Re^6: how to read input from a file, one section at a time?

in reply to Re^5: how to read input from a file, one section at a time?
in thread how to read input from a file, one section at a time?

In the above written script, how can I make the script to spit out the length of the sequence that is being read? So, after the line printf $out_file "Number of proteins = %d\n\n",$num ; in the above code, I tried - printf $out_file "string length = length($num) ; but nothing happens. What am I doing wrong?

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Re^7: how to read input from a file, one section at a time? by poj (Abbot) on Oct 21, 2019 at 10:35 UTC
You need to provide a value to printf for example `printf $out_file "string length = %d\n",length($num) ;` [download] but that gives you the length of the count value not the sequence. You need to calculate the sequence length before the value is changed by this counting regex `$para =~ s/([A-Z])/ ++$prot{ $1 } /eg;` Try making these changes `# Remove comment line(s) and white space $para =~ s/^\s#.//mg; $para =~ s/\s//g; # add my $seq_length = length($para); # add print "[$para]\n"; # optional . . printf $out_file "Number of proteins = %d\n",$num ; printf $out_file "String length = %d\n\n",$seq_length; # add` [download] poj	[reply] [d/l] [select]

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Re^7: how to read input from a file, one section at a time?
by poj (Abbot) on Oct 21, 2019 at 10:35 UTC

You need to provide a value to printf for example

printf $out_file "string length = %d\n",length($num) ;
[download]

$para =~ s/([A-Z])/ ++$prot{ $1 } /eg;

Try making these changes

    # Remove comment line(s) and white space
    $para =~ s/^\s*#.*//mg;
    $para =~ s/\s//g; # add
    my $seq_length = length($para); # add
    print "[$para]\n"; # optional
    .
    .
    printf $out_file "Number of proteins = %d\n",$num ;
    printf $out_file "String length = %d\n\n",$seq_length; # add
[download]

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