Using script in config files

[Sebastien]

Hi, I'm wondering if there is a way to use python scripts in the configuration files. It could be pretty handfull when we need some scripting between steps.

[Eduardo Andres Leon]

Ummm I'm sure what you mean. Could you explain it a little more ?

Thanks

[Sebastien]

Hum for example. I use miARma to make quality, adapter trimming, alignment. Then I use a personal script for the DE analysis. Then I use miARma to make target prediction.

I would like for example to add scripts between the [ReadCount] and the [TargetPrediction]. The script will run DE analysis the way I want and move the results file (in .xls format) to a "EdgeR_Results" folder so miARma can detect it.

Do you understand what I mean?

Thanks

[Eduardo Andres Leon]

Now I understand!. It can be done but in a very different way and using only perl. miARma has been created as perl packages. So from perl you can call a package (for example ReadCount.pm), then you can do what every you want and finally call another package to process data in a compatible format. Take a look to: https://bitbucket.org/cbbio/miarma/src/5e3a903c0c3c11e876be08f93ff4c2bb0ca18f80/Examples/advanced_examples/miRNAs/

for example: https://bitbucket.org/cbbio/miarma/src/5e3a903c0c3c11e876be08f93ff4c2bb0ca18f80/Examples/advanced_examples/miRNAs/4.ReadCount/4.Read_Count.pl?at=master&fileviewer=file-view-default

Edu

[Sebastien]

Ho ok I see thank you ;)

Unfortunately I don't know perl but I think my collegues can do some things with that.

Thanks

Sebastien