Hello Monks, i need your help in searching my two files,in first file(result)frist word of each line represents geneset and rest of the words of that line represents genes represent in that geneset{We can compare it with a draw having number of files in it, i.e geneset is nothing but a draw and files in that draw are genes,I hope you can get my point}each line may contain few hundreds of words and now i need to search each gene(words except first word)in second file(map) and print that line, which has information about genes.


Just have a look at my files
My First file: 
 
#RAW data
chr1q21    na    S100A3    S100A6    HRNR    DRD5P2    .......    
HSA04910_INSULIN_SIGNALING_PATHWAY    na    XRCC5 HRAS    ....
V$YY1_02    na    B3GALT6    DZIP1    RAB1B    SART3    FLJ20309 ..
MORF_EIF3S2    na    HCCS    XRCC3    LDHB    LDHA    OXA1L    RPL14  
+  ...
module_486    na    CYP3A7    C14orf179    JAG2    INTS1    RBM6    ..
CATABOLIC_PROCESS    na    PGD    HNRPD    USE1    RNF217    RNASEH1
#second word can be eleminated

[download]
My second file 
#Map data
XRCC5    SNP_A-1966881    1
EFNA1    SNP_A-1877994    9
HRNR    SNP_A-1919060    2
XRCC5    SNP_A-1966884    1
XRCC5    SNP_A-1966882    1
HRNR    SNP_A-1829030    1

[download]
My output file should look some thing like this: 
chr1q21 
      HRNR    SNP_A-1829030    1
      HRNR    SNP_A-1919060    2
      EFNA1    SNP_A-1877994    9
HSA04910_INSULIN_SIGNALING_PATHWAY
      XRCC5    SNP_A-1966884    1
      XRCC5    SNP_A-1966882    1
      XRCC5    SNP_A-1966881    1
.......

[download]

I tried doing this by storing each line in array and from there getting genes (searching has to be done), but the thing is that i want to know is there any thing much simpler way to do this???

THANKS IN ADVANCE. Have a look at my code:
#Actually is a subroutine which is a part of my other program:
sub parseGeneEntry {  ##purpose of this function is to return everythi
+ng from the second tab onwards (these are the genes)
    $genesList = $_[0];
    #print $genesList."\n";
    #print "STARTING PARSING \n";
    @genes;
    @genes = split(/\t/,$genesList);
    shift(@genes);              ##removes first entry of array
    #print $#genes." ";         ##for debugging only
    shift(@genes);
    #print $#genes." ";
    #@genes;
    $toReturn = "";
    $counter = 0;
    foreach $element(@genes){
        if ($counter == 0){
            $toReturn = $toReturn.$element;
            $counter++;
        }
        else{
            $toReturn = $toReturn."\t".$element;
        }
    }
    #$toReturn = $toReturn."\n";

    #print length($toReturn)." ".$toReturn."\n\n";
    return($toReturn);
}

[download]

In reply to Searching each word of a file by biomonk

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