Ganesh Shankar wrote:
>
> Hello all,
Hello,
> I'm starting to learn perl to convert files between different
> bioinformatics programs. I'm aware of bioperl but want to learn some
> basic perl before using those modules.
>
> 1) The script is in the same directory as the input folder, so open
> should be able to find it.
>
> 2) The open input folder part works because I get a I get a list of the
> files.
>
> 3) The whole program worked on a single file, but died when I tried to
> convert it to handle a whole directory as input.
>
> 4) I'm developing on a Windows machine, so I think setting file
> permissions are unnecessary, right?
This problem is described is explained in the documentation for the
readdir function.
perldoc -f readdir
[snip]
If you're planning to filetest the return values
out of a `readdir', you'd better prepend the
directory in question. Otherwise, because we
didn't `chdir' there, it would have been testing
the wrong file.
> Here's the code snippet:
>
> use warnings;
> use strict;
>
> my @files = ();
> my $folder = 'input';
> # Open the input folder
> unless (opendir(FOLDER, $folder)) {
> print "Cannot open folder $folder!\n\n";
> exit;
> }
>
> #read the contents of the folder (files and subfolders)
> @files = readdir(FOLDER);
>
> #Close the folder
> print "\n\n Here are the files in the folder\n";
> #print out the filenames, one per line
> print join( "\n", @files), "\n";
> closedir(FOLDER);
>
> foreach my $seqfilename (@files){
> [EMAIL PROTECTED] = @_;
> $seqfilename = '';
> open (TXTFILE,"<$seqfilename") or die $!;
open (TXTFILE,"<$folder/$seqfilename") or die $!;
> close TXTFILE;
>
> my @seqelements = <TXTFILE>;
>
> ...........goes on from here
> I know the conversion routine works, because it worked
> when I specified a single file.
John
--
use Perl;
program
fulfillment
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