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 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   
27 -class Record(object):
28 """Hold information from a PHD file."""
29 - def __init__(self):
30 self.file_name = '' 31 self.comments = {} 32 for kw in CKEYWORDS: 33 self.comments[kw.lower()] = None 34 self.sites = [] 35 self.seq = '' 36 self.seq_trimmed = ''
37 38
39 -def read(handle):
40 """Reads the next PHD record from the file, returning it as a Record object. 41 42 This function reads PHD file data line by line from the handle, 43 and returns a single Record object. 44 """ 45 for line in handle: 46 if line.startswith("BEGIN_SEQUENCE"): 47 record = Record() 48 record.file_name = line[15:].rstrip() 49 break 50 else: 51 return # No record found 52 53 for line in handle: 54 if line.startswith("BEGIN_COMMENT"): 55 break 56 else: 57 raise ValueError("Failed to find BEGIN_COMMENT line") 58 59 for line in handle: 60 line = line.strip() 61 if not line: 62 continue 63 if line == "END_COMMENT": 64 break 65 keyword, value = line.split(":", 1) 66 keyword = keyword.lower() 67 value = value.strip() 68 if keyword in ('chromat_file', 69 'phred_version', 70 'call_method', 71 'chem', 72 'dye', 73 'time', 74 'basecaller_version', 75 'trace_processor_version'): 76 record.comments[keyword] = value 77 elif keyword in ('abi_thumbprint', 78 'quality_levels', 79 'trace_array_min_index', 80 'trace_array_max_index'): 81 record.comments[keyword] = int(value) 82 elif keyword == 'trace_peak_area_ratio': 83 record.comments[keyword] = float(value) 84 elif keyword == 'trim': 85 first, last, prob = value.split() 86 record.comments[keyword] = (int(first), int(last), float(prob)) 87 else: 88 raise ValueError("Failed to find END_COMMENT line") 89 90 for line in handle: 91 if line.startswith('BEGIN_DNA'): 92 break 93 else: 94 raise ValueError("Failed to find BEGIN_DNA line") 95 96 for line in handle: 97 if line.startswith('END_DNA'): 98 break 99 else: 100 # Line is: "site quality peak_location" 101 # Peak location is optional according to 102 # David Gordon (the Consed author) 103 parts = line.split() 104 if len(parts) in [2, 3]: 105 record.sites.append(tuple(parts)) 106 else: 107 raise ValueError("DNA line must contain a base and quality " 108 "score, and optionally a peak location.") 109 110 for line in handle: 111 if line.startswith("END_SEQUENCE"): 112 break 113 else: 114 raise ValueError("Failed to find END_SEQUENCE line") 115 116 record.seq = Seq.Seq(''.join(n[0] for n in record.sites), generic_dna) 117 if record.comments['trim'] is not None: 118 first, last = record.comments['trim'][:2] 119 record.seq_trimmed = record.seq[first:last] 120 121 return record
122 123
124 -def parse(handle):
125 """Iterates over a file returning multiple PHD records. 126 127 The data is read line by line from the handle. The handle can be a list 128 of lines, an open file, or similar; the only requirement is that we can 129 iterate over the handle to retrieve lines from it. 130 131 Typical usage: 132 133 records = parse(handle) 134 for record in records: 135 # do something with the record object 136 """ 137 while True: 138 record = read(handle) 139 if not record: 140 return 141 yield record
142