Micro-QTL project

Scripts created for the micro-QTL project.

create_go_tree.py

Converts the GO flat file to a pickled format optimised for tree traversal.

$ ./create_go_tree.py --output go_tree.pickle.xz go-basic.obo

make_uniprot_idmapping_db.py

Creates ID conversion maps from the Uniprot idmapping file.

# NCBI gene ID to GO-terms lookup table
$ ./make_uniprot_idmapping_db.py --from geneid --to go idmapping_selected.tab.gz output.pickle.xz

morgans_to_coordinates.py

For converting the peak regions obtained by R/qtl from centimorgans to actual coordinates.

$ ./morgans_to_coordinates.py marker_new_map.csv rqtl_peaks.csv > coordinates_output.csv

The R/qtl peaks file (rqtl_peaks.csv) should be formatted as tab-separated CSV:

peak_id	chr	pos_cm
peak_1	2	6.052
peak_2	8	52.64

get_go_in_region.py

Find the GO terms within the given regions using a GFF as a reference (e.g. SL2.40).

$ ./get_go_in_region.py --gff sl240.gff.gz --map output.pickle.xz coordinates_output.csv > peak_terms_output.csv

output.pickle.xz is generated by make_uniprot_idmapping_db.py. coordinates_output.csv is generated by morgans_to_coordinates.py.

go_enrichment.R

Perform the GO term enrichment analysis.

$ ./go_enrichment.R peak_terms_output.csv

peak_terms_output.csv is generated by get_go_in_region.py.