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Re: appending to a file

by Nkuvu (Priest)
on Mar 19, 2009 at 16:41 UTC ( #751784=note: print w/ replies, xml ) Need Help??


in reply to appending to a file

I'd start with error checking. (added: Fletch is more accurate than I am on the functions you'll want to check errors on, consider adding similar error checking to the functions mentioned):
open( my $in, ">>".$seq_dir."/".$fa) or die "Unable to open $seq_dir/$fa for append: $!\n";
Obviously if the file is read only or the path isn't parsed correctly, the open call will fail and you won't be able to write to the file.


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Re^2: appending to a file
by lomSpace (Scribe) on Mar 19, 2009 at 17:05 UTC
    The file test has not failed

      The -e checks for the existence of a file, not writability. So the file test in question won't guarantee that your file can be opened for appending.

        The file is open for appending. I am writing to it.
        13132HU.fa,13132HD.fa,13132Ltvec_small.FA 13132HU.fa,13132HD.fa,13132Ltvec_small.FA 13132HU.fa,13132HD.fa,13132Ltvec_small.FA
        Those strings are being appended to the file.
        I want the contents of these files, not the strings
        of the file names.
Re^2: appending to a file
by lomSpace (Scribe) on Mar 19, 2009 at 17:19 UTC
    I can append to the file, but am having trouble accessing the file contents. I am
    appending the file names not the contents. Example
    13132HU.fa,13132HD.fa,13132Ltvec_small.FA 13132HU.fa,13132HD.fa,13132Ltvec_small.FA 13132HU.fa,13132HD.fa,13132Ltvec_small.FA 13132HU.fa,13132HD.fa,13132Ltvec_small.FA
    This is what is being appended to the file. I want the contents
    of those files to be appended to the file.
    Any ideas?

      I can't see how that's possible. The only thing you append to the file is a newline.

      Here's a guess on what you're really looking for. You want to append the three files to the $fa file. You'll need to open each in turn, read from it, then print the contents to the $fa file (those variable names could really be more descriptive, by the way).

      So I think what you want is something like this:

      #!/usr/bin/perl use strict; use Data::Dumper; use File::Glob ':glob'; my @dirs = glob("C:/Documents and Settings/mydir/Desktop/KOMP/*"); foreach my $maid_dir (@dirs) { # Combined the first two conditionals to reduce indentation if (-d $maid_dir and $maid_dir=~m%\d+\s[A-Z]%){ # match the dir na +me my $seq_dir = $maid_dir."/sequencing/"; chdir ($maid_dir) or die "Can't chdir to $maid_dir: $!\n"; next if (-M $seq_dir > 1.0); chdir ($seq_dir) or die "Can't chdir to $seq_dir: $!\n"; #print Dumper ($maid_dir, $seq_dir); opendir my $dh, "$seq_dir" or die "Can't open $seq_dir: $!\n"; if(-d $seq_dir){ my @files = readdir $dh; #my $path = @_; for my $f(@files){ if($f=~ m%^(\d*)(HU.fa|HD.fa|Ltvec_small.FA|_fasta)$%) +{ my ($fa, $hu, $hd, $lt)= ($1."_fasta", $1."HU.fa", + $1."HD.fa", $1."Ltvec_small.FA"); if(-e $fa){ # This is output, not input. Renamed variable +accordingly. open( my $out, ">>".$seq_dir."/".$fa) or die " +Can't open $seq_dir/$fa for append: $!\n"; # Append the contents of the three files to $f +a open my $hu_file, '<', $hu or die "Can't open +$hu: $!\n"; while (my $line = <$hu_file>) { print $out $line; } open my $hd_file, '<', $hd or die "Can't open +$hd: $!\n"; while (my $line = <$hd_file>) { print $out $line; } open my $lt_file, '<', $lt or die "Can't open +$lt: $!\n"; while (my $line = <$lt_file>) { print $out $line; } #open( my $out, ">>".$seq_dir."/".$fa); print $out, "\n" ;#"$hu,$hd,$lt\n"; print Dumper($f); close($out); close($hu_file); close($hd_file); close($lt_file); } } } } } }

      Note that this is a very quick revision of your code, with added error checks (and just noticed I missed the readdir, doh). And it may not be at all what you want. If not, please provide more detail on what you're trying to do.

        I want to append the three files to my $out file.
        I only need each file appended once. The loop is appending each file
        four times. Any ideas?

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