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'
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
$annotation_filename = $ARGV[0];
my $protein_filename = "$ARGV[1]";
#input parameter;
my $domain_param = "$ARGV[2]";
print "domain_param->".$domain_param."\n";
#open annotation file and assign file handle
open(ANN,$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;
my $proteinID = $ANN[0];
my $domain = $ANN[1];
my $start = $ANN[2];
my $stop = $ANN[3];
#call up the getseq program
$seq = `getseq.pl $start $stop $proteinID $protein_filename`;
#print the identifier and then the sequence
print ">".$proteinID." ".$domain_param." ".$domain." ".$start."
".$stop."\n".$seq;
}
close(ANN);
and the getseq.pl program that gets pulled up by line 29 is:
>(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'
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