left_column_offset, right_column_offset ): + new_read = fastqSequencingRead.get_class_by_format( self.format )() + new_read.identifier = self.identifier + new_read.sequence = self.get_sequence()[left_column_offset:right_column_offset] + new_read.description = self.description + if self.is_ascii_encoded(): + new_read.quality = self.quality[left_column_offset:right_column_offset] + else: + quality = map( str, self.get_decimal_quality_scores()[left_column_offset:right_column_offset] ) + if quality: + new_read.quality = "%s " % " ".join( quality ) + else: + new_read.quality = '' + return new_read + def is_valid_format( self ): + if self.is_ascii_encoded(): + for val in self.get_ascii_quality_scores(): + val = ord( val ) + if val < self.ascii_min or val > self.ascii_max: + return False + else: + for val in self.get_decimal_quality_scores(): + if val < self.quality_min or val > self.quality_max: + return False + if not self.is_valid_sequence(): + return False + return True + def is_valid_sequence( self ): + for base in self.get_sequence(): + if base not in self.valid_sequence_list: + return False + return True + def insufficient_quality_length( self ): + return len( self.get_ascii_quality_scores() ) < len( self.sequence ) + def assert_sequence_quality_lengths( self ): + qual_len = len( self.get_ascii_quality_scores() ) + seq_len = len( self.sequence ) + assert qual_len == seq_len, "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i)" % ( qual_len, seq_len ) + def reverse( self, clone = True ): + #need to override how decimal quality scores are reversed + if clone: + rval = self.clone() + else: + rval = self + rval.sequence = transform.reverse( self.sequence ) + if rval.is_ascii_encoded(): + rval.quality = rval.quality[::-1] + else: + rval.quality = reversed( rval.get_decimal_quality_scores() ) + rval.quality = "%s " % " ".join( map( str, rval.quality ) ) + return rval + +class fastqSangerRead( fastqSequencingRead ): + format = 'sanger' + ascii_min = 33 + ascii_max = 126 + quality_min = 0 + quality_max = 93 + score_system = 'phred' + sequence_space = 'base' + +class fastqIlluminaRead( fastqSequencingRead ): + format = 'illumina' + ascii_min = 64 + ascii_max = 126 + quality_min = 0 + quality_max = 62 + score_system = 'phred' + sequence_space = 'base' + +class fastqSolexaRead( fastqSequencingRead ): + format = 'solexa' + ascii_min = 59 + ascii_max = 126 + quality_min = -5 + quality_max = 62 + score_system = 'solexa' + sequence_space = 'base' + +class fastqSolidRead( fastqSequencingRead ): + format = 'solid' #color space + ascii_min = 33 + ascii_max = 126 + quality_min = 0 + quality_max = 93 + score_system = 'phred' + sequence_space = 'color' + valid_sequence_list = map( str, range( 7 ) ) + [ '.' ] + def __len__( self ): + if self.has_adapter_base(): #Adapter base is not counted in length of read + return len( self.sequence ) - 1 + return fastqSequencingRead.__len__( self ) + def has_adapter_base( self ): + if self.sequence and self.sequence[0] in string.letters: #adapter base must be a letter + return True + return False + def insufficient_quality_length( self ): + if self.has_adapter_base(): + return len( self.get_ascii_quality_scores() ) + 1 < len( self.sequence ) + return fastqSequencingRead.insufficient_quality_length( self ) + def assert_sequence_quality_lengths( self ): + if self.has_adapter_base(): + qual_len = len( self.get_ascii_quality_scores() ) + seq_len = len( self.sequence ) + assert qual_len + 1 == seq_len, "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i with adapter base)" % ( qual_len, seq_len ) + else: + return fastqSequencingRead.assert_sequence_quality_lengths( self ) + def get_sequence( self ): + if self.has_adapter_base(): + return self.sequence[1:] + return self.sequence + def reverse( self, clone = True ): + #need to override how color space is reversed + if clone: + rval = self.clone() + else: + rval = self + if rval.has_adapter_base(): + adapter = rval.sequence[0] + #sequence = rval.sequence[1:] + rval.sequence = self.color_space_converter.to_color_space( transform.reverse( self.color_space_converter.to_base_space( rval.sequence ) ), adapter_base = adapter ) + else: + rval.sequence = transform.reverse( rval.sequence ) + + if rval.is_ascii_encoded(): + rval.quality = rval.quality[::-1] + else: + rval.quality = reversed( rval.get_decimal_quality_scores() ) + rval.quality = "%s " % " ".join( map( str, rval.quality ) ) + return rval + def complement( self, clone = True ): + #need to override how color space is complemented + if clone: + rval = self.clone() + else: + rval = self + if rval.has_adapter_base(): #No adapter, color space stays the same + adapter = rval.sequence[0] + sequence = rval.sequence[1:] + if adapter.lower() != 'u': + adapter = transform.DNA_complement( adapter ) + else: + adapter = transform.RNA_complement( adapter ) + rval.sequence = "%s%s" % ( adapter, sequence ) + return rval + def change_adapter( self, new_adapter, clone = True ): + #if new_adapter is empty, remove adapter, otherwise replace with new_adapter + if clone: + rval = self.clone() + else: + rval = self + if rval.has_adapter_base(): + if new_adapter: + if new_adapter != rval.sequence[0]: + rval.sequence = rval.color_space_converter.to_color_space( rval.color_space_converter.to_base_space( rval.sequence ), adapter_base = new_adapter ) + else: + rval.sequence = rval.sequence[1:] + elif new_adapter: + rval.sequence = "%s%s" % ( new_adapter, rval.sequence ) + return rval + + +FASTQ_FORMATS = {} +for format in [ fastqIlluminaRead, fastqSolexaRead, fastqSangerRead, fastqSolidRead ]: + FASTQ_FORMATS[ format.format ] = format + + +class fastqAggregator(): + VALID_FORMATS = FASTQ_FORMATS.keys() + def __init__( self, ): + self.ascii_values_used = [] #quick lookup of all ascii chars used + self.seq_lens = {} #counts of seqs by read len + self.nuc_index_quality = [] #counts of scores by read column + self.nuc_index_base = [] #counts of bases by read column + def consume_read( self, fastq_read ): + #ascii values used + for val in fastq_read.get_ascii_quality_scores(): + if val not in self.ascii_values_used: + self.ascii_values_used.append( val ) + #lengths + seq_len = len( fastq_read ) + self.seq_lens[ seq_len ] = self.seq_lens.get( seq_len, 0 ) + 1 + #decimal qualities by column + for i, val in enumerate( fastq_read.get_decimal_quality_scores() ): + if i == len( self.nuc_index_quality ): + self.nuc_index_quality.append( {} ) + self.nuc_index_quality[ i ][ val ] = self.nuc_index_quality[ i ].get( val, 0 ) + 1 + #bases by column + for i, nuc in enumerate( fastq_read.get_sequence() ): + if i == len( self.nuc_index_base ): + self.nuc_index_base.append( {} ) + nuc = nuc.upper() + self.nuc_index_base[ i ][ nuc ] = self.nuc_index_base[ i ].get( nuc, 0 ) + 1 + def get_valid_formats( self, check_list = None ): + if not check_list: + check_list = self.VALID_FORMATS + rval = [] + sequence = [] + for nuc_dict in self.nuc_index_base: + for nuc in nuc_dict.keys(): + if nuc not in sequence: + sequence.append( nuc ) + sequence = "".join( sequence ) + quality = "".join( self.ascii_values_used ) + for fastq_format in check_list: + fastq_read = fastqSequencingRead.get_class_by_format( fastq_format )() + fastq_read.quality = quality + fastq_read.sequence = sequence + if fastq_read.is_valid_format(): + rval.append( fastq_format ) + return rval + def get_ascii_range( self ): + return ( min( self.ascii_values_used ), max( self.ascii_values_used ) ) + def get_decimal_range( self ): + decimal_values_used = [] + for scores in self.nuc_index_quality: + decimal_values_used.extend( scores.keys() ) + return ( min( decimal_values_used ), max( decimal_values_used ) ) + def get_length_counts( self ): + return self.seq_lens + def get_max_read_length( self ): + return len( self.nuc_index_quality ) + def get_read_count_for_column( self, column ): + if column >= len( self.nuc_index_quality ): + return 0 + return sum( self.nuc_index_quality[ column ].values() ) + def get_read_count( self ): + return self.get_read_count_for_column( 0 ) + def get_base_counts_for_column( self, column ): + return self.nuc_index_base[ column ] + def get_score_list_for_column( self, column ): + return self.nuc_index_quality[ column ].keys() + def get_score_min_for_column( self, column ): + return min( self.nuc_index_quality[ column ].keys() ) + def get_score_max_for_column( self, column ): + return max( self.nuc_index_quality[ column ].keys() ) + def get_score_sum_for_column( self, column ): + return sum( score * count for score, count in self.nuc_index_quality[ column ].iteritems() ) + def get_score_at_position_for_column( self, column, position ): + score_value_dict = self.nuc_index_quality[ column ] + scores = sorted( score_value_dict.keys() ) + for score in scores: + if score_value_dict[ score ] <= position: + position -= score_value_dict[ score ] + else: + return score + def get_summary_statistics_for_column( self, i ): + def _get_med_pos( size ): + halfed = int( size / 2 ) + if size % 2 == 1: + return [ halfed ] + return[ halfed - 1, halfed ] + read_count = self.get_read_count_for_column( i ) + + min_score = self.get_score_min_for_column( i ) + max_score = self.get_score_max_for_column( i ) + sum_score = self.get_score_sum_for_column( i ) + mean_score = float( sum_score ) / float( read_count ) + #get positions + med_pos = _get_med_pos( read_count ) + if 0 in med_pos: + q1_pos = [ 0 ] + q3_pos = [ read_count - 1 ] + else: + q1_pos = _get_med_pos( min( med_pos ) ) + q3_pos = [] + for pos in q1_pos: + q3_pos.append( max( med_pos ) + 1 + pos ) + #get scores at position + med_score = float( sum( [ self.get_score_at_position_for_column( i, pos ) for pos in med_pos ] ) ) / float( len( med_pos ) ) + q1 = float( sum( [ self.get_score_at_position_for_column( i, pos ) for pos in q1_pos ] ) ) / float( len( q1_pos ) ) + q3 = float( sum( [ self.get_score_at_position_for_column( i, pos ) for pos in q3_pos ] ) ) / float( len( q3_pos ) ) + #determine iqr and step + iqr = q3 - q1 + step = 1.5 * iqr + + #Determine whiskers and outliers + outliers = [] + score_list = sorted( self.get_score_list_for_column( i ) ) + left_whisker = q1 - step + for score in score_list: + if left_whisker <= score: + left_whisker = score + break + else: + outliers.append( score ) + + right_whisker = q3 + step + score_list.reverse() + for score in score_list: + if right_whisker >= score: + right_whisker = score + break + else: + outliers.append( score ) + + column_stats = { 'read_count': read_count, + 'min_score': min_score, + 'max_score': max_score, + 'sum_score': sum_score, + 'mean_score': mean_score, + 'q1': q1, + 'med_score': med_score, + 'q3': q3, + 'iqr': iqr, + 'left_whisker': left_whisker, + 'right_whisker': right_whisker, + 'outliers': outliers } + return column_stats + +class fastqReader( object ): + def __init__( self, fh, format = 'sanger' ): + self.file = fh + self.format = format + def close( self ): + return self.file.close() + def next(self): + while True: + fastq_header = self.file.readline() + if not fastq_header: + raise StopIteration + fastq_header = fastq_header.rstrip( '\n\r' ) + #remove empty lines, apparently extra new lines at end of file is common? + if fastq_header: + break + + assert fastq_header.startswith( '@' ), 'Invalid fastq header: %s' % fastq_header + rval = fastqSequencingRead.get_class_by_format( self.format )() + rval.identifier = fastq_header + while True: + line = self.file.readline() + if not line: + raise Exception( 'Invalid FASTQ file: could not parse second instance of sequence identifier.' ) + line = line.rstrip( '\n\r' ) + if line.startswith( '+' ) and ( len( line ) == 1 or line[1:].startswith( fastq_header[1:] ) ): + rval.description = line + break + rval.append_sequence( line ) + while rval.insufficient_quality_length(): + line = self.file.readline() + if not line: + break + rval.append_quality( line ) + rval.assert_sequence_quality_lengths() + return rval + def __iter__( self ): + while True: + yield self.next() + +class fastqNamedReader( object ): + def __init__( self, fh, format = 'sanger' ): + self.file = fh + self.format = format + self.reader = fastqReader( self.file, self.format ) + #self.last_offset = self.file.tell() + self.offset_dict = {} + self.eof = False + def close( self ): + return self.file.close() + def get( self, sequence_id ): + rval = None + if sequence_id in self.offset_dict: + initial_offset = self.file.tell() + seq_offset = self.offset_dict[ sequence_id ].pop( 0 ) + if not self.offset_dict[ sequence_id ]: + del self.offset_dict[ sequence_id ] + self.file.seek( seq_offset ) + rval = self.reader.next() + #assert rval.identifier == sequence_id, 'seq id mismatch' #should be able to remove this + self.file.seek( initial_offset ) + else: + while True: + offset = self.file.tell() + try: + fastq_read = self.reader.next() + except StopIteration: + self.eof = True + break #eof, id not found, will return None + if fastq_read.identifier == sequence_id: + rval = fastq_read + break + else: + if fastq_read.identifier not in self.offset_dict: + self.offset_dict[ fastq_read.identifier ] = [] + self.offset_dict[ fastq_read.identifier ].append( offset ) + return rval + def has_data( self ): + #returns a string representation of remaining data, or empty string (False) if no data remaining + eof = self.eof + count = 0 + rval = '' + if self.offset_dict: + count = sum( map( len, self.offset_dict.values() ) ) + if not eof: + offset = self.file.tell() + try: + fastq_read = self.reader.next() + except StopIteration: + eof = True + self.file.seek( offset ) + if count: + rval = "There were %i known sequence reads not utilized. " + if not eof: + rval = "%s%s" % ( rval, "An additional unknown number of reads exist in the input that were not utilized." ) + return rval + +class fastqWriter( object ): + def __init__( self, fh, format = None, force_quality_encoding = None ): + self.file = fh + self.format = format + self.force_quality_encoding = force_quality_encoding + def write( self, fastq_read ): + if self.format: + fastq_read = fastq_read.convert_read_to_format( self.format, force_quality_encoding = self.force_quality_encoding ) + self.file.write( str( fastq_read ) ) + def close( self ): + return self.file.close() + +class fastaWriter( object ): + def __init__( self, fh ): + self.file = fh + def write( self, fastq_read ): + #this will include SOLiD adapter base if applicable + self.file.write( ">%s\n%s\n" % ( fastq_read.identifier[1:], fastq_read.sequence ) ) + def close( self ): + return self.file.close() + +class fastqJoiner( object ): + def __init__( self, format, force_quality_encoding = None ): + self.format = format + self.force_quality_encoding = force_quality_encoding + def join( self, read1, read2 ): + if read1.identifier.endswith( '/2' ) and read2.identifier.endswith( '/1' ): + #swap 1 and 2 + tmp = read1 + read1 = read2 + read2 = tmp + del tmp + if read1.identifier.endswith( '/1' ) and read2.identifier.endswith( '/2' ): + identifier = read1.identifier[:-2] + else: + identifier = read1.identifier + + #use force quality encoding, if not present force to encoding of first read + force_quality_encoding = self.force_quality_encoding + if not force_quality_encoding: + if read1.is_ascii_encoded(): + force_quality_encoding = 'ascii' + else: + force_quality_encoding = 'decimal' + + new_read1 = read1.convert_read_to_format( self.format, force_quality_encoding = force_quality_encoding ) + new_read2 = read2.convert_read_to_format( self.format, force_quality_encoding = force_quality_encoding ) + rval = FASTQ_FORMATS[ self.format ]() + rval.identifier = identifier + if len( read1.description ) > 1: + rval.description = "+%s" % ( identifier[1:] ) + else: + rval.description = '+' + if rval.sequence_space == 'color': + #need to handle color space joining differently + #convert to nuc space, join, then convert back + rval.sequence = rval.convert_base_to_color_space( new_read1.convert_color_to_base_space( new_read1.sequence ) + new_read2.convert_color_to_base_space( new_read2.sequence ) ) + else: + rval.sequence = new_read1.sequence + new_read2.sequence + if force_quality_encoding == 'ascii': + rval.quality = new_read1.quality + new_read2.quality + else: + rval.quality = "%s %s" % ( new_read1.quality.strip(), new_read2.quality.strip() ) + return rval + def get_paired_identifier( self, fastq_read ): + identifier = fastq_read.identifier + if identifier[-2] == '/': + if identifier[-1] == "1": + identifier = "%s2" % identifier[:-1] + elif identifier[-1] == "2": + identifier = "%s1" % identifier[:-1] + return identifier + +class fastqSplitter( object ): + def split( self, fastq_read ): + length = len( fastq_read ) + #Only reads of even lengths can be split + if length % 2 != 0: + return None, None + half = int( length / 2 ) + read1 = fastq_read.slice( 0, half ) + read1.identifier += "/1" + if len( read1.description ) > 1: + read1.description += "/1" + read2 = fastq_read.slice( half, None ) + read2.identifier += "/2" + if len( read2.description ) > 1: + read2.description += "/2" + return read1, read2 + +class fastaSequence( ): + def __init__( self ): + self.identifier = None + self.sequence = '' #holds raw sequence string: no whitespace + def __len__( self ): + return len( self.sequence ) + def __str__( self ): + return "%s\n%s\n" % ( self.identifier, self.sequence ) + +class fastaReader( object ): + def __init__( self, fh ): + self.file = fh + def close( self ): + return self.file.close() + def next( self ): + line = self.file.readline() + #remove header comment lines + while line and line.startswith( '#' ): + line = self.file.readline() + if not line: + raise StopIteration + assert line.startswith( '>' ), "FASTA headers must start with >" + rval = fastaSequence() + rval.identifier = line.strip() + offset = self.file.tell() + while True: + line = self.file.readline() + if not line or line.startswith( '>' ): + if line: + self.file.seek( offset ) + return rval + #454 qual test data that was used has decimal scores that don't have trailing spaces + #so we'll need to parse and build these sequences not based upon de facto standards + #i.e. in a less than ideal fashion + line = line.rstrip() + if ' ' in rval.sequence or ' ' in line: + rval.sequence = "%s%s " % ( rval.sequence, line ) + else: + rval.sequence += line + offset = self.file.tell() + def __iter__( self ): + while True: + yield self.next() + +class fastaNamedReader( object ): + def __init__( self, fh ): + self.file = fh + self.reader = fastaReader( self.file ) + self.offset_dict = {} + self.eof = False + def close( self ): + return self.file.close() + def get( self, sequence_id ): + rval = None + if sequence_id in self.offset_dict: + initial_offset = self.file.tell() + seq_offset = self.offset_dict[ sequence_id ].pop( 0 ) + if not self.offset_dict[ sequence_id ]: + del self.offset_dict[ sequence_id ] + self.file.seek( seq_offset ) + rval = self.reader.next() + self.file.seek( initial_offset ) + else: + while True: + offset = self.file.tell() + try: + fasta_seq = self.reader.next() + except StopIteration: + self.eof = True + break #eof, id not found, will return None + if fasta_seq.identifier == sequence_id: + rval = fasta_seq + break + else: + if fasta_seq.identifier not in self.offset_dict: + self.offset_dict[ fasta_seq.identifier ] = [] + self.offset_dict[ fasta_seq.identifier ].append( offset ) + return rval + def has_data( self ): + #returns a string representation of remaining data, or empty string (False) if no data remaining + eof = self.eof + count = 0 + rval = '' + if self.offset_dict: + count = sum( map( len, self.offset_dict.values() ) ) + if not eof: + offset = self.file.tell() + try: + fasta_seq = self.reader.next() + except StopIteration: + eof = True + self.file.seek( offset ) + if count: + rval = "There were %i known sequences not utilized. " % count + if not eof: + rval = "%s%s" % ( rval, "An additional unknown number of sequences exist in the input that were not utilized." ) + return rval + +class fastqCombiner( object ): + def __init__( self, format ): + self.format = format + def combine(self, fasta_seq, quality_seq ): + fastq_read = fastqSequencingRead.get_class_by_format( self.format )() + fastq_read.identifier = "@%s" % fasta_seq.identifier[1:] + fastq_read.description = '+' + fastq_read.sequence = fasta_seq.sequence + fastq_read.quality = quality_seq.sequence + return fastq_read diff -r 03dbef081cf2 -r 9dd990a2fa94 lib/galaxy_utils/sequence/sequence.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy_utils/sequence/sequence.py Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,61 @@ +#Dan Blankenberg +import transform +import string +from copy import deepcopy + +class SequencingRead( object ): + color_space_converter = transform.ColorSpaceConverter() + valid_sequence_list = string.letters + def __init__( self ): + self.identifier = None + self.sequence = '' #holds raw sequence string: no whitespace + self.description = None + self.quality = '' #holds raw quality string: no whitespace, unless this contains decimal scores + def __len__( self ): + return len( self.sequence ) + def __str__( self ): + return "%s\n%s\n%s\n%s\n" % ( self.identifier, self.sequence, self.description, self.quality ) + def append_sequence( self, sequence ): + self.sequence += sequence.rstrip( '\n\r' ) + def append_quality( self, quality ): + self.quality += quality.rstrip( '\n\r' ) + def is_DNA( self ): + return 'u' not in self.sequence.lower() + def clone( self ): + return deepcopy( self ) + def reverse( self, clone = True ): + if clone: + rval = self.clone() + else: + rval = self + rval.sequence = transform.reverse( self.sequence ) + rval.quality = rval.quality[::-1] + return rval + def complement( self, clone = True ): + if clone: + rval = self.clone() + else: + rval = self + if rval.is_DNA(): + rval.sequence = transform.DNA_complement( rval.sequence ) + else: + rval.sequence = transform.RNA_complement( rval.sequence ) + return rval + def reverse_complement( self, clone = True ): + #need to reverse first, then complement + rval = self.reverse( clone = clone ) + return rval.complement( clone = False ) #already working with a clone if requested + def sequence_as_DNA( self, clone = True ): + if clone: + rval = self.clone() + else: + rval = self + rval.sequence = transform.to_DNA( rval.sequence ) + return rval + def sequence_as_RNA( self, clone = True ): + if clone: + rval = self.clone() + else: + rval = self + rval.sequence = transform.to_RNA( rval.sequence ) + return rval diff -r 03dbef081cf2 -r 9dd990a2fa94 lib/galaxy_utils/sequence/transform.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy_utils/sequence/transform.py Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,74 @@ +#Dan Blankenberg +#Contains methods to tranform sequence strings +import string + +#FIXME: This should Handle ambiguity codes... +#Translation table for reverse Complement +DNA_COMPLEMENT = string.maketrans( "ACGTacgt", "TGCAtgca" ) +RNA_COMPLEMENT = string.maketrans( "ACGUacgu", "UGCAugca" ) +#Translation table for DNA <--> RNA +DNA_TO_RNA = string.maketrans( "Tt", "Uu" ) +RNA_TO_DNA = string.maketrans( "Uu", "Tt" ) + +#reverse sequence string +def reverse( sequence ): + return sequence[::-1] +#complement DNA sequence string +def DNA_complement( sequence ): + return sequence.translate( DNA_COMPLEMENT ) +#complement RNA sequence string +def RNA_complement( sequence ): + return sequence.translate( RNA_COMPLEMENT ) +#returns the reverse complement of the sequence +def DNA_reverse_complement( self, sequence ): + sequence = reverse( sequence ) + return DNA_complement( sequence ) +def RNA_reverse_complement( self, sequence ): + sequence = reverse( sequence ) + return RNA_complement( sequence ) +def to_DNA( sequence ): + return sequence.translate( DNA_TO_RNA ) +def to_RNA( sequence ): + return sequence.translate( RNA_TO_DNA ) + +class ColorSpaceConverter( object ): + unknown_base = 'N' + unknown_color = '.' + color_to_base_dict = {} + color_to_base_dict[ 'A' ] = { '0':'A', '1':'C', '2':'G', '3':'T', '4':'N', '5':'N', '6':'N', '.':'N' } + color_to_base_dict[ 'C' ] = { '0':'C', '1':'A', '2':'T', '3':'G', '4':'N', '5':'N', '6':'N', '.':'N' } + color_to_base_dict[ 'G' ] = { '0':'G', '1':'T', '2':'A', '3':'C', '4':'N', '5':'N', '6':'N', '.':'N' } + color_to_base_dict[ 'T' ] = { '0':'T', '1':'G', '2':'C', '3':'A', '4':'N', '5':'N', '6':'N', '.':'N' } + color_to_base_dict[ 'N' ] = { '0':'N', '1':'N', '2':'N', '3':'N', '4':'N', '5':'N', '6':'N', '.':'N' } + base_to_color_dict = {} + for base, color_dict in color_to_base_dict.iteritems(): + base_to_color_dict[ base ] = {} + for key, value in color_dict.iteritems(): + base_to_color_dict[ base ][ value ] = key + base_to_color_dict[ base ][ 'N' ] = '4' #force ACGT followed by N to be '4', because this is now 'processed' data; we could force to '.' (non-processed data) also + base_to_color_dict[ 'N' ].update( { 'A':'5', 'C':'5', 'G':'5', 'T':'5', 'N':'6' } ) + def __init__( self, fake_adapter_base = 'G' ): + assert fake_adapter_base in self.base_to_color_dict, 'A bad fake adapter base was provided: %s.' % fake_adapter_base + self.fake_adapter_base = fake_adapter_base + def to_color_space( self, sequence, adapter_base = None ): + if adapter_base is None: + adapter_base = self.fake_adapter_base + last_base = adapter_base #we add a fake adapter base so that the sequence can be decoded properly again + rval = last_base + for base in sequence: + rval += self.base_to_color_dict.get( last_base, self.base_to_color_dict[ self.unknown_base ] ).get( base, self.unknown_color ) + last_base = base + return rval + def to_base_space( self, sequence ): + if not isinstance( sequence, list ): + sequence = list( sequence ) + if sequence: + last_base = sequence.pop( 0 ) + else: + last_base = None + assert last_base in self.color_to_base_dict, 'A valid adapter base must be included when converting to base space from color space. Found: %s' % last_base + rval = '' + for color_val in sequence: + last_base = self.color_to_base_dict[ last_base ].get( color_val, self.unknown_base ) + rval += last_base + return rval diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/3.fastqsanger --- a/test-data/3.fastqsanger Tue Feb 23 16:12:20 2010 -0500 +++ b/test-data/3.fastqsanger Tue Feb 23 16:48:07 2010 -0500 @@ -18,4 +18,3 @@ TATCAAAAAAGAATATAATCTGAATCAACACTACAACCTATTAGTGTGTAGAATAGGAAGTAGAGGCCTGCG +HWI-EAS91_1_30788AAXX:7:64:947:234 hhhhhhhhhhhhhhhhhhhhhhhRhhehhahhhhhJhhhhhhhh^hPhWfhhhhThWUhhfhh_hhNIVPUd - diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/boxplot_summary_statistics_out.png Binary file test-data/boxplot_summary_statistics_out.png has changed diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/combine_phiX_out_1.fastqsolid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combine_phiX_out_1.fastqsolid Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,576 @@ +@1831_573_1004_F3 +T00030133312212111300011021310132222 ++ +4 29 27 34 5 5 24 24 20 17 10 34 29 20 27 13 30 27 22 24 11 28 19 17 27 17 24 17 25 27 7 24 14 12 22 +@1831_573_1050_F3 +T03330322230322112131010221102122113 ++ +8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 5 10 13 6 5 10 6 16 11 +@1831_573_1067_F3 +T00023032023103330112220321200200002 ++ +13 10 10 2 4 7 6 11 4 14 3 11 10 5 16 2 5 8 11 8 5 10 6 9 6 9 4 2 3 5 2 4 7 6 3 +@1831_573_1219_F3 +T11211130300300301021212330201121310 ++ +31 31 31 28 19 14 10 8 20 8 19 15 23 30 6 21 21 20 29 9 14 20 30 27 21 16 6 26 27 18 11 25 11 20 12 +@1831_573_1242_F3 +T02132003121011302100130302112221121 ++ +29 29 29 25 25 29 16 22 28 32 20 30 31 31 28 26 22 32 28 26 17 13 21 15 29 23 17 27 23 28 22 19 10 26 26 +@1831_573_1333_F3 +T00200312330110101013212313222303112 ++ +8 28 6 31 2 4 18 28 13 29 8 14 18 19 9 16 16 22 11 11 14 21 12 19 10 13 24 22 19 17 19 20 21 27 8 +@1831_573_1362_F3 +T21203131001102231121211101111321131 ++ +34 33 31 31 30 31 31 30 31 34 31 33 32 30 31 29 31 27 31 23 32 31 30 31 6 13 23 6 30 16 22 25 11 10 30 +@1831_573_1448_F3 +T23101211223113320132212331313312022 ++ +22 22 28 32 8 30 11 13 31 32 31 31 25 31 31 27 28 14 22 8 31 27 12 2 23 21 21 17 4 24 21 16 18 5 10 +@1831_573_1490_F3 +T31312310323301210002210123101021011 ++ +31 31 31 31 30 11 31 30 30 31 3 29 27 28 29 10 4 14 9 29 9 16 11 8 30 17 21 5 16 17 6 24 4 22 13 +@1831_573_1523_F3 +T10322001220012223202202222001230222 ++ +7 11 14 14 9 11 2 23 6 6 13 21 6 6 21 6 17 5 17 22 14 23 15 8 4 5 2 15 6 4 2 9 11 17 6 +@1831_573_1578_F3 +T21202302100010020121100311022120111 ++ +31 30 28 31 27 31 34 31 30 31 31 30 30 28 29 31 26 22 27 27 23 27 21 24 19 8 18 20 16 16 7 10 16 27 13 +@1831_573_1647_F3 +T10222233301013033120132223202022123 ++ +28 30 31 31 27 31 31 30 30 30 26 32 28 28 31 31 26 24 30 31 30 18 28 26 21 13 19 14 26 21 25 28 14 26 19 +@1831_573_1684_F3 +T13310013212312012302121010221231123 ++ +22 29 16 25 23 27 31 18 24 31 31 30 30 24 28 26 31 31 27 29 30 31 31 27 26 27 30 22 29 22 21 30 24 29 30 +@1831_573_1769_F3 +T33220123030232212032021032302233131 ++ +22 20 19 22 19 24 5 5 22 21 22 4 14 22 26 18 3 12 22 26 18 2 11 18 14 14 2 11 19 20 14 2 5 15 21 +@1831_573_1853_F3 +T11000012111222211310103212122102331 ++ +21 19 13 14 33 31 31 22 17 33 10 14 19 30 31 30 22 30 10 31 24 14 10 24 24 13 6 8 17 27 17 5 8 17 5 +@1831_573_1943_F3 +T20300123032210232001222122001132111 ++ +7 29 14 9 16 11 8 11 31 12 8 6 15 9 29 20 6 3 14 30 21 31 14 13 5 30 23 14 7 6 8 32 19 18 11 +@1831_573_1977_F3 +T22212302221310332321002303112011311 ++ +31 31 30 21 31 23 31 31 24 32 31 28 19 21 18 18 32 22 30 24 30 27 18 25 10 22 29 6 31 4 31 30 4 18 17 +@1831_574_109_F3 +T13122332123301331032220222133301033 ++ +15 22 21 20 16 2 19 23 16 22 29 31 21 20 27 17 25 23 19 22 16 21 28 22 23 23 27 16 24 24 20 13 22 30 21 +@1831_574_148_F3 +T01200113123030012202302312200010231 ++ +27 26 12 29 18 26 26 18 29 14 14 29 15 26 26 22 28 11 28 19 12 19 14 10 29 15 17 24 27 24 27 21 17 19 26 +@1831_574_185_F3 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+T00032312310201201333221212000011030 ++ +,@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ +@1831_576_1987_F3 +T30022313313231221213220132001011320 ++ +)##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ +@1831_576_2014_F3 +T31123201010100321122111102113021003 ++ +@@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 +@1831_576_2028_F3 +T20131211210311112023201213120201100 ++ +5<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ +@1831_577_40_F3 +T11111212330120012020200031313303003 ++ +92/4('.')(<*?#$)%&<,/39<(.2,+<=@611 +@1831_577_119_F3 +T33111010021103320103213121313000102 ++ +9>?C11)-1/)#;#/,850*+.+$$5550+%-.40 +@1831_577_133_F3 +T33213323012231300122223032223331322 ++ +/4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) +@1831_577_255_F3 +T00332022110020300332022020202002232 ++ +7<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# +@1831_577_281_F3 +T03032301231212301013112222111210000 ++ +7-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? +@1831_577_288_F3 +T01031120221303100221230021013201130 ++ +5;/79??&=B::298*6.7/+4&21,7,6?.7#'6 +@1831_577_322_F3 +T12003213220230103303201000130312202 ++ +9=;>4506;255464-<#7+194&2<?65968)7/ +@1831_577_362_F3 +T31203302330110131230331210121110220 ++ +62B?:@?@<?958=,3:,90:&'-99,6<5.($+6 +@1831_577_382_F3 +T32312123033111120321303230201332100 ++ +12957/:1))=76(*24;,3+:<.&.&-=1=2/5* +@1831_577_464_F3 +T13020221011130013102221333131203302 ++ +3=<7/<826)>#.'&4204+5#/041.7*91&756 +@1831_577_488_F3 +T13200302330322110200323132101120301 ++ +:48.,*>6566<?8=<=<2>6;94>;=9>@8924@ +@1831_577_511_F3 +T32232133031023313331312220133230333 ++ +#7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ +@1831_577_545_F3 +T00112131333222303222210031322103233 ++ +>><<9?<>?A<481@<@8==@76/61<95.5988- +@1831_577_559_F3 +T32321101303233120102011130022122002 ++ +.<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' +@1831_577_562_F3 +T32331101301233110121000220031120031 ++ +#((&*&0%)1%)#($2-,***%/-,,))&,-.1'* +@1831_577_637_F3 +T22113312122202103031023120301031110 ++ +8-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, +@1831_577_641_F3 +T13031301101121223221212020032131113 ++ +&47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' +@1831_577_692_F3 +T01122320200330103121202301211100220 ++ +@B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/fastq_combiner_in_1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_combiner_in_1.fasta Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,14 @@ +>SRR014849.50939 EIXKN4201BA2EC length=135 +GAAATTTCAGGGCCACCTTTTTTTT +GATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGA +GAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG +>SRR014849.110027 EIXKN4201APUB0 length=131 +CTTCAAATGATTC +CGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCC +TTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGAC +CAGAACGATCCG +>SRR014849.203935 EIXKN4201B4HU6 length=144 +AACCCGTCCCA +TCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACC +CCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTT +TAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/fastq_combiner_in_1.qual454 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_combiner_in_1.qual454 Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,22 @@ +>SRR014849.110027 EIXKN4201APUB0 length=131 +=B::@<':=5A9?7EA0:=<<?6@7<3?5< +@;%D?-B=)::0=4<D? +-EA/D@2";B;B: +B:A9;;=<B;;<B;<B;<B;:A;<A;8FB7 ++=<B;B:A9<1:=FB6(<=<<EA0956;<2 +==A8===:@8= +>SRR014849.203935 EIXKN4201B4HU6 length=144 +A;@;%75?:#<<9EA1;=EA3%B;B;A;B; +@;%9EA1EA1EA3%<B;A;8EA0D@ +3$EA1 +=B;A;B;B;:=:B;:B:A9:EA0A9<FA81 ++&"D?-B;4<::/<;=:A98-5?6=C>+8< +<3;=4:DA3%<;=8-9.A=):B=* +>SRR014849.50939 EIXKN4201BA2EC length=135 +;C?-EA/=<EA/B;<B;D>60,)%"<=:5< +@8<B;=B;<;E +A4'@8FB6*<:=<<===<= +;=B:A9<<B;=B;=EA0:<B:<<=<<FA81 ++$?6;<A9=<3>5@7@8<A<(B=*A=)<<2 +?57B=*B=*D?-:=4 + diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/fastq_stats_1_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_stats_1_out.tabular Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,37 @@ +#column count min max sum mean Q1 med Q3 IQR lW rW outliers A_Count C_Count G_Count T_Count N_Count other_bases other_base_count +1 9 23 34 288 32.0 33.0 33.0 33.0 0.0 33 33 23,34 3 1 4 1 0 +2 9 28 33 287 31.8888888889 30.5 33.0 33.0 2.5 28 33 3 3 2 1 0 +3 9 13 34 268 29.7777777778 27.5 33.0 33.5 6.0 27 34 13 5 1 0 3 0 +4 9 17 33 261 29.0 24.5 33.0 33.0 8.5 17 33 1 2 3 3 0 +5 9 22 33 269 29.8888888889 26.0 33.0 33.0 7.0 22 33 3 3 3 0 0 +6 9 22 33 277 30.7777777778 29.0 33.0 33.0 4.0 28 33 22 5 3 0 1 0 +7 9 21 33 258 28.6666666667 23.0 33.0 33.0 10.0 21 33 4 1 3 1 0 +8 9 12 33 263 29.2222222222 26.5 33.0 33.0 6.5 21 33 12 2 1 1 5 0 +9 9 29 33 290 32.2222222222 31.5 33.0 33.0 1.5 30 33 29 3 3 2 1 0 +10 9 23 33 277 30.7777777778 28.0 33.0 33.0 5.0 23 33 1 4 2 2 0 +11 9 12 33 245 27.2222222222 21.0 31.0 33.0 12.0 12 33 5 2 1 1 0 +12 9 13 33 214 23.7777777778 14.0 24.0 33.0 19.0 13 33 2 4 2 1 0 +13 9 5 33 249 27.6666666667 26.5 31.0 33.0 6.5 24 33 5 2 1 1 5 0 +14 9 5 33 233 25.8888888889 19.5 33.0 33.0 13.5 5 33 3 3 2 1 0 +15 9 15 33 251 27.8888888889 22.5 33.0 33.0 10.5 15 33 5 1 1 2 0 +16 9 23 34 269 29.8888888889 23.5 33.0 33.0 9.5 23 34 3 1 2 3 0 +17 9 13 34 266 29.5555555556 27.0 33.0 33.0 6.0 21 34 13 2 3 1 3 0 +18 9 21 34 272 30.2222222222 26.0 33.0 33.0 7.0 21 34 0 5 1 3 0 +19 9 5 34 244 27.1111111111 24.0 30.0 33.0 9.0 21 34 5 4 4 1 0 0 +20 9 11 34 241 26.7777777778 17.0 32.0 33.0 16.0 11 34 3 4 2 0 0 +21 9 13 33 240 26.6666666667 22.5 27.0 33.0 10.5 13 33 1 4 0 4 0 +22 9 5 33 190 21.1111111111 9.0 21.0 33.0 24.0 5 33 1 4 0 3 1 +23 9 5 33 205 22.7777777778 14.0 26.0 33.0 19.0 5 33 4 4 1 0 0 +24 9 5 33 247 27.4444444444 24.5 31.0 33.0 8.5 21 33 5 1 5 1 2 0 +25 9 11 34 241 26.7777777778 18.5 33.0 33.0 14.5 11 34 3 4 0 2 0 +26 9 5 33 212 23.5555555556 11.5 31.0 33.0 21.5 5 33 0 6 0 3 0 +27 9 5 33 227 25.2222222222 20.0 26.0 33.0 13.0 5 33 3 4 1 1 0 +28 9 21 33 255 28.3333333333 22.5 31.0 33.0 10.5 21 33 2 4 3 0 0 +29 9 5 33 228 25.3333333333 19.5 30.0 33.0 13.5 5 33 2 4 1 2 0 +30 9 10 33 213 23.6666666667 13.5 28.0 33.0 19.5 10 33 3 4 2 0 0 +31 9 5 33 236 26.2222222222 21.0 31.0 33.0 12.0 5 33 1 4 1 3 0 +32 9 5 33 210 23.3333333333 11.5 29.0 33.0 21.5 5 33 3 3 0 3 0 +33 9 5 33 183 20.3333333333 8.0 21.0 33.0 25.0 5 33 1 4 2 2 0 +34 9 5 33 150 16.6666666667 6.0 17.0 25.5 19.5 5 33 3 4 1 1 0 +35 9 13 33 217 24.1111111111 19.5 24.0 31.0 11.5 13 33 1 4 1 3 0 +36 9 5 33 195 21.6666666667 11.5 21.0 32.5 21.0 5 33 3 2 1 3 0 diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/fastq_to_fasta_python_1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_to_fasta_python_1.out Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,4 @@ +>FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC +>FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/fastq_to_fasta_python_2.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_to_fasta_python_2.out Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,4 @@ +>FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +G2131313131313131313131313131313131313131313131313131313131313131313131313131313131313131313131 +>FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +G3131313131313131313131313131313131313131313131313131313131313131313131313131313131313131313131 diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/fastq_trimmer_out1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_trimmer_out1.fastqsanger Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +CGTA ++ +NOPQ +@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +ATGC ++ +QPON diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/illumina_full_range_as_sanger.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illumina_full_range_as_sanger.fastqsanger Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0005 Original version has PHRED scores from 0 to 62 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG ++ +!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_ +@FAKE0006 Original version has PHRED scores from 62 to 0 inclusive (in that order) +GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA ++ +_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/illumina_full_range_as_solexa.fastqsolexa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illumina_full_range_as_solexa.fastqsolexa Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0005 Original version has PHRED scores from 0 to 62 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG ++ +;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ +@FAKE0006 Original version has PHRED scores from 62 to 0 inclusive (in that order) +GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA ++ +~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJHGFECB@>;; diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/illumina_full_range_as_solid.fastqsolid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illumina_full_range_as_solid.fastqsolid Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0005 Original version has PHRED scores from 0 to 62 inclusive (in that order) +G213131313131313131313131313131313131313131313131313131313131313 ++ +!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_ +@FAKE0006 Original version has PHRED scores from 62 to 0 inclusive (in that order) +G031313131313131313131313131313131313131313131313131313131313131 ++ +_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/illumina_full_range_original_illumina.fastqillumina --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illumina_full_range_original_illumina.fastqillumina Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0005 Original version has PHRED scores from 0 to 62 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG ++ +@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ +@FAKE0006 Original version has PHRED scores from 62 to 0 inclusive (in that order) +GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA ++ +~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@ diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/sanger_full_range_as_decimal_sanger.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_as_decimal_sanger.fastqsanger Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC ++ +0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 +@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA ++ +93 92 91 90 89 88 87 86 85 84 83 82 81 80 79 78 77 76 75 74 73 72 71 70 69 68 67 66 65 64 63 62 61 60 59 58 57 56 55 54 53 52 51 50 49 48 47 46 45 44 43 42 41 40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0 diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/sanger_full_range_as_illumina.fastqillumina --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_as_illumina.fastqillumina Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC ++ +@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@ diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/sanger_full_range_as_rna.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_as_rna.fastqsanger Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +ACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUAC ++ +!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ +@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +CAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCAUGCA ++ +~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/sanger_full_range_as_solexa.fastqsolexa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_as_solexa.fastqsolexa Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC ++ +;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJHGFECB@>;; diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/sanger_full_range_as_solid.fastqsolid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_as_solid.fastqsolid Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +G2131313131313131313131313131313131313131313131313131313131313131313131313131313131313131313131 ++ +!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ +@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +G3131313131313131313131313131313131313131313131313131313131313131313131313131313131313131313131 ++ +~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/sanger_full_range_original_sanger.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_original_sanger.fastqsanger Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC ++ +!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ +@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA ++ +~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/sanger_full_range_rev_comp.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_rev_comp.fastqsanger Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT ++ +~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! +@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATG ++ +!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/sanger_full_range_rev_comp_1_seq.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_rev_comp_1_seq.fastqsanger Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) +GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT ++ +~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! +@FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) +CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA ++ +~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"! diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/solexa_full_range_as_decimal_solexa.fastqsolexa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/solexa_full_range_as_decimal_solexa.fastqsolexa Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0003 Original version has Solexa scores from -5 to 62 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT ++ +-5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 +@FAKE0004 Original version has Solexa scores from 62 to -5 inclusive (in that order) +TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA ++ +62 61 60 59 58 57 56 55 54 53 52 51 50 49 48 47 46 45 44 43 42 41 40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0 -1 -2 -3 -4 -5 diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/solexa_full_range_as_illumina.fastqillumina --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/solexa_full_range_as_illumina.fastqillumina Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0003 Original version has Solexa scores from -5 to 62 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT ++ +AABBCCDDEEFGHIJJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ +@FAKE0004 Original version has Solexa scores from 62 to -5 inclusive (in that order) +TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA ++ +~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJJIHGFEEDDCCBBAA diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/solexa_full_range_as_sanger.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/solexa_full_range_as_sanger.fastqsanger Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0003 Original version has Solexa scores from -5 to 62 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT ++ +""##$$%%&&'()*++,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_ +@FAKE0004 Original version has Solexa scores from 62 to -5 inclusive (in that order) +TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA ++ +_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,++*)('&&%%$$##"" diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/solexa_full_range_as_solid.fastqsolid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/solexa_full_range_as_solid.fastqsolid Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0003 Original version has Solexa scores from -5 to 62 inclusive (in that order) +G21313131313131313131313131313131313131313131313131313131313131313131 ++ +""##$$%%&&'()*++,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_ +@FAKE0004 Original version has Solexa scores from 62 to -5 inclusive (in that order) +G11313131313131313131313131313131313131313131313131313131313131313131 ++ +_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,++*)('&&%%$$##"" diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/solexa_full_range_original_solexa.fastqsolexa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/solexa_full_range_original_solexa.fastqsolexa Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,8 @@ +@FAKE0003 Original version has Solexa scores from -5 to 62 inclusive (in that order) +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT ++ +;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ +@FAKE0004 Original version has Solexa scores from 62 to -5 inclusive (in that order) +TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA ++ +~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<; diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/split_pair_reads_1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split_pair_reads_1.fastqsanger Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,20 @@ +@HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 +GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC ++HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_30788AAXX:7:22:1621:462/1 +ATAATGGCTATTATTGTGGGGGGGATGATGCTGGAA ++HWI-EAS91_1_30788AAXX:7:22:1621:462/1 +hhhhhhhhhhhhQAhh@hhhhNhhhfhMbCIScC?h +@HWI-EAS91_1_30788AAXX:7:45:408:807/1 +TACCCGATTTTTTGCTTTCCACTTTATCCTACCCTT ++HWI-EAS91_1_30788AAXX:7:45:408:807/1 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_30788AAXX:7:49:654:1439/1 +CTAACTCTATTTATTGTATTTCAACTAAAAATCTCA ++HWI-EAS91_1_30788AAXX:7:49:654:1439/1 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_30788AAXX:7:64:947:234/1 +TATCAAAAAAGAATATAATCTGAATCAACACTACAA ++HWI-EAS91_1_30788AAXX:7:64:947:234/1 +hhhhhhhhhhhhhhhhhhhhhhhRhhehhahhhhhJ diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/split_pair_reads_2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split_pair_reads_2.fastqsanger Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,20 @@ +@HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 +GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA ++HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 +hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR +@HWI-EAS91_1_30788AAXX:7:22:1621:462/2 +ACTAGCCCCAATATCAATCCTATATCAAATCTCACC ++HWI-EAS91_1_30788AAXX:7:22:1621:462/2 +hJhhhhChhhJhhhRhhKhePhc\KhhV\KhXhJhh +@HWI-EAS91_1_30788AAXX:7:45:408:807/2 +ATGAGTGCTAGGATCAGGATGGAGAGGATTAGGGCT ++HWI-EAS91_1_30788AAXX:7:45:408:807/2 +hhhhhhhhhhhhhhhhhh`hhhZh`hhhhhRXhhYh +@HWI-EAS91_1_30788AAXX:7:49:654:1439/2 +TAGGTTTATTGATAGTTGTGTTGTTGGTGTAAATGG ++HWI-EAS91_1_30788AAXX:7:49:654:1439/2 +hhhhhhhhhhhhhhhhhhhhhhhhhdhh_hG\XhU@ +@HWI-EAS91_1_30788AAXX:7:64:947:234/2 +CCTATTAGTGTGTAGAATAGGAAGTAGAGGCCTGCG ++HWI-EAS91_1_30788AAXX:7:64:947:234/2 +hhhhhhhh^hPhWfhhhhThWUhhfhh_hhNIVPUd diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/split_paired_reads_out_1.fastqsanger --- a/test-data/split_paired_reads_out_1.fastqsanger Tue Feb 23 16:12:20 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -@HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 -GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC -+HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 -hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh -@HWI-EAS91_1_30788AAXX:7:22:1621:462/1 -ATAATGGCTATTATTGTGGGGGGGATGATGCTGGAA -+HWI-EAS91_1_30788AAXX:7:22:1621:462/1 -hhhhhhhhhhhhQAhh@hhhhNhhhfhMbCIScC?h -@HWI-EAS91_1_30788AAXX:7:45:408:807/1 -TACCCGATTTTTTGCTTTCCACTTTATCCTACCCTT -+HWI-EAS91_1_30788AAXX:7:45:408:807/1 -hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh -@HWI-EAS91_1_30788AAXX:7:49:654:1439/1 -CTAACTCTATTTATTGTATTTCAACTAAAAATCTCA -+HWI-EAS91_1_30788AAXX:7:49:654:1439/1 -hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh -@HWI-EAS91_1_30788AAXX:7:64:947:234/1 -TATCAAAAAAGAATATAATCTGAATCAACACTACAA -+HWI-EAS91_1_30788AAXX:7:64:947:234/1 -hhhhhhhhhhhhhhhhhhhhhhhRhhehhahhhhhJ diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/split_paired_reads_out_2.fastqsanger --- a/test-data/split_paired_reads_out_2.fastqsanger Tue Feb 23 16:12:20 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -@HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 -GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA -+HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 -hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR -@HWI-EAS91_1_30788AAXX:7:22:1621:462/2 -ACTAGCCCCAATATCAATCCTATATCAAATCTCACC -+HWI-EAS91_1_30788AAXX:7:22:1621:462/2 -hJhhhhChhhJhhhRhhKhePhc\KhhV\KhXhJhh -@HWI-EAS91_1_30788AAXX:7:45:408:807/2 -ATGAGTGCTAGGATCAGGATGGAGAGGATTAGGGCT -+HWI-EAS91_1_30788AAXX:7:45:408:807/2 -hhhhhhhhhhhhhhhhhh`hhhZh`hhhhhRXhhYh -@HWI-EAS91_1_30788AAXX:7:49:654:1439/2 -TAGGTTTATTGATAGTTGTGTTGTTGGTGTAAATGG -+HWI-EAS91_1_30788AAXX:7:49:654:1439/2 -hhhhhhhhhhhhhhhhhhhhhhhhhdhh_hG\XhU@ -@HWI-EAS91_1_30788AAXX:7:64:947:234/2 -CCTATTAGTGTGTAGAATAGGAAGTAGAGGCCTGCG -+HWI-EAS91_1_30788AAXX:7:64:947:234/2 -hhhhhhhh^hPhWfhhhhThWUhhfhh_hhNIVPUd diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/wrapping_as_illumina.fastqillumina --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wrapping_as_illumina.fastqillumina Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,12 @@ +@SRR014849.50939 EIXKN4201BA2EC length=135 +GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG ++ +Zb^Ld`N\[d`NaZ[aZc]UOKHDA[\YT[_W[aZ\aZ[Zd`SF_WeaUI[Y\[[\\\[\Z\aY`X[[aZ\aZ\d`OY[aY[[\[[e`WPJC^UZ[`X\[R]T_V_W[`[Ga\I`\H[[Q^TVa\Ia\Ic^LY\S +@SRR014849.110027 EIXKN4201APUB0 length=131 +CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG ++ +\aYY_[FY\T`X^Vd`OY\[[^U_V[R^T[_ZDc^La\HYYO\S[c^Ld`Nc_QAZaZaYaY`XZZ\[aZZ[aZ[aZ[aZY`Z[`ZWeaVJ\[aZaY`X[PY\eaUG[\[[d`OXTUZ[Q\\`W\\\Y_W\ +@SRR014849.203935 EIXKN4201B4HU6 length=144 +AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT ++ +`Z_ZDVT^YB[[Xd`PZ\d`RDaZaZ`ZaZ_ZDXd`Pd`Pd`RD[aZ`ZWd`Oc_RCd`P\aZ`ZaZaZY\YaZYaY`XYd`O`X[e`WPJEAc^LaZS[YYN[Z\Y`XWLT^U\b]JW[[RZ\SYc`RD[Z\WLXM`\HYa\I diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/wrapping_as_sanger.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wrapping_as_sanger.fastqsanger Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,12 @@ +@SRR014849.50939 EIXKN4201BA2EC length=135 +GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG ++ +;C?-EA/=<EA/B;<B;D>60,)%"<=:5<@8<B;=B;<;EA4'@8FB6*<:=<<===<=;=B:A9<<B;=B;=EA0:<B:<<=<<FA81+$?6;<A9=<3>5@7@8<A<(B=*A=)<<2?57B=*B=*D?-:=4 +@SRR014849.110027 EIXKN4201APUB0 length=131 +CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG ++ +=B::@<':=5A9?7EA0:=<<?6@7<3?5<@;%D?-B=)::0=4<D?-EA/D@2";B;B:B:A9;;=<B;;<B;<B;<B;:A;<A;8FB7+=<B;B:A9<1:=FB6(<=<<EA0956;<2==A8===:@8= +@SRR014849.203935 EIXKN4201B4HU6 length=144 +AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT ++ +A;@;%75?:#<<9EA1;=EA3%B;B;A;B;@;%9EA1EA1EA3%<B;A;8EA0D@3$EA1=B;A;B;B;:=:B;:B:A9:EA0A9<FA81+&"D?-B;4<::/<;=:A98-5?6=C>+8<<3;=4:DA3%<;=8-9.A=):B=* diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/wrapping_as_sanger_decimal.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wrapping_as_sanger_decimal.fastqsanger Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,12 @@ +@SRR014849.50939 EIXKN4201BA2EC length=135 +GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG ++ +26 34 30 12 36 32 14 28 27 36 32 14 33 26 27 33 26 35 29 21 15 11 8 4 1 27 28 25 20 27 31 23 27 33 26 28 33 26 27 26 36 32 19 6 31 23 37 33 21 9 27 25 28 27 27 28 28 28 27 28 26 28 33 25 32 24 27 27 33 26 28 33 26 28 36 32 15 25 27 33 25 27 27 28 27 27 37 32 23 16 10 3 30 21 26 27 32 24 28 27 18 29 20 31 22 31 23 27 32 27 7 33 28 9 32 28 8 27 27 17 30 20 22 33 28 9 33 28 9 35 30 12 25 28 19 +@SRR014849.110027 EIXKN4201APUB0 length=131 +CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG ++ +28 33 25 25 31 27 6 25 28 20 32 24 30 22 36 32 15 25 28 27 27 30 21 31 22 27 18 30 20 27 31 26 4 35 30 12 33 28 8 25 25 15 28 19 27 35 30 12 36 32 14 35 31 17 1 26 33 26 33 25 33 25 32 24 26 26 28 27 33 26 26 27 33 26 27 33 26 27 33 26 25 32 26 27 32 26 23 37 33 22 10 28 27 33 26 33 25 32 24 27 16 25 28 37 33 21 7 27 28 27 27 36 32 15 24 20 21 26 27 17 28 28 32 23 28 28 28 25 31 23 28 +@SRR014849.203935 EIXKN4201B4HU6 length=144 +AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT ++ +32 26 31 26 4 22 20 30 25 2 27 27 24 36 32 16 26 28 36 32 18 4 33 26 33 26 32 26 33 26 31 26 4 24 36 32 16 36 32 16 36 32 18 4 27 33 26 32 26 23 36 32 15 35 31 18 3 36 32 16 28 33 26 32 26 33 26 33 26 25 28 25 33 26 25 33 25 32 24 25 36 32 15 32 24 27 37 32 23 16 10 5 1 35 30 12 33 26 19 27 25 25 14 27 26 28 25 32 24 23 12 20 30 21 28 34 29 10 23 27 27 18 26 28 19 25 35 32 18 4 27 26 28 23 12 24 13 32 28 8 25 33 28 9 diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/wrapping_as_solexa.fastqsolexa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wrapping_as_solexa.fastqsolexa Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,12 @@ +@SRR014849.50939 EIXKN4201BA2EC length=135 +GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG ++ +Zb^Ld`N\[d`NaZ[aZc]UOKGB;[\YT[_W[aZ\aZ[Zd`SE_WeaUH[Y\[[\\\[\Z\aY`X[[aZ\aZ\d`OY[aY[[\[[e`WPJ@^UZ[`X\[R]T_V_W[`[Fa\H`\G[[Q^TVa\Ha\Hc^LY\S +@SRR014849.110027 EIXKN4201APUB0 length=131 +CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG ++ +\aYY_[EY\T`X^Vd`OY\[[^U_V[R^T[_ZBc^La\GYYO\S[c^Ld`Nc_Q;ZaZaYaY`XZZ\[aZZ[aZ[aZ[aZY`Z[`ZWeaVJ\[aZaY`X[PY\eaUF[\[[d`OXTUZ[Q\\`W\\\Y_W\ +@SRR014849.203935 EIXKN4201B4HU6 length=144 +AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT ++ +`Z_ZBVT^Y>[[Xd`PZ\d`RBaZaZ`ZaZ_ZBXd`Pd`Pd`RB[aZ`ZWd`Oc_R@d`P\aZ`ZaZaZY\YaZYaY`XYd`O`X[e`WPJC;c^LaZS[YYN[Z\Y`XWLT^U\b]JW[[RZ\SYc`RB[Z\WLXM`\GYa\H diff -r 03dbef081cf2 -r 9dd990a2fa94 test-data/wrapping_original_sanger.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wrapping_original_sanger.fastqsanger Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,24 @@ +@SRR014849.50939 EIXKN4201BA2EC length=135 +GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG ++ +;C?-EA/=<EA/B;<B;D>60,)%"<=:5< +@8<B;=B;<;EA4'@8FB6*<:=<<===<= +;=B:A9<<B;=B;=EA0:<B:<<=<<FA81 ++$?6;<A9=<3>5@7@8<A<(B=*A=)<<2 +?57B=*B=*D?-:=4 +@SRR014849.110027 EIXKN4201APUB0 length=131 +CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG ++ +=B::@<':=5A9?7EA0:=<<?6@7<3?5< +@;%D?-B=)::0=4<D?-EA/D@2";B;B: +B:A9;;=<B;;<B;<B;<B;:A;<A;8FB7 ++=<B;B:A9<1:=FB6(<=<<EA0956;<2 +==A8===:@8= +@SRR014849.203935 EIXKN4201B4HU6 length=144 +AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT ++ +A;@;%75?:#<<9EA1;=EA3%B;B;A;B; +@;%9EA1EA1EA3%<B;A;8EA0D@3$EA1 +=B;A;B;B;:=:B;:B:A9:EA0A9<FA81 ++&"D?-B;4<::/<;=:A98-5?6=C>+8< +<3;=4:DA3%<;=8-9.A=):B=* diff -r 03dbef081cf2 -r 9dd990a2fa94 tool_conf.xml.sample --- a/tool_conf.xml.sample Tue Feb 23 16:12:20 2010 -0500 +++ b/tool_conf.xml.sample Tue Feb 23 16:48:07 2010 -0500 @@ -127,6 +127,7 @@ <tool file="plotting/scatterplot.xml" /> <tool file="plotting/bar_chart.xml" /> <tool file="plotting/xy_plot.xml" /> + <tool file="plotting/boxplot.xml" /> <tool file="visualization/GMAJ.xml" /> <tool file="visualization/LAJ.xml" /> <tool file="visualization/build_ucsc_custom_track.xml" /> @@ -174,7 +175,17 @@ <tool file="fastx_toolkit/fastx_collapser.xml" /> </section> <section name="NGS: QC and manipulation" id="cshl_library_information"> - <label text="Generic FASTQ data" id="fastq" /> + <label text="Generic FASTQ data" id="new_fastq" /> + <tool file="fastq/fastq_combiner.xml" /> + <tool file="fastq/fastq_groomer.xml" /> + <tool file="fastq/fastq_paired_end_joiner.xml" /> + <tool file="fastq/fastq_paired_end_splitter.xml" /> + <tool file="fastq/fastq_stats.xml" /> + <tool file="fastq/fastq_filter.xml" /> + <tool file="fastq/fastq_trimmer.xml" /> + <tool file="fastq/fastq_manipulation.xml" /> + <tool file="fastq/fastq_to_fasta.xml" /> + <label text="Deprecated: Generic FASTQ data" id="fastq" /> <tool file="next_gen_conversion/fastq_gen_conv.xml" /> <tool file="fastx_toolkit/fastq_quality_converter.xml" /> <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> diff -r 03dbef081cf2 -r 9dd990a2fa94 tools/fastq/fastq_combiner.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastq/fastq_combiner.py Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,45 @@ +#Dan Blankenberg +import sys, os, shutil +from galaxy_utils.sequence.fastq import fastqWriter, fastaReader, fastaNamedReader, fastqSequencingRead, fastqCombiner + +def main(): + #Read command line arguments + fasta_filename = sys.argv[1] + fasta_type = sys.argv[2] or 'fasta' #should always be fasta or csfasta? what if txt? + qual_filename = sys.argv[3] + qual_type = sys.argv[4] or 'qualsanger' #qual454 qualsolid + output_filename = sys.argv[5] + force_quality_encoding = sys.argv[6] + if force_quality_encoding == 'None': + force_quality_encoding = None + + format = 'sanger' + if fasta_type == 'csfasta' or qual_type == 'qualsolid': + format = 'solid' + elif qual_type == 'qualsolexa': + format = 'solexa' + elif qual_type == 'qualillumina': + format = 'illumina' + + out = fastqWriter( open( output_filename, 'wb' ), format = format, force_quality_encoding = force_quality_encoding ) + qual_input = fastaNamedReader( open( qual_filename, 'rb' ) ) + fastq_combiner = fastqCombiner( format ) + i = None + skip_count = 0 + for i, sequence in enumerate( fastaReader( open( fasta_filename, 'rb' ) ) ): + quality = qual_input.get( sequence.identifier ) + if quality: + fastq_read = fastq_combiner.combine( sequence, quality ) + #Should we check that fastq read is valid? for now, assume groomer will be used to verify + out.write( fastq_read ) + else: + skip_count += 1 + out.close() + if i is None: + print "Your file contains no valid FASTA sequences." + else: + print qual_input.has_data() + print 'Combined %s of %s sequences with quality scores (%.2f%%).' % ( i - skip_count + 1, i + 1, float( i - skip_count + 1 ) / float( i + 1 ) * 100.0 ) + +if __name__ == "__main__": + main() diff -r 03dbef081cf2 -r 9dd990a2fa94 tools/fastq/fastq_combiner.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastq/fastq_combiner.xml Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,55 @@ +<tool id="fastq_combiner" name="Combine FASTA and QUAL" version="1.0.0"> + <description>into FASTQ</description> + <command interpreter="python">fastq_combiner.py '$fasta_file' '${fasta_file.extension}' '$qual_file' '${qual_file.extension}' '$output_file' '$force_quality_encoding'</command> + <inputs> + <param name="fasta_file" type="data" format="fasta,csfasta" label="FASTA File" /> + <param name="qual_file" type="data" format="qual" label="Quality Score File" /> + <param name="force_quality_encoding" type="select" label="Force Quality Score encoding"> + <option value="None">Use Source Encoding</option> + <option value="ascii" selected="True">ASCII</option> + <option value="decimal">Decimal</option> + </param> + </inputs> + <outputs> + <data name="output_file" format="fastqsanger"> + <change_format> + <when input_dataset="fasta_file" attribute="extension" value="csfasta" format="fastqsolid" /> + <when input_dataset="qual_file" attribute="extension" value="qualsolid" format="fastqsolid" /> + <when input_dataset="qual_file" attribute="extension" value="qualsolexa" format="fastqsolexa" /> + <when input_dataset="qual_file" attribute="extension" value="qualillumina" format="fastqillumina" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" /> + <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" /> + <param name="force_quality_encoding" value="None" /> + <output name="output_file" file="combine_phiX_out_1.fastqsolid" /> + </test> + <test> + <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" /> + <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" /> + <param name="force_quality_encoding" value="ascii" /> + <output name="output_file" file="combine_phiX_out_2.fastqsolid" /> + </test> + <test> + <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" /> + <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" /> + <param name="force_quality_encoding" value="None" /> + <output name="output_file" file="wrapping_as_sanger.fastqsanger" /> + </test> + <test> + <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" /> + <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" /> + <param name="force_quality_encoding" value="decimal" /> + <output name="output_file" file="wrapping_as_sanger_decimal.fastqsanger" /> + </test> + </tests> + <help> +**What it does** + +This tool joins a FASTA file to a Quality Score file, creating a single FASTQ block for each read. + + </help> +</tool> diff -r 03dbef081cf2 -r 9dd990a2fa94 tools/fastq/fastq_filter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastq/fastq_filter.py Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,34 @@ +#Dan Blankenberg +import sys, os, shutil +from galaxy_utils.sequence.fastq import fastqReader, fastqWriter + +def main(): + #Read command line arguments + input_filename = sys.argv[1] + script_filename = sys.argv[2] + output_filename = sys.argv[3] + additional_files_path = sys.argv[4] + input_type = sys.argv[5] or 'sanger' + + #Save script file for debuging/verification info later + os.mkdir( additional_files_path ) + shutil.copy( script_filename, os.path.join( additional_files_path, 'debug.txt' ) ) + + out = fastqWriter( open( output_filename, 'wb' ), format = input_type ) + + i = None + reads_kept = 0 + for i, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): + local = {'fastq_read':fastq_read, 'ret_val':False} + execfile( script_filename, {}, local ) + if local['ret_val']: + out.write( fastq_read ) + reads_kept += 1 + out.close() + if i is None: + print "Your file contains no valid fastq reads." + else: + print 'Kept %s of %s reads (%.2f%%).' % ( reads_kept, i + 1, float( reads_kept ) / float( i + 1 ) * 100.0 ) + +if __name__ == "__main__": + main() diff -r 03dbef081cf2 -r 9dd990a2fa94 tools/fastq/fastq_filter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastq/fastq_filter.xml Tue Feb 23 16:48:07 2010 -0500 @@ -0,0 +1,311 @@ +<tool id="fastq_filter" name="Filter FASTQ" version="1.0.0"> + <description>reads by quality score and length</description> + <command interpreter="python">fastq_filter.py $input_file $fastq_filter_file $output_file $output_file.files_path '${input_file.extension[len( 'fastq' ):]}'</command> + <inputs> + <page> + <param name="input_file" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqsolid" label="FASTQ File" help="Requires groomed data: if your data does not appear here try using the FASTQ groomer."/> + <param name="min_size" label="Minimum Size" value="0" type="integer"> + <validator type="in_range" message="Minimum size must be positive" min="0"/> + </param> + <param name="max_size" label="Maximum Size" value="0" type="integer" help="A maximum size less than 1 indicates no limit."/> + <param name="min_quality" label="Minimum Quality" value="0" type="float"/> + <param name="max_quality" label="Maximum Quality" value="0" type="float" help="A maximum quality less than 1 indicates no limit."/> + <param name="max_num_deviants" label="Maximum number of bases allowed outside of quality range" value="0" type="integer"> + <validator type="in_range" message="Maximum number of deviate bases must be positive" min="0"/> + </param> + <param name="paired_end" label="This is paired end data" type="boolean" truevalue="paired_end" falsevalue="single_end" checked="False"/> + <repeat name="fastq_filters" title="Quality Filter on a Range of Bases" help="The above settings do not apply to these filters."> + <conditional name="offset_type"> + <param name="base_offset_type" type="select" label="Define Base Offsets as"> + <option value="offsets_absolute" selected="true">Absolute Values</option> + <option value="offsets_percent">Percentage of Read Length</option> + </param> + <when value="offsets_absolute"> + <param name="left_column_offset" label="Absolute Left Base Offset" value="0" type="integer" help="Values start at 0, increasing from the left"> + <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> + <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> + </param> + <param name="right_column_offset" label="Absolute Right Base Offset" value="0" type="integer" help="Values start at 0, increasing from the right"> + <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> + <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> + </param> + </when> + <when value="offsets_percent"> + <param name="left_column_offset" label="Percentage Left Base Offset" value="0" type="float"> + <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> + </param> + <param name="right_column_offset" label="Percentage Right Base Offset" value="0" type="float"> + <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> + </param> + </when> + </conditional> + <param name="score_operation" type="select" label="Aggregate read score for specified range"> + <option value="min" selected="True">min score</option> + <option value="max">max score</option> + <option value="sum">sum of scores</option> + <option value="mean">mean of scores</option> + </param> + <param name="score_comparison" type="select" label="Keep read when aggregate score is"> + <option value=">">></option> + <option value=">=" selected="true">>=</option> + <option value="==">==</option> + <option value="<"><</option> + <option value="<="><=</option> + <sanitizer sanitize="False"/> + </param> + <param name="score" label="Quality Score" value="0" type="float" /> + </repeat> + </page> + </inputs> + <configfiles> + <configfile name="fastq_filter_file"> +def fastq_read_pass_filter( fastq_read ): + def mean( score_list ): + return float( sum( score_list ) ) / float( len( score_list ) ) + if len( fastq_read ) < $min_size: + return False + if $max_size > 0 and len( fastq_read ) > $max_size: + return False + num_deviates = $max_num_deviants + qual_scores = fastq_read.get_decimal_quality_scores() + for qual_score in qual_scores: + if qual_score < $min_quality or ( $max_quality > 0 and qual_score > $max_quality ): + if num_deviates == 0: + return False + else: + num_deviates -= 1 +#if $paired_end.value == 'single_end': + qual_scores_split = [ qual_scores ] +#else: + qual_scores_split = [ qual_scores[ 0:int( len( qual_scores ) / 2 ) ], qual_scores[ int( len( qual_scores ) / 2 ): ] ] +#end if +#for $fastq_filter in $fastq_filters: + for split_scores in qual_scores_split: + left_column_offset = $fastq_filter[ 'offset_type' ][ 'left_column_offset' ] + right_column_offset = $fastq_filter[ 'offset_type' ][ 'right_column_offset' ] +#if $fastq_filter[ 'offset_type' ]['base_offset_type'] == 'offsets_percent': + left_column_offset = int( round( float( left_column_offset ) / 100.0 * float( len( split_scores ) ) ) ) + right_column_offset = int( round( float( right_column_offset ) / 100.0 * float( len( split_scores ) ) ) ) +#end if + if right_column_offset > 0: + split_scores = split_scores[ left_column_offset:-right_column_offset] + else: + split_scores = split_scores[ left_column_offset:] + if split_scores: ##if a read doesn't have enough columns, it passes by default + if not ( ${fastq_filter[ 'score_operation' ]}( split_scores ) $fastq_filter[ 'score_comparison' ] $fastq_filter[ 'score' ] ): + return False +#end for + return True +ret_val = fastq_read_pass_filter( fastq_read ) +</configfile> + </configfiles> + <outputs> + <data format="input" name="output_file" /> + </outputs> + <tests> + <!-- Do nothing filter --> + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/> + <param name="min_size" value="0"/> + <param name="max_size" value="0"/> + <param name="min_quality" value="0"/> + <param name="max_quality" value="0"/> + <param name="max_num_deviants" value="0"/> + <param name="paired_end" value="single_end"/> + <param name="base_offset_type" value="offsets_absolute"/> + <param name="left_column_offset" value="0"/> + <param name="right_column_offset" value="0"/> + <param name="score_operation" value="min"/> + <param name="score_comparison" value=">="/> + <param name="score" value="0"/> + <output name="out_file1" file="sanger_full_range_original_sanger.fastqsanger"/> + </test> + <test> + <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa"/> + <param name="min_size" value="0"/> + <param name="max_size" value="0"/> + <param name="min_quality" value="-5"/> + <param name="max_quality" value="0"/> + <param name="max_num_deviants" value="0"/> + <param name="paired_end" value="single_end"/> + <param name="base_offset_type" value="offsets_absolute"/> + <param name="left_column_offset" value="0"/> + <param name="right_column_offset" value="0"/> + <param name="score_operation" value="min"/> + <param name="score_comparison" value=">="/> + <param name="score" value="-5"/> + <output name="out_file1" file="solexa_full_range_original_solexa.fastqsolexa"/> + </test> + <!-- No trim, so does not remove Adapter from solid --> + <test> + <param name="input_file" value="sanger_full_range_as_solid.fastqsolid" ftype="fastqsolid"/> + <param name="min_size" value="0"/> + <param name="max_size" value="0"/> + <param name="min_quality" value="0"/> + <param name="max_quality" value="0"/> + <param name="max_num_deviants" value="0"/> + <param name="paired_end" value="single_end"/> + <param name="base_offset_type" value="offsets_absolute"/> + <param name="left_column_offset" value="0"/> + <param name="right_column_offset" value="0"/> + <param name="score_operation" value="min"/> + <param name="score_comparison" value=">="/> + <param name="score" value="0"/> + <output name="out_file1" file="sanger_full_range_as_solid.fastqsolid"/> + </test> + <!-- Remove all Filter --> + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/> + <param name="min_size" value="0"/> + <param name="max_size" value="0"/> + <param name="min_quality" value="1"/> + <param name="max_quality" value="0"/> + <param name="max_num_deviants" value="0"/> + <param name="paired_end" value="single_end"/> + <param name="base_offset_type" value="offsets_absolute"/> + <param name="left_column_offset" value="0"/> + <param name="right_column_offset" value="0"/> + <param name="score_operation" value="min"/> + <param name="score_comparison" value=">="/> + <param name="score" value="0"/> + <output name="out_file1" file="empty_file.dat"/> + </test> + <test> + <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa"/> + <param name="min_size" value="0"/> + <param name="max_size" value="0"/> + <param name="min_quality" value="-4"/> + <param name="max_quality" value="0"/> + <param name="max_num_deviants" value="0"/> + <param name="paired_end" value="single_end"/> + <param name="base_offset_type" value="offsets_absolute"/> + <param name="left_column_offset" value="0"/> + <param name="right_column_offset" value="0"/> + <param name="score_operation" value="min"/> + <param name="score_comparison" value=">="/> + <param name="score" value="-5"/>