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POHow can I grep lines involving tabs?
 

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  1. POHow can I grep lines involving tabs?
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    <p>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.</p> <pre><code>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 </code></pre> <p>I hope to grep some lines which appear in both files:</p> <pre><code>cat FC_DEL_50r.bed |grep `cat FM_DEL_50r.bed |head -2|tail -1|awk '{print $2"\t"$3}'` </code></pre> <p>However there's error: </p> <pre><code>grep: 4392064: No such file or directory </code></pre> <p>I tried <code>cat FM_DEL_50r.bed |head -2|tail -1|awk '{print $2"\t"$3}'</code>, it actually works and outputs <code>4011952 4392064</code></p> <p>So maybe we cannot grep format like 'number"\t"number"? thx</p> <p>edit: how stupid I am. I should use double-quotes..........(I first used single-quote and didn't work...)</p> <pre><code>cat FC_DEL_50r.bed |grep "`cat FM_DEL_50r.bed |head -2|tail -1|awk '{print $2"\t"$3}'`" </code></pre> <p>Follow-up questions: I wrote a bash script, based on the questions above:</p> <pre><code>#!/bin/bash for((c=1;c&lt;=542;c++)) do LINE=`head -$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"\t"$X1" fi done </code></pre> <p>However it produces </p> <pre><code>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 </code></pre> <p>Seems it splits all columns of one line and cannot recognize them. What's the problem this time? thx</p>
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