Question

之前我问过这个类似的问题，但之前的解决方案并没有解决我的问题。我一直在思考和测试事情，但没有任何工作正常。

我有一个包含500多个序列的fasta文件，从该文件我需要构建一个表，所以我正在尝试编写一个脚本来执行它而不是手动执行，使用复制粘贴。我正在使用Biopython读取文件：seq=SeqIO.parse(handle, "fasta")

从每个序列我想知道蛋白质序列所属的种类，蛋白质的名称和Uniprot ID。当我使用SeqIO来解析一个fasta文件时，我注意到我可以解析的信息不多。

这是我的fasta文件的一个子集：

>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

有没有办法从这些序列中获得蛋白质名称，Uniprot ID和生物体？例如，我想从seq.description解析genebank id，然后在带有该ID的genebank中搜索，但我认为不能制作，并非所有序列都有genebank ID。有什么建议怎么做？任何帮助都会非常感激。

所需输出的示例：

name    organism    uniprot id  family
GF11270 Sophophora  B3MFN0  
GA20796 Sophophora  Q291S4

Answer 1

您也可以询问biostar：http://www.biostars.org/

从你的fasta标题中提取ACN。例如：GF11270

并使用uniprot REST API检索与此ACN相关联的记录

http://www.uniprot.org/uniprot/?query=GF11270&sort=score&format=xml

http://www.uniprot.org/uniprot/?query=GF11270&sort=score&format=txt

http://www.uniprot.org/uniprot/?query=GF11270&sort=score&format=tab

从SeqIO.parse python创建表

1 个答案: