CODEWITHSUNDEEP
perlfile-io
olala
olala

Reputation: 4436

Cannot open file handle from a variable

Initially I have run the shell script and direct the output into a file and then use Perl to reading the file and parse it. I wanted to put these two steps together into one Perl script.

And I tried to write something like this:

my $in = 'file.txt';
my $read = qx(samtools view -S $in |cut -f 3|sort|uniq -c|awk '{OFS="\t";print \$2,\$1}');

open (IN,"<",$read) || die "cannot open $read: $!";

I got the error message that $in can't be opened and the result from the qx() command was printed out on the screen.

I couldn't understand why this didn't work and how to make it work..

EDIT:

The error from the open line is:

File name too long

Upvotes: 0

Views: 1363

Answers (2)

Rajit
Rajit

Reputation: 808

Your code will read the output of the shell commands that you have run and store that output (anything written to STDOUT) in $in.

I doubt the shell command will run correctly as you are attempting to use $in within it, and it is probably not defined.

You can spot this if you use strict; at the top of the script.

my $in = qx(samtools view -S $in |cut -f 3|sort|uniq -c|awk '{OFS="\t";print \$2,\$1}');

// No need to open anything here, just inspect $in

I'm not familiar with 'samtools', but you will likely need to fix the shell command and use the right thing instead of $in in view -S $in

EDIT:

Okay, you're saying that your shell command writes to a file, which you then want to read. I misunderstood!

What I have stated above remains true, but to solve your issue more fully you will need to do something like this:

my $in = 'file.txt';
my $cmd_output = qx(samtools view -S $in |cut -f 3|sort|uniq -c|awk '{OFS="\t";print \$2,\$1}');

open my $fh, '<', $in or die "ERROR: Couldn't open $in for reading: $!";

2ND EDIT, answering question in comments:

In order to parse the output line by line, you can just do something like this:

foreach my $line (split /\n/, $cmd_output) {
    // Do something with $line
}

To be honest, you might even find it easier to do this on the shell with:

$ samtools view -S $in |cut -f 3|sort|uniq -c|awk '{OFS="\t";print \$2,\$1}' | perl -lne '... do something with $_ ...'

Upvotes: 3

amon
amon

Reputation: 57590

The string produced by the shell command probably contains a newline at the end. Remove it via chomp:

chomp $in;

Also, please use normal variables for file handles:

open my $fh, "<", $in or die qq(Can't open "$in": $!);

Upvotes: 4

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