Merge VastDB input mode into rna_maps.py with minus-strand fix#12
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Bear-Bee89 wants to merge 5 commits intoulelab:mainfrom
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Merge VastDB input mode into rna_maps.py with minus-strand fix#12Bear-Bee89 wants to merge 5 commits intoulelab:mainfrom
Bear-Bee89 wants to merge 5 commits intoulelab:mainfrom
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New standalone script that accepts VastDB EVENT ID lists with pre-assigned categories (enhanced, silenced, control, constitutive) instead of rMATS output, parsing coordinates directly from a VastDB EVENT_INFO annotation file. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ranch Adds dedicated VastDB section at the top covering inputs, usage, outputs, and a comparison table vs the original rMATS-based script. Original rna_maps.py docs preserved below. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
Merges the standalone
rna_maps_vastdb_only.pyintorna_maps.pyas asecond input mode, so a single script handles both rMATS and VastDB inputs
with a shared downstream pipeline.
What changed
Two input tracks, one shared pipeline
-i): unchanged interface, all original arguments preserved--vastdb_mode): takes--vastdb_enhanced,--vastdb_silenced,--vastdb_control,--vastdb_constitutiveID list files +--vastdb_annotationshared BED creation, coverage calculation, plotting, and heatmap generation
Minus-strand fix for rMATS flanking exon coordinates
rMATS labels
upstreamES/EEanddownstreamES/EEby genomic position (lowercoords = "upstream"), which is inverted for minus-strand genes. The original
script compensated with cross-exon column pairing in
get_ss_bed()calls.This merge instead swaps the columns at load time in
load_rmats_data()sothat upstream/downstream always mean transcript direction after loading. Both
modes then use identical same-exon
get_ss_bed()calls.New features
--seedflag (default 42) for reproducible control/constitutive subsettingtables (these were missing from the standalone script)
_RMATS_with_categories.tsvvs_VastDB_with_categories.tsvFiles changed
rna_maps.py— replaced with merged versionREADME.md— rewritten to document both modesrna_maps_vastdb_only.py— superseded (can be removed)Testing
Tested on KCL CREATE HPC:
ran to completion, outputs match standalone script
ran to completion with correct category counts
(4448 enhanced, 2256 silenced, 52158 constitutive, 8354 control)
Breaking changes
minus-strand genes compared to the original script. This is a bug fix —
the original cross-exon pairing produced correct results through
compensating logic, but the new approach is clearer and consistent with
VastDB mode.
rna_maps_vastdb_only.pyis no longer needed as a separate script.