Editing SecStrAnnotator:Analysis (section)

==Procedure==

===Data preparation===

The directory <code>scripts/secstrapi_data_preparation/</code> contains a pipeline for annotating the whole protein family, including: 

* downloading the list of family members defined by CATH and Pfam, 
* downloading their structures, 
* selecting a non-redundant set, 
* annotation, 
* multiple sequence alignment for individual SSEs, 
* formatting into [[SecStrAnnotator:SecStrAPI#SecStrAPI_format | SecStrAPI format]], 
* formatting into TSV format for further analyses.

The whole pipeline can be executed by <code>scripts/SecStrAPI_pipeline.py</code>

Example usage:

  python3 scripts/SecStrAPI_pipeline.py scripts/SecStrAPI_pipeline_settings.json --resume

Before running, modify the settings in <code>SecStrAPI_pipeline_settings.json</code> to set your family of interest, annotation template, data directory etc (see <code>README.txt</code> for more details).

===Data analysis===

The directory <code>scripts/R_sec_str_anatomy_analysis/</code> contains a pipeline for statistical analysis of the annotation results on the whole protein family, including:

* reading the annotation results from TSV,
* generating plots,
* performing statistical test to compare eukaryotic and bacterial structures (or any two sets of structures).

Example usage:

* Launch <code>rstudio</code> from the said directory
* In <code>sec_str_anatomy.R</code>, set DATADIR to the path to your annotation data created in [[#Data preparation]]
* In <code>sec_str_anatomy_settings.R</code>, modify the family-specific settings (list of helices and strands)
* Run <code>sec_str_anatomy.R</code> line by line