get names from fasta file

Question

[zzzahiri]

How can I get the name of proteins from fasta file in R for example: P13639 from

sp|P13639|EF2_HUMAN Elongation factor 2 OS=Homo sapiens GN=EEF2 PE=1 SV=4 MVNFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAGIIASARAGETRFTDTR KDEQERCITIKSTAISLFYELSENDLNFIKQSKDGAGFLINLIDSPGHVDFSSEVTAALR VTDGALVVVDCVSGVCVQTETVLRQAIAERIKPVLMMNKMDRALLELQLEPEELYQTFQR IVENVNVIISTYGEGESGPMGNIMIDPVLGTVGFGSGLHGWAFTLKQFAEMYVAKFAAKG EGQLGPAERAKKVEDMMKKLWGDRYFDPANGKFSKSATSPEGKKLPRTFCQLILDPIFKV FDAIMNFKKEETAKLIEKLDIKLDSEDKDKEGKPLLKAVMRRWLPAGDALLQMITIHLPS PVTAQKYRCELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYAFGRVFSGL VSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCGNIVGLVGVDQFLV KTGTITTFEHAHNMRVMKFSVSPVVRVAVEAKNPADLPKLVEGLKRLAKSDPMVQCIIEE SGEHIIAGAGELHLEICLKDLEEDHACIPIKKSDPVVSYRETVSEESNVLCLSKSPNKHN RLYMKARPFPDGLAEDIDKGEVSARQELKQRARYLAEKYEWDVAEARKIWCFGPDGTGPN ILTDITKGVQYLNEIKDSVVAGFQWATKEGALCEENMRGVRFDVHDVTLHADAIHRGGGQ IIPTARRCLYASVLTAQPRLMEPIYLVEIQCPEQVVGGIYGVLNRKRGHVFEESQVAGTP MFVVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETRK RKGLKEGIPALDNFLDKL

Answer 1

[Medhat]

from

http://www.bioconductor.org/packages/2.13/bioc/html/Biostrings.html

you can use

library("Biostrings")
myFastaFile <- readAAStringSet("my.fasta")
seqName = names(myFastaFile)

and if you have a big file you can refer to

http://stackoverflow.com/questions/23173215/how-to-subset-sequences-in-fasta-file-based-on-sequence-id-or-name

[zzzahiri]

Thanks But the result of this code is sp|P13639|EF2_HUMAN but I want to have P13639 :-(

[Ram]

maybe use gsub?

[Medhat]

what about using split?

strsplit(seq, "|")[[1]][2]