$ARGV[0] not $ARG[0]
You have defined $sbjct_scr, yet are attempting to use $sbjct_srs
You have defined %query_counts, yet are attempting to use %query_conunts
You are attempting to use the while() command, yet are calling it wile...
Typos and code don't mix. Ever.
Learn to proof read your e-mails as well, it will make you a better coder.
Ever noticed how few people that post solutions here have typos in their
e-mails? I don't think it's coincidence.
John
-----Original Message-----
From: webmaster [mailto:[EMAIL PROTECTED]]
Sent: 21 August 2001 14:48
To: perl
Subject: inquiry
what does
Global symbol "@ARG" requires explicit package name at testbio1.pl line 4.
Global symbol "$sbjct_scr" requires explicit package name at testbio1.pl
line 29
.
Global symbol "%query_conunts" requires explicit package name at
testbio1.pl lin
e 46.
Global symbol "$sbjct_srs" requires explicit package name at testbio1.pl
line 48
mean?
and why on this lines I am getting a comp error...
{
while ($query_src=~ /$pattern/g)
{
$query_conunts{$pattern}++;
}
wile ($sbjct_srs=~ /$pattern/g)
{
$sbjct_counts{ $pattern }++;
}
}
the whole wource code is here:
#!/usr/bin/perl
use strict;
my $REPORT_FILE="report.txt";
my $blast_file=$ARG[0]||'blast.dat';
unless (-e $blast_file)
{
die "$0: error:missing file: $blast_file";
}
#slurp all the seqs in to the scalar
my ($query_src,$sbjct_src);
#open the blast data file and end prg (DIE) if we can't find it open(IN,
#$blast_file) or die
open (IN, $blast_file) or die "$0: ERROR: $blast_file: $!";
#go trought the blast file line by line, concat all the query and sbj seqs
while (my $line=<IN>)
{
chomp $line;
print "processing line $. \n";
open (IN, $blast_file) or die "$0: ERROR: $blast_file: $!";
my @words=split /\s+/, $line;
if ($line=~ /^Query/)
{
$query_src .=$words[2];
}
elsif ($line =~ /^Sbjct/)
{
$sbjct_scr .=$words[2];
}
}
#next line closes the blast file
close IN;
#analysis part
my @patterns=('gtccca', 'gcaatg', 'cagct', 'tcggga', '-');
#find the patterns and sotore them in to the hashes
my (%query_counts, %sbjct_counts);
#search and store
foreach my $pattern (@patterns)
{
while ($query_src=~ /$pattern/g)
{
$query_conunts{$pattern}++;
}
wile ($sbjct_srs=~ /$pattern/g)
{
$sbjct_counts{ $pattern }++;
}
}
#create an empty report fele
open (OUT, ">$REPORT_FILE" or die "$0: ERROR: cant write $REPORT_FILE";
#print the header of the report file
print OUT "Seq report \n",
"lo que sea ", scalar localtime, "\n",
"\nNOTEdfaasafsaada \n",
"total lenght of the query dseq:",
lenght $query_src, " characters \n", "results for 'Query' :\n";
#print the query mathces
foreach (my $key (sort @patterns)
{
print OUT "\t '$key ' seen $query_counts{$key}\n";
}
print OUT "\nTOTAL lenght of 'Sbjct' seq: ",
lenght $sbjct_src, "cahracters\n", "resoults for 'Sbjct':\n";
#print the sbjct mathces
foreach my $key (sort @patterns)
{
print OUT "\t'$key' seen $sbjct_counts{$key}\n";
}
close OUT;
__END__
cheers
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