[2] | 1 | #Dan Blankenberg |
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| 2 | |
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| 3 | class fastaSequence( object ): |
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| 4 | def __init__( self ): |
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| 5 | self.identifier = None |
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| 6 | self.sequence = '' #holds raw sequence string: no whitespace |
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| 7 | def __len__( self ): |
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| 8 | return len( self.sequence ) |
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| 9 | def __str__( self ): |
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| 10 | return "%s\n%s\n" % ( self.identifier, self.sequence ) |
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| 11 | |
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| 12 | class fastaReader( object ): |
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| 13 | def __init__( self, fh ): |
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| 14 | self.file = fh |
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| 15 | def close( self ): |
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| 16 | return self.file.close() |
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| 17 | def next( self ): |
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| 18 | line = self.file.readline() |
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| 19 | #remove header comment lines |
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| 20 | while line and line.startswith( '#' ): |
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| 21 | line = self.file.readline() |
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| 22 | if not line: |
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| 23 | raise StopIteration |
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| 24 | assert line.startswith( '>' ), "FASTA headers must start with >" |
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| 25 | rval = fastaSequence() |
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| 26 | rval.identifier = line.strip() |
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| 27 | offset = self.file.tell() |
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| 28 | while True: |
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| 29 | line = self.file.readline() |
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| 30 | if not line or line.startswith( '>' ): |
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| 31 | if line: |
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| 32 | self.file.seek( offset ) #this causes sequence id lines to be read twice, once to determine previous sequence end and again when getting actual sequence; can we cache this to prevent it from being re-read? |
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| 33 | return rval |
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| 34 | #454 qual test data that was used has decimal scores that don't have trailing spaces |
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| 35 | #so we'll need to parse and build these sequences not based upon de facto standards |
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| 36 | #i.e. in a less than ideal fashion |
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| 37 | line = line.rstrip() |
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| 38 | if ' ' in rval.sequence or ' ' in line: |
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| 39 | rval.sequence = "%s%s " % ( rval.sequence, line ) |
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| 40 | else: |
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| 41 | rval.sequence += line |
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| 42 | offset = self.file.tell() |
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| 43 | def __iter__( self ): |
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| 44 | while True: |
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| 45 | yield self.next() |
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| 46 | |
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| 47 | class fastaNamedReader( object ): |
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| 48 | def __init__( self, fh ): |
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| 49 | self.file = fh |
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| 50 | self.reader = fastaReader( self.file ) |
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| 51 | self.offset_dict = {} |
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| 52 | self.eof = False |
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| 53 | def close( self ): |
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| 54 | return self.file.close() |
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| 55 | def get( self, sequence_id ): |
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| 56 | if not isinstance( sequence_id, basestring ): |
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| 57 | sequence_id = sequence_id.identifier |
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| 58 | rval = None |
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| 59 | if sequence_id in self.offset_dict: |
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| 60 | initial_offset = self.file.tell() |
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| 61 | seq_offset = self.offset_dict[ sequence_id ].pop( 0 ) |
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| 62 | if not self.offset_dict[ sequence_id ]: |
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| 63 | del self.offset_dict[ sequence_id ] |
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| 64 | self.file.seek( seq_offset ) |
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| 65 | rval = self.reader.next() |
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| 66 | self.file.seek( initial_offset ) |
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| 67 | else: |
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| 68 | while True: |
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| 69 | offset = self.file.tell() |
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| 70 | try: |
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| 71 | fasta_seq = self.reader.next() |
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| 72 | except StopIteration: |
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| 73 | self.eof = True |
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| 74 | break #eof, id not found, will return None |
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| 75 | if fasta_seq.identifier == sequence_id: |
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| 76 | rval = fasta_seq |
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| 77 | break |
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| 78 | else: |
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| 79 | if fasta_seq.identifier not in self.offset_dict: |
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| 80 | self.offset_dict[ fasta_seq.identifier ] = [] |
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| 81 | self.offset_dict[ fasta_seq.identifier ].append( offset ) |
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| 82 | return rval |
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| 83 | def has_data( self ): |
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| 84 | #returns a string representation of remaining data, or empty string (False) if no data remaining |
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| 85 | eof = self.eof |
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| 86 | count = 0 |
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| 87 | rval = '' |
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| 88 | if self.offset_dict: |
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| 89 | count = sum( map( len, self.offset_dict.values() ) ) |
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| 90 | if not eof: |
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| 91 | offset = self.file.tell() |
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| 92 | try: |
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| 93 | fasta_seq = self.reader.next() |
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| 94 | except StopIteration: |
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| 95 | eof = True |
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| 96 | self.file.seek( offset ) |
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| 97 | if count: |
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| 98 | rval = "There were %i known sequences not utilized. " % count |
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| 99 | if not eof: |
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| 100 | rval = "%s%s" % ( rval, "An additional unknown number of sequences exist in the input that were not utilized." ) |
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| 101 | return rval |
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| 102 | |
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| 103 | class fastaWriter( object ): |
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| 104 | def __init__( self, fh ): |
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| 105 | self.file = fh |
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| 106 | def write( self, fastq_read ): |
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| 107 | #this will include color space adapter base if applicable |
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| 108 | self.file.write( ">%s\n%s\n" % ( fastq_read.identifier[1:], fastq_read.sequence ) ) |
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| 109 | def close( self ): |
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| 110 | return self.file.close() |
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