Help: Count characters

[Amy Lee]

Hello,

I make a small perl script to count how many sequences in a fasta
formation file. In fasta formation file every sequence starts with a ">",
so I can count how many ">" in a file.

There's my code:

if (@ARGV != 0)
{
foreach $file (@ARGV)
{
unless (-e $file)
{
print "***Error: $file dose not exist.\n";
next;
}
unless (open $FILE_IN, '<', $file)
{
print "***Error: Cannot read $file.\n";
next;
}
$full_size = (stat($file))[7];
while (<$FILE_IN>)
{
s/>//g;
}
$mod_size = (stat($FILE_IN))[7];
$num = $full_size-$mod_size;
close $FILE_IN;
print "$file ==> $num seq.\n"
}
}

However, when I run this script, it always shows "0 seqs". I don't know
what happened. And is there any better way to count ">"?

Thank you very much~

Regards,

Amy Lee

 

[Ron Bergin]

Hello,

I make a small perl script to count how many sequences in a fasta
formation file. In fasta formation file every sequence starts with a ">",
so I can count how many ">" in a file.

There's my code:

if (@ARGV != 0)
{
foreach $file (@ARGV)
{
unless (-e $file)
{
print "***Error: $file dose not exist.\n";
next;
}
unless (open $FILE_IN, '<', $file)
{
print "***Error: Cannot read $file.\n";
next;
}
$full_size = (stat($file))[7];
while (<$FILE_IN>)
{
s/>//g;
}

You're not maintaining a count of the number of substitutions.

$mod_size = (stat($FILE_IN))[7];
$num = $full_size-$mod_size;
close $FILE_IN;
print "$file ==> $num seq.\n"
}

Since the file was opened in read only mode, its size will not have
been changed.

}

However, when I run this script, it always shows "0 seqs". I don't know
what happened. And is there any better way to count ">"?

perldoc -q "how do I count the number of lines in a file"