Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Need help comparing Base Pairs within PERL
Top Forums Shell Programming and Scripting Need help comparing Base Pairs within PERL Post 302652701 by ddreggors on Thursday 7th of June 2012 02:34:45 PM
Old 06-07-2012
make sure that "file1.txt" is changed to point to a files that has 89 columns.

I tested it and it works fine here with 89 columns, given column 1 is the id, column 6 is the Chr data, column 88 is the geno type, and column 89 is the reference.


I added the reference characters to the end of the file I have so that it is at column 89 and I get these results:

Code:
1> ./test5.pl     
4       Exonic  AA
5       Intronic        GC


Here is the code in test5.pl:

Code:
> cat test5.pl  
#!/usr/bin/perl

use strict;
use warnings;
my (@data, $row, @dataline);
open(FILE1,"<","file3.txt") or die $!; @data = <FILE1>; close(FILE1);
foreach $row (@data) {
        next unless $row =~ /^\d/;
        @dataline = split('\s',$row);
        next unless $dataline[87] =~ /$dataline[88]/i;
        print $dataline[0] . "\t" . $dataline[5] . "\t" . $dataline[87] . "\n";
}

Notice that mine says "file3.txt" since I joined "file1.txt" and "file2.txt".

A sample line from that file is:

Code:
> tail -n1 file3.txt 
5 11870 8261 18422 24259 Intronic 15495 23051 4827 26004 2011 30461 17052 20343 5506 815 32209 27172 2468 27703 29545 31868 21221 10972 3873 683 16202 3724 27384 30299 12204 16980 9401 20465 2634 892 21801 18130 23943 26629 11366 25954 24322 28419 13529 29828 29234 12970 24232 31703 7905 21009 30803 29126 31981 1909 29809 15415 5633 24425 12946 17837 8637 22348 5534 11272 23240 27336 29402 14416 21197 8000 7602 12751 3651 21132 9811 118 1334 1276 31821 9240 22285 29856 5598 21499 31765 GC G

This User Gave Thanks to ddreggors For This Post:
drossy
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

perl search and replace pairs

Hello all im facing some kind of problem i have this string : functionA() $" "$ functionB("arg1") $" = "$ i will like to replace all the pairs of opening and closing "$" to be something like that functionA() <#" "#> functionB("arg1") <#" = "#> i cant of course do is with simple ... (1 Reply)
Discussion started by: umen
1 Replies

2. Shell Programming and Scripting

Comparing Variables in Perl

Hi. I have three arrays. @a=('AB','CD','EF'); @b=('AB,'DG',HK'); @c=('DD','TT','MM'); I want to compare the elements of the first two array and if they match then so some substition. I tried using the if statement using the scalar value of the array but its not giving me any output. ... (7 Replies)
Discussion started by: kamitsin
7 Replies

3. Shell Programming and Scripting

Comparing arrays in perl

Hi all, I am trying to compare two arrays in perl using the following code. foreach $item (@arrayA){ push(@arrayC, $item) unless grep(/$item/, @arrayB); ... (1 Reply)
Discussion started by: chriss_58
1 Replies

4. Shell Programming and Scripting

PERL name value pairs substituions

I have a main file with variable tokens like this: name: File1 =========== Destination/Company=@deploy.company@ Destination/Environment=@deploy.env@ Destination/Location=@deploy.location@ Destination/Domain=@deploy.location@ MIG_GatewayAddresses=@deploy.gwaddress@ MIG_URL=@deploy.mig_url@... (1 Reply)
Discussion started by: uandme2k2
1 Replies

5. Shell Programming and Scripting

comparing list values in Perl

Hi, I have tab separated list: KB0005 1019 T IFVATVPVI 0.691 PKC YES KB0005 1036 T YFLQTSQQL 0.785 PKC YES KB0005 1037 S FLQTSQQLK 0.585 DNAPK YES KB0005 508 S ENIISGVSY 0.507 cdc2 YES KB0005 511 S ... (1 Reply)
Discussion started by: karla
1 Replies

6. Shell Programming and Scripting

PERL: simple comparing arrays question

Hi there, i have been trying different methods and i wonder if somebody could explain to me how i would perform a comparison on two arrays for example my @array1 = ("gary" ,"peter", "paul"); my @array2 = ("gary" ,"peter", "joe"); I have two arrays above, and i want to something like this... (5 Replies)
Discussion started by: hcclnoodles
5 Replies

7. Shell Programming and Scripting

Perl: Comparing to two files and displaying the differences

Hi, I'm new to perl and i have to write a perl script that will compare to log/txt files and display the differences. Unfortunately I'm not allowed to use any complied binaries or applications like diff or comm. So far i've across a code like this: use strict; use warnings; my $list1;... (2 Replies)
Discussion started by: dont_be_hasty
2 Replies

8. Shell Programming and Scripting

Perl: Need help comparing huge files

What do i need to do have the below perl program load 205 million record files into the hash. It currently works on smaller files, but not working on huge files. Any idea what i need to do to modify to make it work with huge files: #!/usr/bin/perl $ot1=$ARGV; $ot2=$ARGV; open(mfileot1,... (12 Replies)
Discussion started by: mrn6430
12 Replies

9. Shell Programming and Scripting

Need help in comparing two files using shell or Perl

I have these two file that I am trying to compare using shell arrays. I need to find out the changed or the missing enteries from File2. For example. The line "f nsd1" in file2 is different from file1 and the line "g nsd6" is missing from file2. I dont want to use "for loop" because my files... (2 Replies)
Discussion started by: sags007_99
2 Replies

10. Shell Programming and Scripting

Perl for comparing numbers from previous lines in a file?

Hi everyone I have a question for you, as I am trying to learn more about Perl and work with some weather data. I have an ascii file (shown below) that has 10 lines with different columns. What I would like is have Perl find an "anomalous" value by comparing a field with the values from the last... (2 Replies)
Discussion started by: lucshi09
2 Replies

LEARN ABOUT REDHAT

psc

PSC(1)							      General Commands Manual							    PSC(1)

NAME

       psc - prepare sc files

SYNOPSIS

       psc [-fLkrSPv] [-s cell] [-R n] [-C n] [-n n] [-d c]

DESCRIPTION

       Psc  is used to prepare data for input to the spreadsheet calculator sc(1).  It accepts normal ascii data on standard input.  Standard out-
       put is a sc file.  With no options, psc starts the spreadsheet in cell A0.  Strings are right justified.  All data on a line is entered	on
       the  same row; new input lines cause the output row number to increment by one.	The default delimiters are tab and space.  The column for-
       mats are set to one larger than the number of columns required to hold the largest value in the column.

OPTIONS

       -f     Omit column width calculations.  This option is for preparing data to be merged with an existing spreadsheet.  If the option is  not
	      specified, the column widths calculated for the data read by psc will override those already set in the existing spreadsheet.

       -L     Left justify strings.

       -k     Keep  all  delimiters.   This  option  causes the output cell to change on each new delimiter encountered in the input stream.   The
	      default action is to condense multiple delimiters to one, so that the cell only changes once per input data item.

       -r     Output the data by row first then column.  For input consisting of a single column, this option will result in  output  of  one  row
	      with multiple columns instead of a single column spreadsheet.

       -s cell
	      Start  the  top  left  corner  of the spreadsheet in cell.  For example, -s B33 will arrange the output data so that the spreadsheet
	      starts in column B, row 33.

       -R n   Increment by n on each new output row.

       -C n   Increment by n on each new output column.

       -n n   Output n rows before advancing to the next column.  This option is used when the input is  arranged  in  a  single  column  and  the
	      spreadsheet is to have multiple columns, each of which is to be length n.

       -d c   Use the single character c as the delimiter between input fields.

       -P     Plain numbers only.  A field is a number only when there is no imbedded [-+eE].

       -S     All numbers are strings.

       -v     Print the version of psc

SEE ALSO

       sc(1)

AUTHOR

       Robert Bond

PSC 7.16							 19 September 2002							    PSC(1)
All times are GMT -4. The time now is 12:38 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy