How to run TOFU analysis in the perl ?

[huan]

Now I am working on the Iso_seq Analysis using the Tofu program, I am intended to intergrated all the analysis (including classify,cluster,Removing Redundant Transcripts Analysis,find fusion) in a perl script. But I run into an error when I run the Tofu program by using the following perl script :
`/share/biosoft/smrtanalysis/current/smrtcmds/bin/smrtshell && source /share/software/python_virtualenv/bin/activate && collapse_isoforms_by_sam.py --input $fafile -s $fafile.sorted.sam -o $fafile.sorted.5merge>$fafile.sorted.5merge.log`;.
The program only go into the smrtshell and doesn't run the following script. What is the matter?
Is there any advice to intergrated the Iso_seq Analysis workflow and the TOFU workflow into a perl script?
Thanks a lot!

[Magdoll]

Hi,

I don't really use Perl anymore but I think this issue is not coming from Perl but the fact that you are trying to activate a virtualenv within a script in a shell.

I found a post that encountered the same issue trying to activate a virtualenv in a bash script:

http://stackoverflow.com/questions/13122137/how-to-source-virtualenv-activate-in-a-bash-script

Unfortunately the solution provided in the post (activating a subshell) did not work for me. I'm tempted to suggest that you do the smrtshell -> virtualenv *before* you launch a series of Perl scripts that would string together ToFU script calls. Or you can try googling a bit more to see if people have success with activating virtualenv inside Perl (or bash...)

Best,
--Liz

[bowhan]

Like `bash` command itself, when you directly call "smrtshell" it creates an interactive shell and breaks your flow. But if you gives it a script as an option, it will execute it and return to the parent shell when it finishes. So you can probably do it in this way:
1. wrap Iso-Seq code in a bash script "run_iso-seq.sh"

#! /bin/bash
. /path/to/virtualenv/bin/activate && \
/path/to/collapse_isoforms_by_sam.py ...

2. wrap the above bash script in another bash script "smrtshell_wrap.sh", which calls "smrtshell" to run "run_iso-seq.sh"

#! /bin/bash
/path/to/smrtshell /path/to/run_iso-seq.sh

3. call "smrtshell_wrap.sh" in perl

$ret = `/path/to/smrtshell_wrap.sh 2>&1`

[huan]

Thanks bowhan and MagdollO(∩_∩)O! This problem has troubled me a a lot! Your suggestion solves the problem prefectly~\(≧▽≦)/~