How to run a local program with user input in Perl

Question

I'm trying to get user input from a web page written in Perl and send it to a local program (blastp), then display the results.

This is what I have right now:

(input code)

print $q->p, "Your database: $bd",
$q->p, "Your protein is: $prot",
$q->p, "Executing...";

print $q->p, system("blastp","-db $bd","-query $prot","-out results.out");

Now, I've done a little research, but I can't quite grasp how you're supposed to do things like this in Perl. I've tried opening a file, writing to it, and sending it over to blastp as an input, but I was unsuccessful.

For reference, this line produces a successful output file:

 kold@sazabi ~/BLAST/pataa $ blastp -db pataa -query ../teste.fs -out results.out

I may need to force the bd to load from an absolute path, but that shouldn't be difficult.

edit: Yeah, the DBs have an environmental variable, that's fixed. Ok, all I need is to get the input into a file, pass it to the command, and then print the output file to the CGI page.

edit2: for clarification:

I am receiving user input in $prot, I want to pass it over to blastp in -query, have the program blastp execute, and then print out to the user the results.out file (or just have a link to it, since blastp can output in HTML)

EDIT:

All right, fixed everything I needed to fix. The big problem was me not seeing what was going wrong: I had to install Tiny:Capture and print out stderr, which was when I realized the environmental variable wasn't getting set correctly, so BLAST wasn't finding my databases. Thanks for all the help!

Is $prot going to contain the NAME of the file, or contents? — DVK, May 24 '14 at 14:40
Right now, I was planning on $prot to receive FASTA text, namely something that looks like this: >gi|218093591|emb|CAT70956.1| unnamed protein product [Thermococcus kodakarensis KOD1] MKVLVAAPLHEKAIEVLKNAGFEVVYEEYPDEDRLVELVKDVDAIIVRSKPKVTRKVIEAAPKLKVIGRA GVGLDNIDLKAAEERGIKVVNSPGASSRSVAELAIGLIFAVARKIAFADRKMREGVWAKKQCMGIELEGK TIGVVGFGRIGYQVAKIANALGMKVLFYDPYPNEERAKEVGGKFADLETLLKESDVVTLHVPLVDATYHL INEERLKLMKPTAILINAARGAVVDTDALVKALQEGWIAGAGLDVFEEEPLPADHPLTKLDNVVLTPHIG ASTVEAQMRAGVEVAEKIVEALKG — José Maia, May 24 '14 at 14:42

DVK · Accepted Answer · 2014-05-24T14:50:15.210

0

Write $prot to the file. Assuming you need to do it as-is without processing the text to split it or something:

For a fixed file name (may be problematic):

use File::Slurp;
write_file("../teste.fs", $prot, "\n") or print_error_to_web(); 
      # Implement the latter to print error in nice HTML format

For a temp file (better):

my ($fh, $filename) = tempfile( $template, DIR => "..", CLEANUP => 1);
# You can also create temp directory which is even better, via tempdir()
print $fh "$prot\n";
close $fh;

Step 2: Run your command as you indicated:

my $rc = system("$BLASTP_PATH/blastp", "-db", "pataa"
                ,"-query", "../teste.fs", "-out", "results.out");
# Process $rc for errors
# Use qx[] instead of system() if you want to capture 
#      standard output of the command

Step 3: Read the output file in:

use File::Slurp;
my $out_file_text = read_file("results.out");

Send back to web server
```
print $q->p, $out_file_text;
```

The above code has multiple issues (e.g. you need better file/directory paths, more error handling etc...) but should start you on the right track.

edited May 24 '14 at 14:50

answered May 24 '14 at 14:45

DVK

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Thank you, this has helped a lot. There's still a problem, though: apparently I need to preserve the newlines and write_file isn't doing it correctly. My input file, and the test print I do of $prot, show a newline after the first bit, like the comment I made up there, but the file produced by write_file has everything in one line, making BLAST unable to recognize it. – José Maia May 24 '14 at 15:07
@JoséMaia - that's exactly why I said "Assuming you need to do it as-is without processing the text to split it or something". If you need to know how to do that, look into `split` – DVK May 24 '14 at 15:09
Ok, having fixed the problems, the code is now producing a correct input.fs file, as well as a correct (blastp -db pataa -query input.fs -out results.out) query. However, the results.out file is empty, despite the query working if I execute it manually in the terminal. Is there a place I should be looking at for the logs to figure out what happened? – José Maia May 24 '14 at 15:37
Don't think it's a permissions problem either, seeing as if I su into www-data and execute the code, it works. – José Maia May 24 '14 at 16:15

How to run a local program with user input in Perl

1 Answers1