Re^2: reading files in directory

The file format is

>chr1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGCNNNNNNNNNNNNNNNNGCAT...
+.....
>chr2
ATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNN.
....
EOF
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I have splitted this multifasta into 25 pieces which is present in my current working directory.However, I am confused as to how can I read all these fasta files and store the hash key as header line and value as sequence. Thanks

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Re^3: reading files in directory by Riales (Hermit) on Mar 20, 2012 at 00:21 UTC
Well, the first thing you'll need to do is tell Perl what the relevant files are. The simplest way to do that is to pass it in as a command-line argument. Look for `@ARGV` in `perldoc perlvar` for that. If the files are all in the same directory and there are no other files in the directory (and you don't want to type out 25 separate filenames), you could use a loop on `STDIN` to receive piped into into your script: `my @filenames; push @filenames, $_ while (<STDIN>); chomp@filenames; use Data::Dumper; print Dumper(@filenames);` [download] That way, you can get all your filenames into your script by simply doing: `ls \| my_script.pl` [download] As for actually opening each file for reading, you've already done that. What's confusing about reading the files? Have you checked `perldoc -f open`? As for hashes, they're pretty simple: `my %hash; # Declare your hash. $hash{$key} = $sequence; # Assign $sequence to the hash with key $key. my $sequence_im_looking_for = $hash{$key}; # Get the sequence by looki +ng it up with its key $key.` [download] It looks like you'll be alternating lines; line1 is the key for the sequence in line2, line3 is the key for the sequence in line4, etc.	[reply] [d/l] [select]

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Re^3: reading files in directory
by Riales (Hermit) on Mar 20, 2012 at 00:21 UTC

Well, the first thing you'll need to do is tell Perl what the relevant files are. The simplest way to do that is to pass it in as a command-line argument. Look for @ARGV in perldoc perlvar for that.

If the files are all in the same directory and there are no other files in the directory (and you don't want to type out 25 separate filenames), you could use a loop on STDIN to receive piped into into your script:

my @filenames;
push @filenames, $_ while (<STDIN>);
chomp@filenames;

use Data::Dumper;
print Dumper(@filenames);
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That way, you can get all your filenames into your script by simply doing:

ls | my_script.pl
[download]

As for actually opening each file for reading, you've already done that. What's confusing about reading the files? Have you checked perldoc -f open?

As for hashes, they're pretty simple:

my %hash; # Declare your hash.

$hash{$key} = $sequence; # Assign $sequence to the hash with key $key.

my $sequence_im_looking_for = $hash{$key}; # Get the sequence by looki
+ng it up with its key $key.
[download]

It looks like you'll be alternating lines; line1 is the key for the sequence in line2, line3 is the key for the sequence in line4, etc.

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