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Top Forums Shell Programming and Scripting how to match a numers from file1 to file 2??Ps help me.. Post 302413204 by penchal_boddu on Thursday 15th of April 2010 01:39:14 AM
Old 04-15-2010
[root]# perl -lane "BEGIN { open(FH,'file1');@con=<FH>;}print if grep(/@F[2]/,@con)" file2
rs3737728 1 1061338 A G 0.2845 0.2809 1.018

Thanks,
Penchal

---------- Post updated at 12:39 AM ---------- Previous update was at 12:35 AM ----------

Quote:
Originally Posted by sureshraj
Hi firends,
I need to write a program in perl for following task,
I have a data like following numbers in file1.txt

1061338
1159781
1161717
1920355
1924487
2996733
3121872
3124510

I have to search the matching numbers in file2,my file2 is have a multiple columns like this
rs3934834 1 1045729 A G 0.1791 0.2054 0.8441
rs3737728 1 1061338 A G 0.2845 0.2809 1.018
rs6687776 1 1070488 A G 0.1768 0.1956 0.8833
rs9651273 1 1071463 A G 0.2743 0.2689 1.028
rs4970405 1 1088878 G A 0.0922 0.0757 1.24
rs1272625 1 1089873 G A 0.1369 0.1231 1.13
rs2298217 1 1104902 A G 0.1448 0.1542 0.9286
rs4970362 1 1134661 A G 0.3793 0.3954 0.9346

the underlined column have to matched with file1..But i dont know how to write a program for this task..I need out put like file2 for matching numbers only...Pls any one help me & give me a program in perl..
my output should be like
rs6596796 6 120522 A G 0.1058 0.09469
rs1535053 6 126089 G A 0.2155 0.2151
rs12192106 6 137664 A G 0.06956 0.07949
rs6913464 6 139090 A G 0.1702 0.1663
rs9405480 6 144199 A G 0.1869 0.1771
rs9392299 6 148909 G A 0.07122 0.06203
rs1418708 6 150610 A G 0.1386 0.1374
rs1418707 6 150800 G A 0.192 0.1631
Hi ,

if third coulmn of file2 matches with file1 in above case ,

output must be

rs3737728 1 1061338 A G 0.2845 0.2809 1.018

Am i right

Thanks,
Penchal
 

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DIFF(1) 						      General Commands Manual							   DIFF(1)

NAME
diff - differential file comparator SYNOPSIS
diff [ -efbh ] file1 file2 DESCRIPTION
Diff tells what lines must be changed in two files to bring them into agreement. If file1 (file2) is `-', the standard input is used. If file1 (file2) is a directory, then a file in that directory whose file-name is the same as the file-name of file2 (file1) is used. The normal output contains lines of these forms: n1 a n3,n4 n1,n2 d n3 n1,n2 c n3,n4 These lines resemble ed commands to convert file1 into file2. The numbers after the letters pertain to file2. In fact, by exchanging `a' for `d' and reading backward one may ascertain equally how to convert file2 into file1. As in ed, identical pairs where n1 = n2 or n3 = n4 are abbreviated as a single number. Following each of these lines come all the lines that are affected in the first file flagged by `<', then all the lines that are affected in the second file flagged by `>'. The -b option causes trailing blanks (spaces and tabs) to be ignored and other strings of blanks to compare equal. The -e option produces a script of a, c and d commands for the editor ed, which will recreate file2 from file1. The -f option produces a similar script, not useful with ed, in the opposite order. In connection with -e, the following shell program may help maintain multiple versions of a file. Only an ancestral file ($1) and a chain of version-to-version ed scripts ($2,$3,...) made by diff need be on hand. A `latest version' appears on the standard output. (shift; cat $*; echo '1,$p') | ed - $1 Except in rare circumstances, diff finds a smallest sufficient set of file differences. Option -h does a fast, half-hearted job. It works only when changed stretches are short and well separated, but does work on files of unlimited length. Options -e and -f are unavailable with -h. FILES
/tmp/d????? /usr/lib/diffh for -h SEE ALSO
cmp(1), comm(1), ed(1) DIAGNOSTICS
Exit status is 0 for no differences, 1 for some, 2 for trouble. BUGS
Editing scripts produced under the -e or -f option are naive about creating lines consisting of a single `.'. DIFF(1)
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