Package Bio :: Package SeqIO :: Module PirIO
[hide private]
[frames] | no frames]

Source Code for Module Bio.SeqIO.PirIO

  1  # Copyright 2008-2009 by Peter Cock.  All rights reserved. 
  2  # This code is part of the Biopython distribution and governed by its 
  3  # license.  Please see the LICENSE file that should have been included 
  4  # as part of this package. 
  5  # 
  6  # This module is for reading and writing PIR or NBRF format files as 
  7  # SeqRecord objects.  The code is based on Bio.SeqIO.FastaIO 
  8   
  9  """Bio.SeqIO support for the "pir" (aka PIR or NBRF) file format. 
 10   
 11  You are expected to use this module via the Bio.SeqIO functions, or if 
 12  the file contains a sequence alignment, optionally via Bio.AlignIO instead. 
 13   
 14  This format was introduced for the Protein Information Resource (PIR), a 
 15  project of the National Biomedical Research Foundation (NBRF).  The PIR 
 16  database itself is now part of UniProt. 
 17   
 18  The file format is described online at: 
 19  http://www.ebi.ac.uk/help/pir_frame.html 
 20  http://www.cmbi.kun.nl/bioinf/tools/crab_pir.html (currently down) 
 21   
 22  An example file in this format would be: 
 23   
 24  >P1;CRAB_ANAPL 
 25  ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). 
 26    MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR 
 27    SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH 
 28    GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ 
 29    SDVPERSIPI TREEKPAIAG AQRK* 
 30   
 31  >P1;CRAB_BOVIN 
 32  ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). 
 33    MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPA STSLSPFYLR 
 34    PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV 
 35    HGKHEERQDE HGFISREFHR KYRIPADVDP LAITSSLSSD GVLTVNGPRK 
 36    QASGPERTIP ITREEKPAVT AAPKK* 
 37   
 38  Or, an example of a multiple sequence alignment: 
 39   
 40  >P1;S27231 
 41  rhodopsin - northern leopard frog 
 42  MNGTEGPNFY IPMSNKTGVV RSPFDYPQYY LAEPWKYSVL AAYMFLLILL GLPINFMTLY 
 43  VTIQHKKLRT PLNYILLNLG VCNHFMVLCG FTITMYTSLH GYFVFGQTGC YFEGFFATLG 
 44  GEIALWSLVV LAIERYIVVC KPMSNFRFGE NHAMMGVAFT WIMALACAVP PLFGWSRYIP 
 45  EGMQCSCGVD YYTLKPEVNN ESFVIYMFVV HFLIPLIIIS FCYGRLVCTV KEAAAQQQES 
 46  ATTQKAEKEV TRMVIIMVIF FLICWVPYAY VAFYIFTHQG SEFGPIFMTV PAFFAKSSAI 
 47  YNPVIYIMLN KQFRNCMITT LCCGKNPFGD DDASSAATSK TEATSVSTSQ VSPA* 
 48   
 49  >P1;I51200 
 50  rhodopsin - African clawed frog 
 51  MNGTEGPNFY VPMSNKTGVV RSPFDYPQYY LAEPWQYSAL AAYMFLLILL GLPINFMTLF 
 52  VTIQHKKLRT PLNYILLNLV FANHFMVLCG FTVTMYTSMH GYFIFGPTGC YIEGFFATLG 
 53  GEVALWSLVV LAVERYIVVC KPMANFRFGE NHAIMGVAFT WIMALSCAAP PLFGWSRYIP 
 54  EGMQCSCGVD YYTLKPEVNN ESFVIYMFIV HFTIPLIVIF FCYGRLLCTV KEAAAQQQES 
 55  LTTQKAEKEV TRMVVIMVVF FLICWVPYAY VAFYIFTHQG SNFGPVFMTV PAFFAKSSAI 
 56  YNPVIYIVLN KQFRNCLITT LCCGKNPFGD EDGSSAATSK TEASSVSSSQ VSPA* 
 57   
 58  >P1;JN0120 
 59  rhodopsin - Japanese lamprey 
 60  MNGTEGDNFY VPFSNKTGLA RSPYEYPQYY LAEPWKYSAL AAYMFFLILV GFPVNFLTLF 
 61  VTVQHKKLRT PLNYILLNLA MANLFMVLFG FTVTMYTSMN GYFVFGPTMC SIEGFFATLG 
 62  GEVALWSLVV LAIERYIVIC KPMGNFRFGN THAIMGVAFT WIMALACAAP PLVGWSRYIP 
 63  EGMQCSCGPD YYTLNPNFNN ESYVVYMFVV HFLVPFVIIF FCYGRLLCTV KEAAAAQQES 
 64  ASTQKAEKEV TRMVVLMVIG FLVCWVPYAS VAFYIFTHQG SDFGATFMTL PAFFAKSSAL 
 65  YNPVIYILMN KQFRNCMITT LCCGKNPLGD DE-SGASTSKT EVSSVSTSPV SPA* 
 66   
 67   
 68  As with the FASTA format, each record starts with a line beginning with ">" 
 69  character.  There is then a two letter sequence type (P1, F1, DL, DC, RL, 
 70  RC, or XX), a semi colon, and the identification code.  The second like is 
 71  free text description.  The remaining lines contain the sequence itself, 
 72  terminating in an asterisk.  Space separated blocks of ten letters as shown 
 73  above are typical. 
 74   
 75  Sequence codes and their meanings: 
 76   
 77  P1 - Protein (complete) 
 78  F1 - Protein (fragment) 
 79  D1 - DNA (e.g. EMBOSS seqret output) 
 80  DL - DNA (linear) 
 81  DC - DNA (circular) 
 82  RL - RNA (linear) 
 83  RC - RNA (circular) 
 84  N3 - tRNA 
 85  N1 - Other functional RNA 
 86  XX - Unknown 
 87  """ 
 88   
 89  from __future__ import print_function 
 90   
 91  from Bio.Alphabet import single_letter_alphabet, generic_protein, \ 
 92      generic_dna, generic_rna 
 93  from Bio.Seq import Seq 
 94  from Bio.SeqRecord import SeqRecord 
 95   
 96  _pir_alphabets = {"P1": generic_protein, 
 97                    "F1": generic_protein, 
 98                    "D1": generic_dna, 
 99                    "DL": generic_dna, 
100                    "DC": generic_dna, 
101                    "RL": generic_rna, 
102                    "RC": generic_rna, 
103                    "N3": generic_rna, 
104                    "XX": single_letter_alphabet, 
105                    } 
106   
107   
108 -def PirIterator(handle):
109 """Generator function to iterate over Fasta records (as SeqRecord objects). 110 111 handle - input file 112 alphabet - optional alphabet 113 title2ids - A function that, when given the title of the FASTA 114 file (without the beginning >), will return the id, name and 115 description (in that order) for the record as a tuple of strings. 116 117 If this is not given, then the entire title line will be used 118 as the description, and the first word as the id and name. 119 120 Note that use of title2ids matches that of Bio.Fasta.SequenceParser 121 but the defaults are slightly different. 122 """ 123 #Skip any text before the first record (e.g. blank lines, comments) 124 while True: 125 line = handle.readline() 126 if line == "": 127 return # Premature end of file, or just empty? 128 if line[0] == ">": 129 break 130 131 while True: 132 if line[0] != ">": 133 raise ValueError( 134 "Records in PIR files should start with '>' character") 135 pir_type = line[1:3] 136 if pir_type not in _pir_alphabets or line[3] != ";": 137 raise ValueError( 138 "Records should start with '>XX;' " 139 "where XX is a valid sequence type") 140 identifier = line[4:].strip() 141 description = handle.readline().strip() 142 143 lines = [] 144 line = handle.readline() 145 while True: 146 if not line: 147 break 148 if line[0] == ">": 149 break 150 #Remove trailing whitespace, and any internal spaces 151 lines.append(line.rstrip().replace(" ", "")) 152 line = handle.readline() 153 seq = "".join(lines) 154 if seq[-1] != "*": 155 #Note the * terminator is present on nucleotide sequences too, 156 #it is not a stop codon! 157 raise ValueError( 158 "Sequences in PIR files should include a * terminator!") 159 160 #Return the record and then continue... 161 record = SeqRecord(Seq(seq[:-1], _pir_alphabets[pir_type]), 162 id=identifier, name=identifier, 163 description=description) 164 record.annotations["PIR-type"] = pir_type 165 yield record 166 167 if not line: 168 return # StopIteration 169 assert False, "Should not reach this line"
170 171 if __name__ == "__main__": 172 print("Running quick self test") 173 174 import os 175 176 for name in ["clustalw", "DMA_nuc", "DMB_prot", "B_nuc", "Cw_prot"]: 177 print(name) 178 filename = "../../Tests/NBRF/%s.pir" % name 179 if not os.path.isfile(filename): 180 print("Missing %s" % filename) 181 continue 182 183 records = list(PirIterator(open(filename))) 184 count = 0 185 for record in records: 186 count += 1 187 parts = record.description.split() 188 if "bases," in parts: 189 assert len(record) == int(parts[parts.index("bases,") - 1]) 190 print("Could read %s (%i records)" % (name, count)) 191