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' -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] <http://learn.perl.org/> <http://learn.perl.org/first-response>