5S RNA

T-stretch-extraction.txt

#!/usr/bin/perl

use strict;

if
(($ARGV[0] eq "-h") || ($ARGV[0] eq "--h") || ($ARGV[0] eq
"-

help"
)|| ($ARGV[0] eq "--help")|| (!defined($ARGV[3])))

{

print
"# Obtaining reads covering a part of the reference

sequence

# Argument
0 : reference

# Argument
1 : path to the fasta files for reads mapped on

the
reference

# Argument
2 : beginning of comparaison

# Argument
3 : end comparaison

# Argument
4 : end of the position

# Argument
5 : beginning of position

# Argument
6 : % of difference\n";

die("\n");

}

my
%hash_nuc_ref;

open(F1,"$ARGV[0]")
or die ("ARG fichier $ARGV[0] "); # Obtaining

the
positions of interest of the reference

while(my
$ligne= <F1>){

chomp($ligne);

my
$position;

if
(!($ligne=~/^>/)) {

my
@split_seq= split ("",$ligne);

for(my $i=0;$i<scalar(@split_seq);$i++){

$hash_nuc_ref{$i}=$split_seq[$i];

}

}

}

close F1;

my
%hash_motif_sans_mut;

my
%hash_motif;

my
$position;

open(F1,"$ARGV[1]")
or die ("ARG fichier $ARGV[0] "); #Reading of

the file
containing the reads mapped on the zone of interest

while(my
$ligne= <F1>){

chomp($ligne);

my
$nom_seq;

if ($ligne=~/^>/) {

$nom_seq=$ligne;

my
@split_info_seq= split('\s',"$ligne");

$position =
$split_info_seq[1];

$position=~
s/pos=//;

}

else{

if($ARGV[2]
>= $position ){

my
$limit=$ARGV[3]-$position;

my
$compte_mutation=0;

my
@split_info_seq= split("","$ligne");

my
$i=$ARGV[2]-$position;

for(
$i;$i<=$limit;$i++){

my
$temp=$position+$i-1;

if
($split_info_seq[$i] ne

$hash_nuc_ref{$temp}){

$compte_mutation++;

}

}

if((
$compte_mutation <= $ARGV[6])){

my
$longeur= $ARGV[4]-$ARGV[5];

my $start
=$ARGV[5]-$position;

my $coupe =
substr($ligne,$start,

$longeur);

$hash_motif{$coupe}

{$compte_mutation}++;

}

}

}

}

close F1;

my
$longueur_a_reagarder = $ARGV[4]-$ARGV[5];

close F1;

my
%hash_fichier;

open(F1
,">>motif_clef_$ARGV[1]\_$ARGV[5]\_$ARGV[4]") ; #

Extraction
of the motifs adjacent to the interest zone of the

reference

foreach my
$clef (keys(%hash_motif)){

foreach(keys
%{$hash_motif{$clef}}){

my
$longeur_clef = length($clef);

if
($longeur_clef == $longueur_a_reagarder){

print F1
"$clef\t$hash_motif{$clef}{$_}\t$_\n";

}

}

}

`sort -k2nr
motif_clef_$ARGV[1]\_$ARGV[5]\_$ARGV[4] >

motif_clef_$ARGV[1]\_$ARGV[5]\_$ARGV[4]_sorted`;
# Sorting motifs by

descending order

`rm
motif_clef_$ARGV[1]\_$ARGV[5]\_$ARGV[4]`;

when I run this perl script, the following error occurred, would you tell me how to deal with them? or tell me in detailed how to configure this script parameters. Thanks
perl ../../../bin/T-stretch-extraction.pl
syntax error at ../../../bin/T-stretch-extraction.pl line 59, near "){"
Global symbol "$ligne" requires explicit package name at ../../../bin/T-stretch-extraction.pl line 61.
syntax error at ../../../bin/T-stretch-extraction.pl line 80, near "}"
syntax error at ../../../bin/T-stretch-extraction.pl line 100, near "){"
syntax error at ../../../bin/T-stretch-extraction.pl line 180, near "}"
syntax error at ../../../bin/T-stretch-extraction.pl line 201, near "$clef ("
Global symbol "$clef" requires explicit package name at ../../../bin/T-stretch-extraction.pl line 204.
syntax error at ../../../bin/T-stretch-extraction.pl line 217, near "}"
Execution of ../../../bin/T-stretch-extraction.pl aborted due to compilation errors.