Package Bio :: Package Sequencing :: Module Phd
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Source Code for Module Bio.Sequencing.Phd

  1  # Copyright 2004 by Cymon J. Cox and Frank Kauff.  All rights reserved. 
  2  # Copyright 2008 by Michiel de Hoon.  All rights reserved. 
  3  # Revisions copyright 2009 by Cymon J. Cox.  All rights reserved. 
  4  # Revisions copyright 2009 by Peter Cock.  All rights reserved. 
  5  #  
  6  # This code is part of the Biopython distribution and governed by its 
  7  # license.  Please see the LICENSE file that should have been included 
  8  # as part of this package. 
  9  """ 
 10  Parser for PHD files output by PHRED and used by PHRAP and CONSED. 
 11   
 12  This module can be used used directly which will return Record objects 
 13  which should contain all the original data in the file. 
 14   
 15  Alternatively, using Bio.SeqIO with the "phd" format will call this module 
 16  internally.  This will give SeqRecord objects for each contig sequence. 
 17  """ 
 18   
 19  from Bio import Seq 
 20  from Bio.Alphabet import generic_dna 
 21   
 22  CKEYWORDS=['CHROMAT_FILE','ABI_THUMBPRINT','PHRED_VERSION','CALL_METHOD',\ 
 23          'QUALITY_LEVELS','TIME','TRACE_ARRAY_MIN_INDEX','TRACE_ARRAY_MAX_INDEX',\ 
 24          'TRIM','TRACE_PEAK_AREA_RATIO','CHEM','DYE'] 
 25   
26 -class Record(object):
27 """Hold information from a PHD file."""
28 - def __init__(self):
29 self.file_name = '' 30 self.comments = {} 31 for kw in CKEYWORDS: 32 self.comments[kw.lower()] = None 33 self.sites = [] 34 self.seq = '' 35 self.seq_trimmed = ''
36 37
38 -def read(handle):
39 """Reads the next PHD record from the file, returning it as a Record object. 40 41 This function reads PHD file data line by line from the handle, 42 and returns a single Record object. 43 """ 44 for line in handle: 45 if line.startswith("BEGIN_SEQUENCE"): 46 record = Record() 47 record.file_name = line[15:].rstrip() 48 break 49 else: 50 return # No record found 51 52 for line in handle: 53 if line.startswith("BEGIN_COMMENT"): 54 break 55 else: 56 raise ValueError("Failed to find BEGIN_COMMENT line") 57 58 for line in handle: 59 line = line.strip() 60 if not line: 61 continue 62 if line=="END_COMMENT": 63 break 64 keyword, value = line.split(":", 1) 65 keyword = keyword.lower() 66 value = value.strip() 67 if keyword in ('chromat_file', 68 'phred_version', 69 'call_method', 70 'chem', 71 'dye', 72 'time', 73 'basecaller_version', 74 'trace_processor_version'): 75 record.comments[keyword] = value 76 elif keyword in ('abi_thumbprint', 77 'quality_levels', 78 'trace_array_min_index', 79 'trace_array_max_index'): 80 record.comments[keyword] = int(value) 81 elif keyword=='trace_peak_area_ratio': 82 record.comments[keyword] = float(value) 83 elif keyword=='trim': 84 first, last, prob = value.split() 85 record.comments[keyword] = (int(first), int(last), float(prob)) 86 else: 87 raise ValueError("Failed to find END_COMMENT line") 88 89 for line in handle: 90 if line.startswith('BEGIN_DNA'): 91 break 92 else: 93 raise ValueError("Failed to find BEGIN_DNA line") 94 95 for line in handle: 96 if line.startswith('END_DNA'): 97 break 98 else: 99 # Line is: "site quality peak_location" 100 # Peak location is optional according to 101 # David Gordon (the Consed author) 102 parts = line.split() 103 if len(parts) in [2,3]: 104 record.sites.append(tuple(parts)) 105 else: 106 raise ValueError("DNA line must contain a base and quality " 107 "score, and optionally a peak location.") 108 109 for line in handle: 110 if line.startswith("END_SEQUENCE"): 111 break 112 else: 113 raise ValueError("Failed to find END_SEQUENCE line") 114 115 record.seq = Seq.Seq(''.join([n[0] for n in record.sites]), generic_dna) 116 if record.comments['trim'] is not None: 117 first, last = record.comments['trim'][:2] 118 record.seq_trimmed = record.seq[first:last] 119 120 return record
121
122 -def parse(handle):
123 """Iterates over a file returning multiple PHD records. 124 125 The data is read line by line from the handle. The handle can be a list 126 of lines, an open file, or similar; the only requirement is that we can 127 iterate over the handle to retrieve lines from it. 128 129 Typical usage: 130 131 records = parse(handle) 132 for record in records: 133 # do something with the record object 134 """ 135 while True: 136 record = read(handle) 137 if not record: 138 return 139 yield record
140