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.
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
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.
>>> 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
PirWriter(handle, wrap=60, record2title=None, code=None)¶
Class to write PIR format files.
__init__(self, handle, wrap=60, record2title=None, code=None)¶
Create a PIR writer.
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 a single PIR record to the file.