Re^3: I don't understand error message

So, my problem may be solved with while loops?

If you are interested in looping through all "next" results, that would be a good start.

CountZero

A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James

Comment on Re^3: I don't understand error message

Replies are listed 'Best First'.
Re^4: I don't understand error message by lomSpace (Scribe) on Jun 17, 2009 at 16:00 UTC
I should not have to use a loop. I have tested the program locally and it works. Read more... (2 kB) When I use it as a subroutine in a larger program is when I run into trouble. I have checked and it is reading in the file. Any ideas?	[reply] [d/l]
Re^5: I don't understand error message by CountZero (Bishop) on Jun 17, 2009 at 18:21 UTC
You have this in your standalone program: `my $in = new Bio::SearchIO(-format => 'blast', -file => $maid_dir."/".$maid."aln_hu.aln", -report_type => 'blastn');` [download] But you have this in your sub-routine: `my $in = new Bio::SearchIO(-format => 'blast', -file => ">".$maid_dir."\\".$maid."aln_hu.aln", -report_type => 'blastn');` [download] Could it be that the "`>`" stops Bio::SearchIO from reading/parsing the file? CountZero A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James	[reply] [d/l] [select]