biopython

v1.71.0

biopython v1.71.0 Bio.SeqIO.PirIO

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

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

Link to this section Summary

Functions

PirIterator()

Generator function to iterate over Fasta records (as SeqRecord objects)

Link to this section Functions

Link to this function PirIterator()

Generator function to 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.

Example:

 >>> 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