perl: comparision of field line by line in two files
Hi everybody,
First I apologize if my question seems demasiad you silly, but it really took 4 days struggling with this, I looked at books, forums ... And Also ask help to a friend that is software developer and he told me that it is a bad idea do it by perl... but this is my problem.
I moved to another lab for a couple of months, in which they use perl as tool to analyse DNA data (at my lab I ever use or developed software, command lines to modificate files to use it correctly, and some tools that people of my lab perform previously). Really in the weeks that I'm working here I saw the power of perform your own scripts to solve problem.
The problem is that i must to compare two files and select the lines of one of them whose fields comply a few requirements, which are comparisons with the other file fields.
my files are (of course that are only few lines)
File 1
Coordinate type RefAllele Strain SNPAllele
358909 Int <T> 5083_6_1 >A<
2074234 syn <G> 5083_6_1 >A<
31160 non <G> 5083_6_12 >A<
I must locate the file lines 2, which is within the range Coordinate generated by start and End, and also the strain match. ie I must compare each line of the file 2 with each line of 1.
I started the script many times, the variables are defined ... but can not get results ... I have tried arrays, hash .. I can not.
I include the script (the part that works) and the conditions that must be met.
Code:
#!/usr/bin/perl -w
# insideRecombinantSNP.pl
#Script to analyze the snps inside the recombinat regions
# if the file is not in your working directory, you have to write the complete path
use warnings;
print "Coordinate Type Reference Allele Strain Strain Allele\n";
open IN, "resultsnplinev2.out" or die; # file 1 y file 2 compared files
open INN, "turkish_segments_tabularv2.txt" or die;
while(<IN>){
if(m/^line\s+(\d+\s+\S+\s+\S+\s+\S+\s+\S+)/){
$lineSNP=$1;
$lineSNP =~m/^(\d+)\s+\S+\s+\S+\s+\S+\s+\S+/;
$SNPcoor=$1;
$lineSNP =~m/^\d+\s+\S+\s+\S+\s+(\S+)\s+\S+/;
$SNPstrain=$1;
}
while(<INN>){
if(m/^(\d+\s+\d+\s+\S+\s+\S+\s+\S+\s+.*)/){
$recline=$1;
$recline =~m/^\d+\s+\d+\s+\S+\s+\S+\s+\S+\s+(.*)/;
$recstrain=$1;
$recline =~m/^(\d+)\s+\d+\s+\S+\s+\S+\s+\S+\s+.*/;
$leftcoor=$1;
$recline =~m/^\d+\s+(\d+)\s+\S+\s+\S+\s+\S+\s+.*/;
$rightcoor=$1;
}
}
if (($leftcoor<=$SNPcoor) && ($SNPcoor<=$rightcoor)){
print "$lineSNP\n";
}elsif ($recstrain eq $SNPstrain){
print "$lineSNP\n";
}
}
i have two files and i want to compare these two
it shoud print those lines which are not in 2nd file
a.txt
1236,AB,0
2345,CD,1
5679,EF,1
9123,AA,1
9223,AA,0
b.txt
1234,AB,0
2345,CD,1
5678,EF,1
9123,AA,0
o/p
1236,AB,0
5679,EF,1
9123,AA,1
9223,AA,0 (6 Replies)
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05-07-2012
perl: comparision of field line by line in two files
