####APPLY localizador ON SINGLE CHROMOSOME FILES####

+ BE CAREFUL!, all the next commands have to be executed using the right root. In this case all of them are referred to files saved at a folder called "realdata". 

+ Check that the internal structure of the fields that form the different registers of the main data files (refseq.gff and snpNih.txt) .

    bash$ head -5 refseq.gff snpNih.txt 
                    ==> refseq.gff <== 
                    chr10 refseq cds 141296 141451 . + . NM_006624 
                    chr10 refseq cds 152600 152761 . + . NM_006624 
                    chr10 refseq cds 168242 168319 . + . NM_006624 
                    chr10 refseq cds 168989 169081 . + . NM_006624 
                    chr10 refseq cds 193975 194062 . + . NM_006624 
                    ==> snpNih.txt <== 
                    585 chr1 33352 33353 9493 
                    585 chr1 34188 34189 708393 
                    585 chr1 34596 34597 1064597 
                    585 chr1 55249 55250 241830 
                    587 chr1 268795 268796 12474 

+ Split the corresponding registers of each chromosome at the main file into different files containing each one only the registers of a single chromosome. The folders "chroms" and "snps" should be created before.
              
    bash$ gawk '{ print $0 > "chroms/"$1".gff" }' refseq.gff 
                   
+ Do the same to the SNPs.

    bash$ gawk '{ print $0 > "snps/"$2".txt" }' snpNih.txt 
    
+ If you want to automate the execution of the "Localitzador" program, you shall use the next command line. 
                   
    bash$ ls -1 chroms/chr* | \ 
          perl -ne 'm/^.*chr(.*)\.gff$/o && print "$1\n";' > chrlist.tbl 
      
      + If you want to use the "for" command form the command-line, you should give a list of items. 

	       bash$ for chr in 1 2 3 4 5 6 7 8 9 10; 
	       do { 
	       echo "### Chromosome: $chr"; 
	       }; 
	       done; 
          
      + However, if you want to read from a file, then you shall use the shell's "while" command.

	       bash$ cat chrlist.tbl | while read chr; 
               do { 
               echo "### Executing Localitzador at chromosome: $chr" 1>&2 ; 
               }; 
               done;

+ You can apply it this way:
 
    bash$ cat chrlist.tbl | while read chr ; 
          do { 
          if [ -e snps/chr${chr}.txt -a -e chroms/chr${chr}.gff ]; 
          then 
          echo "### Executing Localitzador at chromosome: $chr" 1>&2 ; 
          ../localitzador snps/chr${chr}.txt chroms/chr${chr}.gff \ 
          > output/chr${chr}.tbl 2> output/chr${chr}.err ; 
          else 
          echo "### ERROR!!! Check files of chromosome: $chr" 1>&2 ; 
          fi; 
          } ; 
          done ;