Question

I came across some problem with playing with grep ; and probably about grepping a tab. I have two files shown as below, both of which are tab-delimited.

FM_DEL_50r.bed
chr1    3392391 3658426 DEL chr1    3392364 3658425 DEL
chr1    4011952 4392064 DEL chr1    4011953 4392062 DEL
chr1    4468526 4665322 DEL chr1    4468523 4665322 DEL

FC_DEL_50r.bed
chr1    2612264 2613324 DEL chr1    2612205 2613007 DEL
chr1    3392391 3658426 DEL chr1    3392391 3658426 DEL
chr1    4011952 4392064 DEL chr1    4011953 4392060 DEL

我希望两处档案中都有一些内容:

cat FC_DEL_50r.bed |grep `cat FM_DEL_50r.bed |head -2|tail -1|awk  {print $2"	"$3} `

但有错误:

grep: 4392064: No such file or directory

I Trial cat _DEL_DEL_bed head hexachloro FM-1FMkprint{ 2, “$3} , 实际操作和产出401 1952 4392064

So maybe we cannot grep format like number" "number"? thx

edit: how stupid I am. I should use double-quotes..........(I first used single-quote and didn t work...)

cat FC_DEL_50r.bed |grep "`cat FM_DEL_50r.bed |head -2|tail -1|awk  {print $2"	"$3} `"

Follow-up questions: I wrote a bash script, based on the questions above:

#!/bin/bash
for((c=1;c<=542;c++))
do
    LINE=`head -$c FM_DEL_50r.bed|tail -1`
        P1=`cat $LINE|awk  {print $1"\t"$2"\t"$3} `
        GREP1=`cat FC_DEL_50r.bed |grep "$P1"`
        X1=`cat $GREP1 |awk  {print $5"\t"$6"\t"$7} `

        P2=`cat $LINE|awk  {print $5"\t"$6"\t"$7} `
        GREP2=`cat MC_DEL_50r.bed |grep "$P2"`
        X2=`cat $GREP2 |awk  {print $5"\t"$6"\t"$7} `

        if [ $X1 -eq $X2 ]
        then 
           echo "$LINE"	"$X1"
        fi
done

然而,它生产的产品

cat: chr1: No such file or directory
cat: 27122653: No such file or directory
cat: 27446984: No such file or directory
cat: DEL: No such file or directory
cat: chr1: No such file or directory
cat: 27880115: No such file or directory
cat: 28225069: No such file or directory
cat: DEL: No such file or directory

Seems it splits all columns of one line and cannot recognize them. What s the problem this time? thx

Answer 1

gr 1-o-1

<代码>grep [options] PATTERN [FILE...]

这是指在[FLE......]档案中显示的颗粒状。

型轴线不能有空间或表象(无所引述),因为然后将评估作为围护理由。因此,在你的情况下,指挥实际上变成了。

<代码> CA_DEL_50r.bed repg 401 1952 4392064

第二部分(After 管道)基本上要求将439206(Which需要作为档案)的401 1952(主人) gr成)。

为了纠正这种情况,在您的第二次发言中增加两点:

cat FC_DEL_50r.bed |grep "cat FM_DEL_50r.bed |head -2|tail -1|awk {print $2" "$3} "

+1 所涉所有细节。

Answer 2

出现错误是因为背书。 <代码>wk输出到<代码>grep 理由清单。因此,你正在做以下工作:

cat FC_DEL_50r.bed |grep 4011952 4392064

<代码>grep, 当然,401 1952<>/code>为: regex and 4392064, 即为档案名称,不能找到后者。



With the double quotes that you have now added around the argument list, you are getting:

cat FC_DEL_50r.bed |grep "4011952 4392064"


如果你想要的是:

cat FC_DEL_50r.bed |grep "4011952	4392064"

困难在于<代码>正在由<代码>wk解释为绕航顺序。若要从<代码>wk上删除一个字面<代码>。

{print $2"\t"$3}

友情链接