Question

我在表单中有一个文件（Input_fasta.txt）

>tr|A0A089QH62|A0A089QH62_MYCTU Histidine kinase OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) GN=LH57_00865 PE=4 SV=1
MTATASGIAATAPNCGEASINDVPIAESERRYLGARSASEYGQEIPLW
>tr|I6WXB4|I6WXB4_MYCTU 30S ribosomal protein S6 OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) GN=rpsF PE=3 SV=1
MRPYEIMVILDPTLDERTVAPSLETFLNVVRKDGGKVEKVDIWGKRRLAYEIAKHAEGIY
VVIDVKAAPATVSELDRQLSLNESVLRTKVMRTDKH
>tr|A0A089SBT4|A0A089SBT4_MYCTU Glycosyl transferase OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) GN=LH57_19775 PE=4 SV=1
MDTETHYSDVWVVIPAFNEAAVIGKVVTDVRSVFDHVVCVDDGSTDGTGDIARRSGAHLV
RHPINLGQGAAIQTGIEYARKQPGAQVFATFDGDGQHRVKDVAAMVDRLGAGDVDVVIGT
RFGRPVGKASASRPPLMKRIVLQTGARLSRRGRRLGLTDTNNGLRVFNKTVADGLNITMS
GMSHATEFIMLIAENHWRVAEEPVEVLYTEYSKSKGQPLLNGVNIIFDGFLRGRMPR
>tr|A0A089QKT1|A0A089QKT1_MYCTU TetR family transcriptional regulator OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) GN=LH57_00800 PE=4 SV=1
MSLTAGRGPGRPPAAKADETRKRILHAARQVFSERGYDGATFQEIAVRADLTRPAINHYF
ANKRVLYQEVVEQTHELVIVAGIERARREPTLMGRLAVVVDFAMEADAQYPASTAFLATT
VLESQRHPELSRTENDAVRATREFLVWAVNDAIERGELAADVDVSSLAETLLVVLCGVGF
YIGFVGSYQRMATITDSFQQLLAGTLWRPPT
>tr|I6YAB3|I6YAB3_MYCTU Iron ABC transporter permease OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) GN=LH57_07380 PE=4 SV=1
MARGLQGVMLRSFGARDHTATVIETISIAPHFVRVRMVSPTLFQDAEAEPAAWLRFWFPD
PNGSNTEFQRAYTISEADPAAGRFAVDVVLHDPAGPASSWARTVKPGATIAVMSLMGSSR
FDVPEEQPAGYLLIGDSASIPGMNGIIETVPNDVPIEMYLEQHDDNDTLIPLAKHPRLRV
RWVMRRDEKSLAEAIENRDWSDWYAWATPEAAALKCVRVRLRDEFGFPKSEIHAQAYWNA
GRAMGTHRATEPAATEPEVGAAPQPESAVPAPARGSWRAQAASRLLAPLKLPLVLSGVLA
ALVTLAQLAPFVLLVELSRLLVSGAGAHRLFTVGFAAVGLLGTGALLAAALTLWLHVIDA
RFARALRLRLLSKLSRLPLGWFTSRGSGSIKKLVTDDTLALHYLVTHAVPDAVAAVVAPV
GVLVYLFVVDWRVALVLFGPVLVYLTITSSLTIQSGPRIVQAQRWAEKMNGEAGSYLEGQ
PVIRVFGAASSSFRRRLDEYIGFLVAWQRPLAGKKTLMDLATRPATFLWLIAATGTLLVA
THRMDPVNLLPFMFLGTTFGARLLGIAYGLGGLRTGLLAARHLQVTLDETELAVREHPRE
PLDGEAPATVVFDHVTFGYRPGVPVIQDVSLTLRPGTVTALVGPSGSGKSTLATLLARFH
DVERGAIRVGGQDIRSLAADELYTRVGFVLQEAQLVHGTAAENIALAVPDAPAEQVQVAA
REAQIHDRVLRLPDGYDTVLGANSGLSGGERQRLTIARAILGDTPVLILDEATAFADPES
EYLVQQALNRLTRDRTVLVIAHRLHTITRADQIVVLDHGRIVERGTHEELLAAGGRYCRL
WDTGQGSRVAVAAAQDGTR
>tr|L0T545|L0T545_MYCTU PPE family protein PPE7 OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) GN=PPE7 PE=4 SV=1
MSVCVIYIPFKGCVKHVSVTIPITTEHLGPYEIDASTINPDQPIDTAFTQTLDFAGSGTV
GAFPFGFGWQQSPGFFNSTTTPSSGFFNSGAGGASGFLNDAAAAVSGLGNVFTETSGFFN
AGGVGIRASKTSATCCRAGRT

和另一个包含模式的文件，如（Pattern.txt）

I6WXB4

I6WXC3

I6WXK8

我需要像

这样的输出

>tr|I6WXB4|I6WXB4_MYCTU 30S ribosomal protein S6 OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) GN=rpsF PE=3 SV=1
MRPYEIMVILDPTLDERTVAPSLETFLNVVRKDGGKVEKVDIWGKRRLAYEIAKHAEGIY
VVIDVKAAPATVSELDRQLSLNESVLRTKVMRTDKH

直到现在我所做的是 grep -f Pattern.txt Input_fasta.txt

如何将输出扩展到下一行直到我点击下一行＆＃34;＆gt;＆＃34;比赛结束后？

尝试awk '/I6WXB4/{copy=1;next} />/{copy=0;next} copy' Input_fasta.txt 提供输出

MRPYEIMVILDPTLDERTVAPSLETFLNVVRKDGGKVEKVDIWGKRRLAYEIAKHAEGIY VVIDVKAAPATVSELDRQLSLNESVLRTKVMRTDKH

但是这里缺少标题。

Answer 1

在awk中：

$ awk 'NR==FNR{a[$0]; next} $2 in a' pattern.txt FS="|" RS=">" input_fasta.tzt
tr|I6WXB4|I6WXB4_MYCTU 30S ribosomal protein S6 OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) GN=rpsF PE=3 SV=1
MRPYEIMVILDPTLDERTVAPSLETFLNVVRKDGGKVEKVDIWGKRRLAYEIAKHAEGIY
VVIDVKAAPATVSELDRQLSLNESVLRTKVMRTDKH

Answer 2

这是一个简单的Python解决方案，使用BioPython：

import sys
import re
from Bio import SeqIO

with open('pattern.txt', 'r') as f:
    patterns = '|'.join([re.escape(pattern.strip()) for pattern in f])

for record in SeqIO.parse('test.fa', 'fasta'):
    if re.search(patterns, record.id):
        SeqIO.write(record, sys.stdout, 'fasta')

请注意，这需要一个行为良好的patterns.txt文件，即不包含任何空行的文件。

Answer 3

bash＆amp; sed解决方案：

while read pattern
do

if [ ! -z $pattern ] ; then

 sed -n "/\|$pattern\|/{:loop;p;n;/>/q;bloop;}" input.txt
fi

done < patternfile.txt

在模式文件上循环（跳过空白行），如果找到模式，只需阅读＆amp;打印文件行直到结束或直到找到>

grep之后打印行直到下一个模式

3 个答案: