Kathryn E. Bushley wrote:
> Hello,
Hello,
> Maybe not a perl question but I'm trying to run my perl program below and
> am getting the following error which I'm fairly certain is from the linux
> system:
>
>>(BC1G_02948.1) AMP 1/1 144 522
> sh: -c: line 0: syntax error near unexpected token `('
> sh: -c: line 0: `getseq.pl 56 374 (BC1G_03519.1) Botrytis_annotations'
perldoc -q "How do I tell the difference between errors from the shell and perl"
Also search for "syntax error" in perldiag.
> The first line of this message is what line 29 of the main program below
> is supposed to print out but then it is also supposed to print dna
> sequence data but instead prints the error. If anyone has any
> suggestions, please help.
>
>
> The main program is:
>
> #!/usr/bin/perl -w
use warnings;
use strict;
> $annotation_filename = $ARGV[0];
> my $protein_filename = "$ARGV[1]";
$ARGV[1] is already a string, why are you putting quotes around it?
> #input parameter;
> my $domain_param = "$ARGV[2]";
Again, why the quotes?
perldoc -q quoting
> print "domain_param->".$domain_param."\n";
Why concatenation instead of interpolation here?
> #open annotation file and assign file handle
> open(ANN,$annotation_filename)|| die "can't open annotation file: $!\n";
>
> #initialize array and store data in the array
> my(@ANN);
> while (<ANN>){
> # split the line on spaces and put fields into array @ANN
> @ANN = split(/\s+/);# print join(",", @ANN), "\n";
> #get rid of carriage returns
> chomp;
Why do you think that there is a carriage return to get rid of and why do you
think that chomp() will get rid of it?
> my $proteinID = $ANN[0];
> my $domain = $ANN[1];
> my $start = $ANN[2];
> my $stop = $ANN[3];
What is the point of using the @ANN array?
my ( $proteinID, $domain, $start, $stop ) = split;
John
--
use Perl;
program
fulfillment
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