Question

我正在使用grep和一个具有多种搜索模式的文件。作为输出，我想获得匹配模式和该特定模式的出现次数。

cat pattern.txt

AT3G09260.1
AT5G50920.1

输入文件如下所示

>AT2G44750.1 | Symbols: TPK2 | thiamin pyrophosphokinase 2 | chr2:18451510-18452754 FORWARD LENGTH=265
>AT2G47140.1 | Symbols:  | NAD(P)-binding Rossmann-fold superfamily protein | chr2:19350970-19352059 REVERSE LENGTH=257
>AT2G47120.1 | Symbols:  | NAD(P)-binding Rossmann-fold superfamily protein 
>AT1G21470.1 | Symbols:  | BEST Arabidopsis thaliana protein match is: CLPC homologue 1 (TAIR:AT5G50920.1); Has 326 Blast hits to 324 proteins in 95 species: Archae - 0; Bacteria - 130; Metazoa - 0; Fungi - 0; Plants - 67; Viruses - 0; Other Eukaryotes - 129 (source: NCBI BLink). | chr1:7516709-7517179 REVERSE LENGTH=118
>AT3G09260.1 | Symbols: PYK10, PSR3.1, BGLU23, LEB | Glycosyl hydrolase superfamily protein | chr3:2840657-2843730 REVERSE LENGTH=524
>AT5G48175.1 | Symbols:  | FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: hypocotyl, male gametophyte, root; BEST Arabidopsis thaliana protein match is: Glycosyl hydrolase superfamily protein (TAIR:AT3G09260.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink). | chr5:19539208-19539676 FORWARD LENGTH=115
>AT5G50920.1 | Symbols: CLPC, ATHSP93-V, HSP93-V, DCA1, CLPC1 | CLPC homologue 1 | chr5:20715710-20719800 REVERSE LENGTH=929

我想得到像

这样的东西

AT3G09260.1    2
AT5G50920.1    2

我试过了

grep -f pattern.txt -c inputfile.txt
4

但它只给出了匹配行的总数（对于所有模式）。我相信这个问题已经在这里提出但从未解决过

how to loop over pattern from a file with grep

谢谢。

Answer 1

你基本上需要 grep -o ，它只打印匹配的组，然后你可以使用sort和uniq这样简单地找到他们的计数

$ grep -of pattern_file input_file | sort | uniq -c
      2 AT3G09260.1
      2 AT5G50920.1

如果您想要交换订单，那么您可以使用awk，如下所示：

$ grep -of pattern_file input_file | sort | uniq -c | awk '{print $2,$1}'
AT3G09260.1 2
AT5G50920.1 2

或者只是使用 awk

$ awk 'FNR==NR{a[$1]=0; next} { for(i in a) {a[i]+=gsub(i,"")} } END{for(i in a){ print i, a[i]} }' pattern_file RS= input_file
AT5G50920.1 2
AT3G09260.1 2

Answer 2

以下awk可以帮助你，因为你的Input_file看起来没有任何行的多次计数，所以无法测试你的输出。

awk '{a[$0]++} END{for(i in a){print i,a[i]}}'  Input_file

Answer 3

尝试

grep -f pattern.txt inputfile.txt| cut -d'|' -f1 |sort | uniq -c

这将grep文件中匹配的行，然后提取ID（第一个管道符号前的所有内容，对它们进行排序，然后计算每个符号的唯一出现次数。

将grep与模式文件一起使用来计算文件中的各个模式匹配

3 个答案: