Add possibility of samples that are arranged in different folders

ProtProtocols / IsoProt

Protocol of the analysis of iTRAQ/TMT proteomics data including quantification, statistical analysis and maybe clustering

https://protprotocols.github.io

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Add possibility of samples that are arranged in different folders #4

Closed jgriss closed 6 years ago

jgriss commented 6 years ago

Add a feature where different samples were processed in different iTRAQ/TMT runs and the files are thus present in different folders.

This workflow should also take the setup into consideration where these samples were fractionated. For example:

Run 1 (18 MGF files)

sample 1 - 8
fraction 1 - 18

Run 2 (18 MGF files)

sample 8 - 15
fraction 1 - 18

jgriss commented 6 years ago

The GUI elements introduced through #27 should then trigger this functionality

veitveit commented 6 years ago

Set the milestone to version 0.1 as this looks like an important feature. At least most of our experimental design do include multiple MS runs of different samples.

veitveit commented 6 years ago

In principle, the following adjustments need to be made:

automatically search for subfolders in the spectra directory and assign them to different runs if they contain mgf files. Error when main folder and subfolders contain mgf files
run separately the database search + peptideshaker for the files in each folder
show a separate Hbox for mapping channels to samples for each folder

I can start working on this but, given my python experience, it could get messy :-)

veitveit commented 6 years ago

I am on it, should get to some results in a week ....

veitveit commented 6 years ago

Should in principle work now at all stages but requires thorough testing. I will close this one for now