Scripts used in "Structural disruption of exonic stem-loops immediately upstream of the intron regulates mammalian splicing"
sjshapePC.py collects icSHAPE enrichment scores upstream of splice junctions. intronHunterPC.py collects icSHAPE enrichment scores upstream of annotated retained introns.
the *_3prime.py versions do the same, but for downstream regions.
Usage is the same for all 4 scripts: scriptname.py icSHAPE_file gtf_file number_of_threads output_file.
where icSHAPE_file is the final output from the icSHAPE pipeline.
The flankFetch_2way* scripts take the output of one of the above scripts, extract the sequence plus up to a specified length of flanking sequence up- and downstream, and use one of three methods to determine PU values for all hexamers across the region of interest.
flankFetch_2way_rnaplfold.py uses RNAplfold. flankFetch_2way_localfold.py uses LocalFold.
Works for 5' or 3' regions; last argument must specify "5" or "3".
Usage is flankFetch_2way_*.py region_file fasta_file gtf_file output_file_base flank_length 5|3
where region_file is an output file from sjshapePC* or intronHunterPC*.
flankFetch_2way_memeris.py uses a modified GetSecondaryStructureValues from MEMERIS to calculate PU values for the desired sequence. This is part of a three-step process:
- for each desired flank length: flankFetch_2way_memeris.py (usage as above)
- for each fasta file produced by step 1: perl -w ../GetSecondaryStructureValues_fix.perl -f file.fa -o file.pu -l 6 -method PU
- meanPU_memeris.py