如何使用 python 从大型 fasta 文件中提取蛋白质序列的子集？

Question

如果蛋白质 ID 在 txt 文件中列出 (Interested proteins.txt).

下面显示了swissprot_canonical-isoforms.fasta中的部分蛋白质序列。蛋白质 ID 显示在两个“|”之间在以“>”开头的行中。例如，"P04637" 是蛋白质 ID。

>sp|P04637|P53_HUMAN Cellular tumor antigen p53 OS=Homo sapiens GN=TP53 PE=1 SV=4
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK
SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE
RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP
PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPG
GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
>sp|P04637-2|P53_HUMAN Isoform 2 of Cellular tumor antigen p53 OS=Homo sapiens GN=TP53
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK
SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE
RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP
PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQDQTSFQKENC
>sp|P04637-3|P53_HUMAN Isoform 3 of Cellular tumor antigen p53 OS=Homo sapiens GN=TP53
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK
SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE
RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP
PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQMLLDLRWCYFLINSS

以下是 Interested proteins.txt

中列出的一些蛋白质 ID

Q6ZWH5
Q8NG66
P51955
P51957
P04629

最终输出应该是这样的（仅列出 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

有什么方法可以用 python 做到这一点吗？任何帮助将不胜感激。

Answer 1

您可以使用 pyfasta，一个来自 python 的 FASTA 格式的接口来做到这一点。

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

如何使用 python 从大型 fasta 文件中提取蛋白质序列的子集？

How to extract a subset of protein sequences from a big fasta file with python?

python

jupyter-notebook

fasta