I have a fasta file with more than 500 sequences, and from that file I need to build a table, so I am trying to write a script to do it instead of doing it by hand, with copy-paste. I am reading the file using Biopython : seq=SeqIO.parse(handle, "fasta")
From each sequence I want to know the specie the protein sequence belongs, the name of the protein and the Uniprot ID. when I use the SeqIO to parse a fasta file I noticed that there is not much info I can parse from it.
Here is an subset of my fasta file:
>gi|194757291|ref|XP_001960898.1| GF11270 [Drosophila ananassae] >gi|190622196|gb|EDV37720.1| GF11270 [Drosophila ananassae] MSAARTSQDCDCTAKCRLRQHGNTITAALTKRSISSQNLAAFVYKTCGNFANILDDLGRSAVHMSASTGRYEILEWLLNH GAYINGQDYESGSSPLHRALYYGSIDCAVLLLRYGASMELLDEDTCCPLQAICRKCDVDDFATDSQNDVLVWGSNKNYNL GVGSEQNTNAPQSVDFFRKSNIWIEQVALGAYHSLFLDKKGHLYAVGHGKGGRLGTGGENTLPAPKRVKVSSKLGSEDSI RCISVSRQHSLVLTHRSLVFACGLNSDCQLGVRDAPEHLAQFKEVVALRDKGASDLVRVIACDQHSIAYGSRCVYVWGAN QGQFGISANIASIVVPTLIKLPARTTIRFVEANNAATVIYSEEKMIYLYYAEKTRAIKTPNYEDLKSISVMGGHIKNSAK GSAAALKLLMLTETNVVYLWYENTQQFYRCNFLPIRLPQIKKILYKCNQVMVLSEDGCVYRGKCNQIALPASELQEKSRP NLDIWQNNDQNRTEISREHVIRIELQRVPNIDRAVDISCDEGFSSFAVLQESQGKYFRKPTLPRKEHSFKKLLHDTSDCD AVHDVVFHVDGEKYPAHKYIIYSRAPGLRELVRMYLDKDIYLNFENLTGKMFELVLKHIYTNYWPTEDDIDCIQQSLGPA NPQNRSRTCQMFLPHLEKFQLTELAKYVKSYVQDHQFPLPSARQRLPRLHRSDYPELYDVKIKCEDGQVLQAHKCMLVAR LEYFEMMFMHSWAERSSVTMEGVPAEYMEPVLDYLYSLEAEAFCKQAYLETFLYNMITICDQYFIESLQNLCELLILDKI SIRKCGEMLEFATMYNCKLLLKGCMDFICQNLARVLCYRSIEQCDGETLKCLNDHYRNMFSRVFDYRQITPFSEAIEDEL LLSFIDGLEVDLEYRMDAESKAKQAAKTKQKDLRKLNARHQYEQRAISSMMRSISISESNPAPEVATSPQESARSETNNW SRVIDKKEQKRKQAETALKVNKTLKQETSPEPEMVPIERTPVNEQTPPPLSPETEPSTPLNKSYNLDFSSLTPQSQKLSQ KQRKRLSSESKSWRGNSSALLESPTTPVPVPNAWGVTTTPSSSFNDSYTSPTTGSSSDPTSFANMMRSQAASSSATSKDQ SQNFSKILADERRQRESYERMRNKSLVHTQIEETAIAELREFYNVDNIDDEKITIARKSRPSDINFSTWIRQ
>gi|198456847|ref|XP_001360463.2| GA20796 [Drosophila pseudoobscura pseudoobscura] >gi|198135774|gb|EAL25038.2| GA20796 [Drosophila pseudoobscura pseudoobscura] MSTAKAQEYDCTAKCTCRQHGNSITAALTKRSIDNQNLGAFIFKTCGNFANIIDDLGRSAVHMSASVARYEILEWLLNHG AYINGLDYESGSSPLHRALYYGSIDCAVLLLRYGASLELLDEDTRCPLQAICRKCDEDFTTESQNDVLVWGSNKNYNLGI GNEQNTNAPQAVDFFRKSNIWIEQVALGAYHSLFCDKKGHLYAVGHGKGGRLGIGVENSLPAPKRVKVSSKLNDDSIMCI SVSRQHSLLLTRRSLVFACGINTDHQLGVRDAPENLTQFREVVALRDKGASDLLRVIACDQHSIAYSTKCVYVWGANQGQ FGISRTTDTIMAPTLIKLPARTSIRFVEANNAATVIYTEEKMITLFYGDKTRYIKTPNYEDLKSIAVIGGHLKSSTKGSA AALKLLMLTETNVVFLWYENTQQFYRCNFSPIRLPEIKKILYKCNQVLILSLDGCVYRGKCNQIALPAGILEEKSKPNMD IWHNNDQNRTEISREHVIRIELQRVPNIDRATDIFCDESFSSFAVLQESHMKYFRKPPLPRREHNFKKLYHDTCESDAVH DVVFHVDGERFAAHKFILYSRAPGLRELTRIYLDKDVYLNFENLTGKMFELILKYIYTSYWPTEDDIDCIQESLGPANPR ERSRACEMFIPHLEMFQLVDLARYLQSYVRDNQFPIPSTRQRFNRLHRSDYPELYDVRIVCEDSKVLEAHKCMLVSRLEY FEMMFTHSWAERTTVNMEGVPAEYMEPVLDYLYSLDTEAFCKQNYTETFLYNMVTFCDQYFIESLQNVCESLILDKISIR KCGEMLDFAAMYNCKLLHKGCMDFICHNLARVLCYRSIEQCDEATLKCLNDHYRKMFSNVFDYRQITPFSEAIEDELLLS FVVDCDIDLDYRMDPETKLKAAAKHKQKDLRRQDARHYYEQQAISSMMRSLSVSESASGPEATTGPQESTRSEGKNWSRV VDKKEQKRKLADTALKVNNTLKLEEPPRPELEVIERALMKEQTPPPTSPAEETSTPLSKSYNLDLSSLTPQSQKLSQKQR KRLSSESKSWRSPLVEQEPTTPVAVPNAWGLPPATPSSSSFTDSPATGSISDPTSFANMMRGQAAAATTPTEKGQSFSRI LADERRQRESFERMRNKSLAHTQIEETAIAELREFYNVDNTDDETITIERKSRPTDINFSTWLKH
>gi|355695434|gb|AES00009.1| inhibitor of Bruton agammaglobulinemia tyrosine kinase [Mustela putorius furo] KPGNKLKLNQKKCSFLCDVTMKSVDGKEFTCHKCVLCARLEYFHSMLSSSWIEASTCTALEMPIHSDILKVILDYLYTDE AVVIKESQNVDFVCSVLVVADQLLITRLKGMCEVALTEKLTLKNAAMILEFAAMYNAEQLKLSCLQFIGLNM
Is there any way I get the Protein name, Uniprot ID and organism from those sequences? For example I thought on parsing the genebank id from the seq.description and then search in genebank with that ID but I think it cannot be made, not all the sequences have genebank ID. Any suggestions how to do this? Any help would be really appreciated.
example of desired output:
name organism uniprot id family
GF11270 Sophophora B3MFN0
GA20796 Sophophora Q291S4
Solution found:
handle = open("seq.fasta")
orchid_dict = SeqIO.to_dict(SeqIO.parse(handle, "fasta"))
handle.close()
for key in orchid_dict:
# print key
#print orchid_dict[key].description
if orchid_dict[key].description.find("|gb|") !=-1:
gb_id=re.findall(r'gb\|([^\|]+)', orchid_dict[key].description)
newstr = str(gb_id).replace("'", "")
newstr = newstr.replace("[", "")
newstr = newstr.replace("]", "")
params = ( ('query',newstr),
('format','tab'),
('columns','protein names,organism,id,families,existence' )
)
data = urllib.urlencode(params)
request = urllib2.Request(url, data)
contact = "" # Please set your email address here to help us debug in case of problems.
request.add_header('User-Agent', 'Python contact')
response = urllib2.urlopen(request)
page = response.read(200000)
f.writelines( page)
You should probably quote where you found this solution. From the orchid reference I guess on the Biopython tutorial?
I used the code from the Biopython tutorial to read the fast file, and to access the Uniprot I found the information here: http://www.uniprot.org/faq/28#downloading
thanks for following up with an answer!
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What you pasted there is not valid Fasta.
Check out the different string split functions in the Python and other like startswith, endswith.