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Top Forums Shell Programming and Scripting Script to read file and extract data by matching pattern Post 302528747 by pravin27 on Wednesday 8th of June 2011 12:50:34 AM
Old 06-08-2011
I am really confused with your last requirement, I have made the changes in the script as per my understanding.I hope this will resolve your issue.
Code:
#!/usr/bin/perl

sub seen_files {
        $filename=shift;
        @seenfld=split(" ",$seen{$filename});
        for($k=1;$k<=$#seenfld;$k++){
                @res=grep(/$seenfld[$k]/,@old_array);
                unless (scalar @res > 0 ) {
                        #print "FILENAME - $seenfld[$k]\n";
                        system("find /data -name $seenfld[$k]");
                        @old_array=(@old_array,$seenfld[$k]);
                }
        }
}

($file1,$file2)=($ARGV[0],$ARGV[1]);
open (FH1,"<","$file1") or die "Fail- $!\n";
open (FH2,"<","$file2") or die "Fail- $!\n";

while (<FH2>) {
        chomp;
        if(/^\//) {
                @flds=split(/\//);
                $filename=$flds[$#flds];
                if($filename=~/(.+?)[\.~](.+?)/) { $filename=$1;} #print $filename,"\n"; }
                $lookup{$filename}++;
        }
}
open (FH3,"<","$file1") or die "Fail- $!\n";
while (<FH3>) {
        chomp;
        if(/^(.+?):/) {
                @fld=split(/,/,substr($_,index($_,":")+1));
                while (<@fld>) {
                        @fld_new=(@fld_new,((split(/\~/))[1]));
                }
                $seen{$1}="@fld_new";
        }
}
while (<FH1>) {
chomp;
if(/^(.+?):/) {
        $fname=((split(/\~/,$1))[1]);
        if ( exists $lookup{$fname}) {
                @flds=split(/,/,substr($_,index($_,":")+1));
                while (<@flds>) {
                        @flds_new=(@flds_new,((split(/\~/))[1]));
                }

                for($i=0;$i<=$#flds_new;$i++) {
                @res=grep(/$flds_new[$i]/,@old_array);
                unless (scalar @res > 0 ) {
                        #print "FILENAME - $flds_new[$i]\n";
                        system("find /data -name $flds_new[$i]");
                        @old_array=(@old_array,$flds_new[$i]);
                        if (exists $seen{$flds_new[$i]} &&  $i > 0 ) {
                                seen_files($flds_new[$i]);
                                @seenfld_old=@seenfld;
                                for($p=1;$p<=$#seenfld_old;$p++){seen_files($seenfld_old[$p]);}
                        }
                        }
                   }
           }

        }
}
close(FH1);
close(FH2);
close(FH3);

 

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BP_SEARCH2TRIBE(1p)					User Contributed Perl Documentation				       BP_SEARCH2TRIBE(1p)

NAME
search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix SYNOPSIS
Usage: search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1 file2 .. DESCRIPTION
This script is probably too slow for most people's uses. It is better to use something like scripts/searchio/fastam9_to_table, -m 9 output from BLAST, or the blast2table from the BLAST O'Reilly book to get a tabular output from these programs and then feed the table into MCL with the mcxdeblast script and the --m9 option. This script will turn a protein Search report (BLASTP, FASTP, SSEARCH) into a Markov Matrix for TribeMCL clustering. The options are: -o filename - the output filename [default STDOUT] -f format - search result format (blast, fasta) (ssearch is fasta format). default is blast. -w or --weight VALUE - Change the default weight for E(0.0) hits to VALUE (default=200 (i.e. 1e-200) ) -h - this help menu Additionally specify the filenames you want to process on the command-line. If no files are specified then STDIN input is assumed. You specify this by doing: search2tribe < file1 file2 file3 AUTHOR
Jason Stajich, jason-at-bioperl-dot-org perl v5.14.2 2012-03-02 BP_SEARCH2TRIBE(1p)
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