如何从python的大fasta文件中提取蛋白质序列的子集？

Question

如果在txt文件( .fasta文件，Interested proteins.txt)中列出了蛋白质in，我想从新文件(selected_proteins.fasta)中的一个蛋白质文件(swissprot_canonical-isoforms.fasta)中提取蛋白质序列的子集。

下面显示了swissprot_canonical-isoforms.fasta中的部分蛋白质序列。蛋白质ID显示在以">“开头的行中的两个”AC.26“之间。例如，"P04637“是一个蛋白质ID。

sp|P04637|P53_HUMAN细胞肿瘤抗原( p53 OS=Homo OS=Homo GN=TP53 PE=1 SV=4 ) GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD >sp P 04637-2倍p53 _人亚型2细胞肿瘤抗原>sp P 04637-3_p5 3_p5 3人细胞肿瘤抗原OS=Homo GN=TP53 PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQMLLDLRWCYFLINSS

3

下面是Interested proteins.txt中列出的一些蛋白质ID

Q6ZWH5
Q8NG66
P51955
P51957
P04629

最后的输出应该如下所示(只列出Q6ZWH5的序列作为示例)：

>sp|Q6ZWH5|NEK10_HUMAN Serine/threonine-protein kinase Nek10 OS=Homo sapiens GN=NEK10 PE=2 SV=3
MPDQDKKVKTTEKSTDKQQEITIRDYSDLKRLRCLLNVQSSKQQLPAINFDSAQNSMTKS
EPAIRAGGHRARGQWHESTEAVELENFSINYKNERNFSKHPQRKLFQEIFTALVKNRLIS
REWVNRAPSIHFLRVLICLRLLMRDPCYQEILHSLGGIENLAQYMEIVANEYLGYGEEQH
TVDKLVNMTYIFQKLAAVKDQREWVTTSGAHKTLVNLLGARDTNVLLGSLLALASLAESQ
ECREKISELNIVENLLMILHEYDLLSKRLTAELLRLLCAEPQVKEQVKLYEGIPVLLSLL
HSDHLKLLWSIVWILVQVCEDPETSVEIRIWGGIKQLLHILQGDRNFVSDHSSIGSLSSA
NAAGRIQQLHLSEDLSPREIQENTFSLQAACCAALTELVLNDTNAHQVVQENGVYTIAKL
ILPNKQKNAAKSNLLQCYAFRALRFLFSMERNRPLFKRLFPTDLFEIFIDIGHYVRDISA
YEELVSKLNLLVEDELKQIAENIESINQNKAPLKYIGNYAILDHLGSGAFGCVYKVRKHS
GQNLLAMKEVNLHNPAFGKDKKDRDSSVRNIVSELTIIKEQLYHPNIVRYYKTFLENDRL
YIVMELIEGAPLGEHFSSLKEKHHHFTEERLWKIFIQLCLALRYLHKEKRIVHRDLTPNN
IMLGDKDKVTVTDFGLAKQKQENSKLTSVVGTILYSCPEVLKSEPYGEKADVWAVGCILY
QMATLSPPFYSTNMLSLATKIVEAVYEPVPEGIYSEKVTDTISRCLTPDAEARPDIVEVS
SMISDVMMKYLDNLSTSQLSLEKKLERERRRTQRYFMEANRNTVTCHHELAVLSHETFEK
ASLSSSSSGAASLKSELSESADLPPEGFQASYGKDEDRACDEILSDDNFNLENAEKDTYS
EVDDELDISDNSSSSSSSPLKESTFNILKRSFSASGGERQSQTRDFTGGTGSRPRPALLP
LDLLLKVPPHMLRAHIKEIEAELVTGWQSHSLPAVILRNLKDHGPQMGTFLWQASAGIAV
SQRKVRQISDPIQQILIQLHKIIYITQLPPALHHNLKRRVIERFKKSLFSQQSNPCNLKS
EIKKLSQGSPEPIEPNFFTADYHLLHRSSGGNSLSPNDPTGLPTSIELEEGITYEQMQTV
IEEVLEESGYYNFTSNRYHSYPWGTKNHPTKR

有没有办法用蟒蛇来做这件事？任何帮助都将不胜感激。

Answer 1

您可以使用pyfasta (从python到FASTA格式的接口)来完成这一操作。

from pyfasta import Fasta

f = Fasta('fasta.fa') # open the file

targets = {"P04637"} # define your target IDs

selection = {}

for key in f:
    candidateKey = key.split("|")[1]
    if candidateKey in targets:
        selection[key] = f[key][:]
        print(key)
        print(selection[key])

输出：

sp|P04637|P53_HUMAN Cellular tumor antigen p53 OS=Homo sapiens GN=TP53 PE=1 SV=4
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAP
TPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAM
AIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKK
KPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD