Bio.SeqIO.PirIO module

Bio.SeqIO support for the “pir” (aka PIR or NBRF) file format.

This module is for reading and writing PIR or NBRF format files as SeqRecord objects.

You are expected to use this module via the Bio.SeqIO functions, or if the file contains a sequence alignment, optionally via Bio.AlignIO instead.

This format was introduced for the Protein Information Resource (PIR), a project of the National Biomedical Research Foundation (NBRF). The PIR database itself is now part of UniProt.

The file format is described online at: http://www.ebi.ac.uk/help/pir_frame.html http://www.cmbi.kun.nl/bioinf/tools/crab_pir.html (currently down)

An example file in this format would be:

>P1;CRAB_ANAPL
ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
  MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
  SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
  GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
  SDVPERSIPI TREEKPAIAG AQRK*

>P1;CRAB_BOVIN
ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
  MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPA STSLSPFYLR
  PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV
  HGKHEERQDE HGFISREFHR KYRIPADVDP LAITSSLSSD GVLTVNGPRK
  QASGPERTIP ITREEKPAVT AAPKK*

Or, an example of a multiple sequence alignment:

>P1;S27231
rhodopsin - northern leopard frog
MNGTEGPNFY IPMSNKTGVV RSPFDYPQYY LAEPWKYSVL AAYMFLLILL GLPINFMTLY
VTIQHKKLRT PLNYILLNLG VCNHFMVLCG FTITMYTSLH GYFVFGQTGC YFEGFFATLG
GEIALWSLVV LAIERYIVVC KPMSNFRFGE NHAMMGVAFT WIMALACAVP PLFGWSRYIP
EGMQCSCGVD YYTLKPEVNN ESFVIYMFVV HFLIPLIIIS FCYGRLVCTV KEAAAQQQES
ATTQKAEKEV TRMVIIMVIF FLICWVPYAY VAFYIFTHQG SEFGPIFMTV PAFFAKSSAI
YNPVIYIMLN KQFRNCMITT LCCGKNPFGD DDASSAATSK TEATSVSTSQ VSPA*

>P1;I51200
rhodopsin - African clawed frog
MNGTEGPNFY VPMSNKTGVV RSPFDYPQYY LAEPWQYSAL AAYMFLLILL GLPINFMTLF
VTIQHKKLRT PLNYILLNLV FANHFMVLCG FTVTMYTSMH GYFIFGPTGC YIEGFFATLG
GEVALWSLVV LAVERYIVVC KPMANFRFGE NHAIMGVAFT WIMALSCAAP PLFGWSRYIP
EGMQCSCGVD YYTLKPEVNN ESFVIYMFIV HFTIPLIVIF FCYGRLLCTV KEAAAQQQES
LTTQKAEKEV TRMVVIMVVF FLICWVPYAY VAFYIFTHQG SNFGPVFMTV PAFFAKSSAI
YNPVIYIVLN KQFRNCLITT LCCGKNPFGD EDGSSAATSK TEASSVSSSQ VSPA*

>P1;JN0120
rhodopsin - Japanese lamprey
MNGTEGDNFY VPFSNKTGLA RSPYEYPQYY LAEPWKYSAL AAYMFFLILV GFPVNFLTLF
VTVQHKKLRT PLNYILLNLA MANLFMVLFG FTVTMYTSMN GYFVFGPTMC SIEGFFATLG
GEVALWSLVV LAIERYIVIC KPMGNFRFGN THAIMGVAFT WIMALACAAP PLVGWSRYIP
EGMQCSCGPD YYTLNPNFNN ESYVVYMFVV HFLVPFVIIF FCYGRLLCTV KEAAAAQQES
ASTQKAEKEV TRMVVLMVIG FLVCWVPYAS VAFYIFTHQG SDFGATFMTL PAFFAKSSAL
YNPVIYILMN KQFRNCMITT LCCGKNPLGD DE-SGASTSKT EVSSVSTSPV SPA*

As with the FASTA format, each record starts with a line beginning with “>” character. There is then a two letter sequence type (P1, F1, DL, DC, RL, RC, or XX), a semi colon, and the identification code. The second like is free text description. The remaining lines contain the sequence itself, terminating in an asterisk. Space separated blocks of ten letters as shown above are typical.

Sequence codes and their meanings:

  • P1 - Protein (complete)

  • F1 - Protein (fragment)

  • D1 - DNA (e.g. EMBOSS seqret output)

  • DL - DNA (linear)

  • DC - DNA (circular)

  • RL - RNA (linear)

  • RC - RNA (circular)

  • N3 - tRNA

  • N1 - Other functional RNA

  • XX - Unknown

Bio.SeqIO.PirIO.PirIterator(handle)

Iterate over Fasta records as SeqRecord objects.

handle - input file alphabet - optional alphabet title2ids - A function that, when given the title of the FASTA file (without the beginning >), will return the id, name and description (in that order) for the record as a tuple of strings.

If this is not given, then the entire title line will be used as the description, and the first word as the id and name.

Note that use of title2ids matches that of Bio.Fasta.SequenceParser but the defaults are slightly different.

Examples

>>> with open("NBRF/DMB_prot.pir") as handle:
...    for record in PirIterator(handle):
...        print("%s length %i" % (record.id, len(record)))
HLA:HLA00489 length 263
HLA:HLA00490 length 94
HLA:HLA00491 length 94
HLA:HLA00492 length 80
HLA:HLA00493 length 175
HLA:HLA01083 length 188
class Bio.SeqIO.PirIO.PirWriter(handle, wrap=60, record2title=None, code=None)

Bases: Bio.SeqIO.Interfaces.SequentialSequenceWriter

Class to write PIR format files.

__init__(self, handle, wrap=60, record2title=None, code=None)

Create a PIR writer.

Arguments:

  • handle - Handle to an output file, e.g. as returned by open(filename, “w”)

  • wrap - Optional line length used to wrap sequence lines. Defaults to wrapping the sequence at 60 characters Use zero (or None) for no wrapping, giving a single long line for the sequence.

  • record2title - Optional function to return the text to be used for the title line of each record. By default a combination of the record.id, record.name and record.description is used.

  • code - Optional sequence code must be one of P1, F1, D1, DL, DC, RL, RC, N3 and XX. By default None is used, which means auto detection based on record alphabet.

You can either use:

handle = open(filename, "w")
writer = PirWriter(handle)
writer.write_file(myRecords)
handle.close()

Or, follow the sequential file writer system, for example:

handle = open(filename, "w")
writer = PirWriter(handle)
writer.write_header() # does nothing for PIR files
...
Multiple writer.write_record() and/or writer.write_records() calls
...
writer.write_footer() # does nothing for PIR files
handle.close()
write_record(self, record)

Write a single PIR record to the file.