Pipe python string to perl script

Question

I want to pipe a file path from Python to a Perl script. Although I'm familiar with Python and Bash I don't known anything about Perl.
I have the following (example) files:

return.py

print( 'data/test.txt' )

uniprot.pl

use strict;
use warnings;
use LWP::UserAgent;

my $list = $ARGV[0]; # File containg list of UniProt identifiers.
my $base = 'http://www.uniprot.org';
my $tool = 'uploadlists';

my $contact = ''; # Please set your email address here to help us debug in case of problems.
my $agent = LWP::UserAgent->new(agent => "libwww-perl $contact");
push @{$agent->requests_redirectable}, 'POST';

my $response = $agent->post("$base/$tool/",
                            [ 'file' => [$list],
                              'format' => 'fasta',
                              'from' => 'ACC+ID',
                              'to' => 'ACC',
                            ],
                            'Content_Type' => 'form-data');

while (my $wait = $response->header('Retry-After')) {
  print STDERR "Waiting ($wait)...\n";
  sleep $wait;
  $response = $agent->get($response->base);
}

$response->is_success ?
  print $response->content :
  die 'Failed, got ' . $response->status_line .
    ' for ' . $response->request->uri . "\n";

When I call the perl file from the shell like: perl uniprot.pl data/test.txt it works fine.

I tried different approaches to pipe the python print to this call, but apparently the wrong ones:

1.

python3 return.py | perl uniprot.pl

This will give: Failed, got 500 Internal Server Error for http://www.uniprot.org/uploadlists/. However as I know the code works (as said above) this has to be caused by wrong piping.

2

python3 return.py | perl uniprot.pl -

This will give: Can't open file -: No such file or directory at /usr/share/perl5/LWP/UserAgent.pm line 476. So it seems that the string is passed to the perl file, however perl is looking in a complete different directory.

3
I changed this line: my $list = $ARGV[0]; --to--> my $list = <STDIN>; and then again calling both the above commands (thus 1 and 2). Both give: Can't open file data/test.txt : No such file or directory at /usr/share/perl5/LWP/UserAgent.pm line 476.

Question How can I pass the string from return.py to uniprot.pl?

Definitly not a Python question - you'd have the same issue with a C program, a shell script or another perl script. — bruno desthuilliers
– bruno desthuilliers, Commented May 14, 2018 at 12:17
Well yes looking back, however I wasn't sure whether I actually should have printed the string or should have done otherwise @brunodesthuilliers — CodeNoob
– CodeNoob, Commented May 14, 2018 at 12:28
If this is the excepted output from your program then yes printing it the right thing to do. — bruno desthuilliers
– bruno desthuilliers, Commented May 14, 2018 at 13:35

tinita · Accepted Answer · 2018-05-14 12:02:36Z

3

You need to check wether the argument is given via command line arguments or comes via STDIN.

my $file;
if (@ARGV) {
    $file = $ARGV[0];
}
else {
    chomp($file = <STDIN>); # chomp removes linebreak
}

answered May 14, 2018 at 12:02

tinita

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2 Comments

CodeNoob Over a year ago

Thankyou so much!

simbabque Over a year ago

That only gives you the first line of input though, doesn't it?

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