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  #1 (permalink)  
Old 05-09-2009
repinementer repinementer is offline
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Create a script for grep
Could any one know how to write a perl script for multiple grep functions like the following. Help would be appreciated.

Quote:
grep -w chr1 BED1 >>f1.txt | grep –w chr2 BED1 >>f2.txt | grep -w chr3 BED1 >>f3.txt | grep -w chr4 BED1 >>f4.txt | grep -w chr5 BED1 >>f5.txt | grep -w chr6 BED1 >>f6.txt | grep -w chr7 BED1 >>f7.txt | grep -w chr8 BED1 >>f8.txt | grep -w chr9 BED1 >>f9.txt | grep -w chr10 BED1 >>f10.txt | grep -w chr11 BED1 >>f11.txt | grep -w chr12 BED1 >>f12.txt | grep -w chr13 BED1 >>f13.txt | grep -w chr14 BED1 >>f14.txt | grep -w chr15 BED1 >>f15.txt | grep -w chr16 BED1 >>f16.txt | grep -w chr17 BED1 >>f17.txt | grep -w chr18 BED1 >>f19.txt | grep -w chr20 BED1 >>f20.txt | grep -w chr21 BED1 >>f21.txt | grep -w chr22 BED1 >>f22.txt | grep -w chrX BED1 >>fX.txt | grep -w chrY BED1 >>fY.txt
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Old 05-09-2009
ghostdog74 ghostdog74 is offline Forum Advisor  
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wow. that's ridiculous...
describe in detail what you are doing...provide sample input files if any.
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Old 05-09-2009
repinementer repinementer is offline
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Atually it's easy
I'm grepping specific lines contain specic words like chr1, chr2......chrx and chr y from a single file by using the same grep command multiple times with the help of a pipe symbol.

input file
chr1 tab 19u384763
chr1 tab 24275y745
chr21 tab 2527855235
output
all chr1 into 0ne file and all chr2 to another vice versa
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Old 05-09-2009
durden_tyler's Avatar
durden_tyler durden_tyler is offline Forum Advisor  
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Quote:
Originally Posted by repinementer View Post
...
output
all chr1 into 0ne file and all chr2 to another vice versa
Something like this:

Code:
$
$ cat input.txt
chr1 tab 19u384763
chr21 tab 2527855236
chr1 tab 24275y745
chr21 tab 2527855235
chrX tab 273849202
chrX tab 3893402u7
$
$
$ sort -k1,1 input.txt | perl -ne '{split;
  if ($_[0] eq $lastread) {$lastread=$_[0]; print OUT $_}
  else {$lastread=$_[0]; $_[0] =~ s/^chr//; open(OUT, ">>f$_[0].txt"); print OUT $_;}
}'
$
$ cat f1.txt
chr1 tab 19u384763
chr1 tab 24275y745
$
$ cat f21.txt
chr21 tab 2527855235
chr21 tab 2527855236
$
$ cat fX.txt
chrX tab 273849202
chrX tab 3893402u7
$
$
tyler_durden

________________________________________________________________________
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Old 05-09-2009
stateperl stateperl is offline
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Thanx
Hey Thanx for your time and replies.
I will try out now. Your codes are comparatively very simple.
Thanx to you and AWK
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Old 05-09-2009
ghostdog74 ghostdog74 is offline Forum Advisor  
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if your file is sorted and Perl is not a must to use
Code:
awk 'p!=$1{i++}{p=$1;print $0>"file_"i}' file
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Old 05-09-2009
devtakh devtakh is offline
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Try this:

Code:
sort -k 1,1 file| awk '{s=substr($1,4,length($1));print $0 > "f"s}'

cheers,
Devaraj Takhellambam
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