Package Bio :: Package SeqIO :: Module PhdIO
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Source Code for Module Bio.SeqIO.PhdIO

  1  # Copyright 2008-2010 by Peter Cock.  All rights reserved. 
  2  # Revisions copyright 2009 by Cymon J. Cox.  All rights reserved. 
  3  # 
  4  # This code is part of the Biopython distribution and governed by its 
  5  # license.  Please see the LICENSE file that should have been included 
  6  # as part of this package. 
  7   
  8  """Bio.SeqIO support for the "phd" file format. 
  9   
 10  PHD files are output by PHRED and used by PHRAP and CONSED. 
 11   
 12  You are expected to use this module via the Bio.SeqIO functions, under the 
 13  format name "phd". See also the underlying Bio.Sequencing.Phd module. 
 14   
 15  For example, using Bio.SeqIO we can read in one of the example PHRED files 
 16  from the Biopython unit tests: 
 17   
 18      >>> from Bio import SeqIO 
 19      >>> for record in SeqIO.parse(open("Phd/phd1"), "phd"): 
 20      ...     print record.id 
 21      ...     print record.seq[:10], "..." 
 22      ...     print record.letter_annotations["phred_quality"][:10], "..." 
 23      34_222_(80-A03-19).b.ab1 
 24      ctccgtcgga ... 
 25      [9, 9, 10, 19, 22, 37, 28, 28, 24, 22] ... 
 26      425_103_(81-A03-19).g.ab1 
 27      cgggatccca ... 
 28      [14, 17, 22, 10, 10, 10, 15, 8, 8, 9] ... 
 29      425_7_(71-A03-19).b.ab1 
 30      acataaatca ... 
 31      [10, 10, 10, 10, 8, 8, 6, 6, 6, 6] ... 
 32   
 33  Since PHRED files contain quality scores, you can save them as FASTQ or as 
 34  QUAL files, for example using Bio.SeqIO.write(...), or simply with the format 
 35  method of the SeqRecord object: 
 36   
 37      >>> print record[:50].format("fastq") 
 38      @425_7_(71-A03-19).b.ab1 
 39      acataaatcaaattactnaccaacacacaaaccngtctcgcgtagtggag 
 40      + 
 41      ++++))'''')(''')$!$''')''''(+.''$!$))))+)))''''''' 
 42      <BLANKLINE> 
 43   
 44  Or, 
 45   
 46      >>> print record[:50].format("qual") 
 47      >425_7_(71-A03-19).b.ab1 
 48      10 10 10 10 8 8 6 6 6 6 8 7 6 6 6 8 3 0 3 6 6 6 8 6 6 6 6 7 
 49      10 13 6 6 3 0 3 8 8 8 8 10 8 8 8 6 6 6 6 6 6 6 
 50      <BLANKLINE> 
 51   
 52  Note these examples only show the first 50 bases to keep the output short. 
 53  """ 
 54   
 55  from Bio.SeqRecord import SeqRecord 
 56  from Bio.Sequencing import Phd 
 57  from Bio.SeqIO.Interfaces import SequentialSequenceWriter 
 58  from Bio.SeqIO import QualityIO 
 59       
 60  #This is a generator function! 
61 -def PhdIterator(handle):
62 """Returns SeqRecord objects from a PHD file. 63 64 This uses the Bio.Sequencing.Phd module to do the hard work. 65 """ 66 phd_records = Phd.parse(handle) 67 for phd_record in phd_records: 68 #Convert the PHY record into a SeqRecord... 69 #The "filename" can contain spaces, e.g. 'HWI-EAS94_4_1_1_602_99 1' 70 #from unit test example file phd_solexa. 71 #This will cause problems if used as the record identifier 72 #(e.g. output for FASTQ format). 73 name = phd_record.file_name.split(None, 1)[0] 74 seq_record = SeqRecord(phd_record.seq, 75 id = name, name = name, 76 description= phd_record.file_name) 77 #Just re-use the comments dictionary as the SeqRecord's annotations 78 seq_record.annotations = phd_record.comments 79 #And store the qualities and peak locations as per-letter-annotation 80 seq_record.letter_annotations["phred_quality"] = \ 81 [int(site[1]) for site in phd_record.sites] 82 try: 83 seq_record.letter_annotations["peak_location"] = \ 84 [int(site[2]) for site in phd_record.sites] 85 except IndexError: 86 # peak locations are not always there according to 87 # David Gordon (the Consed author) 88 pass 89 yield seq_record
90 #All done 91
92 -class PhdWriter(SequentialSequenceWriter):
93 """Class to write Phd format files""" 94
95 - def __init__(self, handle):
97
98 - def write_record(self, record):
99 """Write a single Phd record to the file.""" 100 assert record.seq, "No sequence present in SeqRecord" 101 # This method returns the 'phred_quality' scores or converted 102 # 'solexa_quality' scores if present, else raises a value error 103 phred_qualities = QualityIO._get_phred_quality(record) 104 peak_locations = record.letter_annotations.get("peak_location", None) 105 assert len(record.seq) == len(phred_qualities), "Number of " + \ 106 "phd quality scores does not match length of sequence" 107 if peak_locations: 108 assert len(record.seq) == len(peak_locations), "Number " + \ 109 "of peak location scores does not match length of sequence" 110 if None in phred_qualities: 111 raise ValueError("A quality value of None was found") 112 if record.description.startswith("%s " % record.id): 113 title = record.description 114 else: 115 title = "%s %s" % (record.id, record.description) 116 self.handle.write("BEGIN_SEQUENCE %s\nBEGIN_COMMENT\n" \ 117 % self.clean(title)) 118 for annot in [k.lower() for k in Phd.CKEYWORDS]: 119 value = None 120 if annot == "trim": 121 if record.annotations.get("trim", None): 122 value = "%s %s %.4f" % record.annotations["trim"] 123 elif annot == "trace_peak_area_ratio": 124 if record.annotations.get("trace_peak_area_ratio", None): 125 value = "%.4f" % record.annotations["trace_peak_area_ratio"] 126 else: 127 value = record.annotations.get(annot, None) 128 if value or value == 0: 129 self.handle.write("%s: %s\n" % (annot.upper(), value)) 130 131 self.handle.write("END_COMMENT\nBEGIN_DNA\n") 132 for i, site in enumerate(record.seq): 133 if peak_locations: 134 self.handle.write("%s %i %i\n" % ( 135 site, 136 round(phred_qualities[i]), 137 peak_locations[i]) 138 ) 139 else: 140 self.handle.write("%s %i\n" % ( 141 site, 142 round(phred_qualities[i])) 143 ) 144 145 self.handle.write("END_DNA\nEND_SEQUENCE\n")
146
147 -def _test():
148 """Run the Bio.SeqIO.PhdIO module's doctests. 149 150 This will try and locate the unit tests directory, and run the doctests 151 from there in order that the relative paths used in the examples work. 152 """ 153 import doctest 154 import os 155 if os.path.isdir(os.path.join("..", "..", "Tests")): 156 print "Runing doctests..." 157 cur_dir = os.path.abspath(os.curdir) 158 os.chdir(os.path.join("..", "..", "Tests")) 159 assert os.path.isfile("Phd/phd1") 160 doctest.testmod() 161 os.chdir(cur_dir) 162 del cur_dir 163 print "Done"
164 165 if __name__ == "__main__": 166 _test() 167