Perl issues bash pipe into Java

Question

I am a Perl beginner. I have this Perl snippet

$normal_pileup = "samtools mpileup -q 1 -f XXXX YYYYY";
$tumor_pileup = "samtools mpileup -q 1 -f XXXX ZZZZZ";

bash -c \"java -jar ttt.jar  <\($normal_pileup\) <\($tumor_pileup\) output

They try to issue a system call that pipes input from these commands into a Java program. I couldn't make it work. Can anybody please tell me how to do it?

Is the line 'bash -c...' part of the perl script? It doesn't look like valid perl to me. — matt freake
– matt freake, Commented Aug 29, 2012 at 9:04

choroba · Accepted Answer · 2012-08-29 10:08:11Z

2

You cannot call bash directly from Perl. If you use system, though, /bin/sh will be called which probably does not support the process substitution.

One of possible workarounds is

system qq(echo 'java -jar ttt.jar  <($normal_pileup) <($tumor_pileup) output' | bash);

edited Aug 29, 2012 at 10:08

answered Aug 29, 2012 at 9:52

choroba

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Matteo · Accepted Answer · 2012-08-29 09:24:28Z

1

$normal_pileup = "samtools mpileup -q 1 -f XXXX YYYYY";

will not execute any command but will just store samtools mpileup -q 1 -f XXXX YYYYY as a string. The same for $tumor_pileup.

If you want to execute the command use

$normal_pileup = `samtools mpileup -q 1 -f XXXX YYYYY`;

bash is not a Perl command.

`java -jar ttt.jar  ...`

You "java" is also most likely wrong

with < you specify where STDIN is read. Is supposed to be a file but in your case you are specifying the output of a previous command. This will only work if the output of samtool is a file name.
if you want your java program to process the output of another command you will need a pipe
```
mycommand | java
```

Summarizing I suppose you want

` ( samtools mpileup -q 1 -f XXXX YYYYY; samtools mpileup -q 1 -f XXXX ZZZZZ ) | java -jar ttt.jar output `

edited Aug 29, 2012 at 9:24

answered Aug 29, 2012 at 9:18

Matteo

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3 Comments

user1632530 Over a year ago

thanks very much for your reply. My intention is to run two bash commands "samtools mpileup -q 1 -f XXXX YYYYY" and samtools mpileup -q 1 -f XXXX YYYYY. their output will be directly piped into java program as two parameters.

Matteo Over a year ago

@user1632530 so both will not generate a stream of data but just a string? Could you give us an example output?

user1632530 Over a year ago

the problem is from usage of varscan. the original url is varscan.sourceforge.net/somatic-calling.html

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