[BiO BB] A problem about a subroutin in my code

[Felipe Albrecht]

A just single comment, 

why in :
    my @Motif = split(//,'$origin[$y]');     # This is a loop to get
the motif template from origin8
the variable $origin[$y] is under quotes?
The correct isnt : " my @Motif = split(//,$origin[$y]); " ?

Felipe Albrecht

2005/7/29, Alex Zhang <mayagao1999 at yahoo.com>:
> Dear all, 
>   
> Sorry to bother you. I need some help on my code. I have an input file named
> "origin8.txt" which holds 200 short sequences of width 8. My code is to use
> each 
> short sequence from "origin8.txt" as a template to generate 100 short
> sequences of the same
> width and store them in a txt file A. 
> 
> Then the code will read 100 short sequences from the txt file A and 100 long
> sequences of width 200 from a txt file B , and then replaced a substring of
> each long sequence using each short sequence. This code will lead to two txt
> files C and D. File C will hold 100 replaced long sequences. 
> 
> In other words, I want to input "origin8.txt" to get 200 File D. 
> 
> My code can generates 200 File D but each of them holds nothing. So I guess
> the problem is caused by a failure of passing the data to a subroutine named
> "make_file". 
> 
> Can anybody suggest me how to modify that? Thank you very much in advance! 
> 
> Sincerely, 
> 
>      Alex 
> 
>   
> 
>   
> 
>   
> 
> My code: 
> 
>   
> 
> *******************************************************************
> 
>  #!/usr/bin/perl
> use strict;
> use warnings;
> my (@origin, $y);
> my $N_Sequences = 100; 
> my @Alphabet = split(//,'ACGT');      
> my $P_Consensus = 0.85;               # This is the probability of dominant
> letter
> # ====== Globals ==========================
> my @Probabilities;                    # Stores the
> probability of each character
> 
> 
> # ====== Program ==========================
> 
> open (ORIGIN, "< origin8.txt");       # This file holds 200 sequences used
> for motif template
> chomp (@origin = <ORIGIN>);
> close ORIGIN;
> 
> for ($y=0; $y<=$#origin; $y++) {
>   
> 
>      my @Motif = split(//,'$origin[$y]');     # This is a loop to get the
> motif template from origin8
>     open (OUT_NORM, ">short_sequences8_[$y].txt") or die "Unable to open
> file :$!";
>         for (my $i=0; $i < $N_Sequences; $i++) {
>             for (my $j=0; $j < scalar(@Motif); $j++) {
>                  loadConsensusCharacter($Motif[$j]);    
>                  addNoiseToDistribution();             
>                  convertToIntervals();
>                  print OUT_NORM (getRandomCharacter(rand(1.0)));
>                                                      }
>             print OUT_NORM "\n";
>             make_files();
>                                                }
>                               }
> 
> exit();
> 
> # ====== Subroutines =======================
> #
> sub loadConsensusCharacter {
>     my ($char) = @_;
>     my $Found = 'FALSE';
> 
>     for (my $i=0; $i < scalar(@Alphabet); $i++) {
>         if ( $char eq $Alphabet[$i]) {
>             $Probabilities[$i] = 1.0;
>             $Found = 'TRUE';
>         } else {
>             $Probabilities[$i] = 0.0;
>         }
>     }
>     if ($Found eq 'FALSE') {
>     die("Panic: Motif-Character\"$char\" was not found in Alphabet.
> Aborting.\n");
>     }
> 
> return();
> }
> 
> # ==========================================
> sub addNoiseToDistribution {
> 
> 
>     my $P_NonConsensus = ( 1.0-$P_Consensus) / (scalar(@Alphabet) - 1);
> 
>     for (my $i=0; $i < scalar(@Probabilities); $i++) {
>         if ( $Probabilit ies[$i] == 1.0 ) {     
>             $Probabilities[$i] = $P_Consensus;
>         } else {
>             $Probabilities[$i] = $P_NonConsensus;
>         }
>     }
> 
>     return();
> }
> 
> # ==========================================
> sub convertToIntervals {
> 
>     my $Sum = 0;
> 
>     for (my $i=1; $i < scalar(@Probabilities); $i++) {
>         $Probabilities[$i] += $Probabilities[$i-1];
>     }
> 
>     return();
> }
> 
> # ==========================================
> sub getRandomCharacter {
> 
>     my ($RandomNumber) = @_;
>    & nbsp;my $i=0;
>     for ($i=0; $i < scalar(@Probabilities); $i++) {
>         if ($Probabilities[$i] > $RandomNumber) { last; }
>     }
> 
>     return($Alphabet[$i]);
> }
> 
> # ==========================================
> sub make_files {
> my (@short, @long,$x,$r, $output_norm);
> 
> open (SHORT, "< short_sequences8_[$y].txt");
> chomp (@short = <SHORT>);
> close SHORT;
> 
> open (LONG, "< long_sequences.txt");
> chomp (@long = <LONG>);
> close LONG;
> 
> open (OUT_INITIAL,  "> output8_[$y]1.txt");
> open (OUT_REPLACED, "> output8_[$y]2.txt");
> 
> for ($x=0; $x<=$#short; $x++) {
>   $r=2;
>   print OUT_INITIAL ">SeqName$x\n$long[$x]\n";
>   print OUT_REPLACED "SeqName$x\n" . substr($long[$x], $r, length
> $short[$x]) . "\n";}
> 
> 
> close OUT_INITIAL;
> close OUT_REPLACED;
> 
> } 
> 
> *******************************************************************
> 
>   
> 
>   
> 
> Input file "origin8.txt" holds 200 sequences as: 
> 
>   
> 
>  TTTATAAT
> TGTCAATG
> CGTTGATG
> CGTCCTAG
> GGCTTCCA
> ATTAGCCT
> GTCCTGAT
> TGTAAATC
> CGCTTATT
> TTGACATA
> CCTGATAT
> ATGAATCG
> CGTCCGAT
> TGGCCCAT
> ATCCTGAT
> TGCCCATT
> CCCTAACT
> AAAAAAAA
> TTTTTTTT
> CCCCCCCC
> GGGGGGGG
> AAAAAAAT
> AAAAAAAG
> AAAAAAAC
> AAAAAACC
> AAAAAATT
> AAAAAAGG
> AAAAAACT
> AAAAAACG
> AAAAAACA
> AAAAACAA
> AAAACAAA
> AAACAAAA
> AACAAAAA
> ACAAAAAA
> CAAAAAAA
> AAAAAATA
> AAAAATAA
> AAAATAAA
> AAATAAAA
> AATAAAAA
> ATAAAAAA
> TAAAAAAA
> AAAAAAGA
> AAAAAGAA
> AAAAGAAA
> AAAGAAAA
> AAGAAAAA
> AGAAAAAA
> GAAAAAAA
> AAAACCAA
> AACCAAAA
> CCAAAAAA
> AAAATTAA
> AATTAAAA
> TTAAAAAA
> AAAAACCC
> AAAACCCA
> AAACCCAA
> AACCCAAA
> ACCCAAAA
> CCCAAAAA
> AAAAATTT
> AAAATTTA
> AAATTTAA
> AATTTAAA
> ATTTAAAA
> TTTAAAAA
> AAAAAGGG
> AAAAGGGA
> AAAGGGAA
> AAGGGAAA
> AGGGAAAA
> GGGAAAAA
> AAAACCCC
> AAACCCCA
> AACCCCAA
> ACCCCAAA
> CCCCAAAA
> AAAATTTT
> AAATTTTA
> AATTTTA A
> ATTTTAAA
> TTTTAAAA
> AAAAGGGG
> AAAGGGGA
> AAGGGGAA
> AGGGGAAA
> GGGGAAAA
> AAACCCCC
> AACCCCCA
> ACCCCCAA
> CCCCCAAA
> AAATTTTT
> AATTTTTA
> ATTTTTAA
> TTTTTAAA
> AAAGGGGG
> AAGGGGGA
> AGGGGGAA
> GGGGGAAA
> AAGGGGGG
> AGGGGGGA
> GGGGGGAA
> AACCCCCC
> ACCCCCCA
> CCCCCCAA
> AATTTTTT
> ATTTTTTA
> TTTTTTAA
> ATTTTTTT
> TTTTTTTA
> ACCCCCCC
> CCCCCCCA
> AGGGGGGG
> GGGGGGGA
> ATTTTTTT
> TTTTTTTA
> ATAAAATA
> AATAAATA
> AAATAATA
> AAAATATA
> ACAAAACA
> AACAAACA
> AAACAACA
> AAAACACA
> AGAAAAGA
> AAGAAAGA
> AAAGAAGA
> AAAAGAGA
> ATAAAAGA
> ATAAAACA
> AGAAAATA
> AGAAAACA
> ACAAAAGA
> ACAAAATA
> ATTAAATA
> AATTAATA
> AAATTATA
> ACCAAACA
> AACCAACA
> AAACCACA
> AGGAAAGA
> AAGGAAGA
> AAAGGAGA
> ATTTAATA
> AATTTATA
> ACCCAACA
> AACCCACA
> AGGGAAGA
> AAGGGAGA
> ATTTAACA
> ATTTAAGA
> AATTTACA
> AATTTAGA
> ACCCAATA
> ACCCAAGA
> AACCCATA
> AACCCAGA
> AGGGAACA
> AGGGAATA
> AAGGGATA
> AAGGGACA
> TTGGGACA
> C CGGGACA< BR>AGAAGGGA
> TGCCCATA
> TAAAAAAT
> TGCCTATA
> CCGTAGTC
> ACTTGACT
> CTGATCCC
> TGTGACTA
> CCTGATCC
> CCTGAACC
> TGATCACG
> GGGTAACC
> CTTTTGAA
> TTGTATGA
> CCTGATAA
> CTGGTTAG
> CCCCGACC
> TTGGGGAC
> GGTTTGAC
> GCTTAGAC
> GTTACACC
> TTGTACCA
> TGGTACCA
> CCGTACAT
> CCCTTGCC
> GTGTTGGT
> ATCGATCG
> ACGTACGT
> TCAGTCAG
> GCTATACG
> GTCCATAC
> CCGTCCGT
> ATATATCC
> GTGTCCCC 
> 
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