Creating Table From Fasta File In Python

Question

[Peiska]

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

[Neilfws]

What you pasted there is not valid Fasta.

[Thaman]

Check out the different string split functions in the Python and other like startswith, endswith.

Answer 1

[Peiska]

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)

[skymningen]

You should probably quote where you found this solution. From the orchid reference I guess on the Biopython tutorial?

[Peiska]

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

[Istvan Albert]

thanks for following up with an answer!