Im running a script where it should read a 4 line txt which will point it to the input files. But its not. Im getting the:
WARNING there is no vector and splice information in the assignment file for the library
error as is at the bottom, but was confused by the way its checking the assignment file. Its definitely reading the .txt in the first place, and the paths in the .txt are correct, but im not perl-skilled enough (yet!) to be certain the script is right. so here we go!
Its got loads of $'s all through the 2100 line script and cant really paste all that but its the reading the $assignments (which is the .txt as defined earlier) that im concerned with
The script: 
       # Now we can run lucy several times, one for each library
        my $lib;my $in_s; my $in_q; my $vec; my $spli; my $out_s; my $
+out_q;
        for ($i=0;$i<$num_libraries;$i++){
                if ($success){  # if something went wrong we should st
+op
                        $lib=$libraries[$i];
                        $in_s=$in_seq."$separator".$libraries[$i];
                        $in_q=$in_qual."$separator".$libraries[$i];
                        my $num_lib=position1(@{$$assignments{librarie
+s}},$lib);
                        $out_s=$out_seq."$separator".$libraries[$i];
                        $out_q=$out_qual."$separator".$libraries[$i];
                        #it could be libraries without vector and spli
+ce site information, in that case we just copy 
                        #the input file to the output file
                        if ($num_lib){
                                $vec=${$$assignments{vector_files}}[$n
+um_lib-1];
                                $spli=${$$assignments{splice_files}}[$
+num_lib-1];
                                $success=run_lucy($config,$lib,$in_s,$
+in_q,$vec,$spli,$out_s,$out_q,$log,$bin_lucy);
                        }else{
                                print localtime().": WARNING there is 
+no vector and splice information in the assignment file for the libra
+ry $lib\n";
                                system ("ln -sf $in_s $out_s\n");
                                system ("ln -sf $in_q $out_q\n");
                                system ('echo "'.$lib.'" >> '.$not_luc
+y);
                        }
                }
        }

[download]

The assignments.txt (I have a definitive structure to adhere to and this is definitely right): 
assignment
library: gammarus
vector file: /home/sbi6dap/est2uni/data/vector.fasta
vector splice site file: /home/sbi6dap/est2uni/data/splice.fasta

[download]

Thanks for looking guys n galls

In reply to why is my pm not finding the correct files by tangledupinperl

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