003337bf766f61f102c61cb924af98ad09372ad0
markd
  Tue Aug 5 12:41:24 2025 -0700
added size and splice junction filters to recount3

diff --git src/hg/makeDb/outside/recount3/junctionsToBed.py src/hg/makeDb/outside/recount3/junctionsToBed.py
index 0600aa0cbb9..f9c3c321d32 100755
--- src/hg/makeDb/outside/recount3/junctionsToBed.py
+++ src/hg/makeDb/outside/recount3/junctionsToBed.py
@@ -1,28 +1,28 @@
 #!/usr/bin/env python3
 import sys
 import csv
 import os
 import re
 import csv
 import argparse
 import textwrap
 from collections import namedtuple
 from math import log
-sys.path.append('/hive/groups/browser/pycbio/lib')
+#sys.path.append('/hive/groups/browser/pycbio/lib')
 from pycbio.hgdata.bed import Bed, BedBlock, BedReader, intArraySplit
-
+from pycbio.sys import fileOps
 
 
 def main():
 	parser = argparse.ArgumentParser(
 	formatter_class=argparse.RawDescriptionHelpFormatter,
 	description=textwrap.dedent('''\
 Converts gff to bed format, adding expression values and CDS from separate files.
 Also outputs a decorator bed file, see https://genome.ucsc.edu/goldenPath/help/decorator.html
 
         '''))
 	#group = parser.add_argument_group('required arguments')
 	parser.add_argument('--junctions', required=True, type=str, help='annotated gff')
 	parser.add_argument('--bed', required=True, type=str, help='output bed')
 	parser.add_argument('--decorator', required=True, type=str, help='output decorator bed')
 	parser.add_argument('--compilation', required=True, type=str,
@@ -71,55 +71,57 @@
 				extraCols=extraCols)
 	rightObj.write(outFH)
 
 
 def junction_to_bed(outputfile, junctions, decoratorfile, compilation):
 	'''Parses intron lines, extracts ID info from last field, assigns score'''
 	urlbase = '<a href="https://snaptron.cs.jhu.edu/snaptron-studies/jxn2studies?compilation='+compilation
 	urlfill = '&jid={jid}&coords={chrom}:{start}-{end}" target="_blank">link to snaptron</a>'
 #'https://snaptron.cs.jhu.edu/snaptron-studies/jxn2studies?compilation=<COMPILATION_ID>&jid=<JXN_ID>&coords=<CHROMOSOME:START-END>'
 #	url = '<a href="https://snaptron.cs.jhu.edu/gtexv2/snaptron?regions={chrom}:{start}-{end}" target="_blank">{text}</a>'
 	decFile = open(decoratorfile, 'wt')
 	with open(outputfile, 'wt') as outfile:
 		writer = csv.writer(outfile, delimiter='\t', lineterminator=os.linesep)
 		# extract all exons from the gff, keep exons grouped by transcript
 		maxScore=1
-		for line in open(junctions, 'rt'):  
+		infh = fileOps.opengz(junctions, 'rt')
+		for line in infh:
 			if line.startswith('#'):
 				continue
 			[snaptron_id, chrom, start, end, length, strand, annotated,
 				left_motif, right_motif, left_annotated, right_annotated, samples,
 				samples_count, coverage_sum, coverage_avg, coverage_median,
 				source_dataset_id] = line.rstrip().split('\t')
 			# skip non-genome chromosomes
 			if any(chrom.startswith(prefix) for prefix in ('ERCC', 'SIRV', 'GL', 'JH', 'chrEBV')):
 				continue
 			# turn left and right motifs into donor and acceptor
 			donor = left_motif.upper()
 			acc = right_motif.upper()
 			if strand == '?':
 				strand = '.'
 			elif strand == '-':
 				complement = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C'}
 				donor = ''.join(complement[base] for base in reversed(acc))
 				acc = ''.join(complement[base] for base in reversed(left_motif.upper()))
 			# link out to sample information for each junction
 			link = urlbase + urlfill.format(jid=snaptron_id, chrom=chrom, start=start, end=end)
 			# correct coordinates
 			start = int(start)-1
 			end = int(end)
 			# score scaling
 			score = int(10*log(int(coverage_sum))) # score field only accepts integers
 			maxScore = max(score, maxScore)
-			extraCols = [coverage_sum, samples_count, donor, acc, link] 
+			size = end - start
+			extraCols = [size, coverage_sum, samples_count, donor, acc, link, donor + '/' + acc]
 			# create bed object
 			bedObj = Bed(chrom, start, end, name=snaptron_id, strand=strand, score=score,
 				thickStart=start, thickEnd=end, numStdCols=9, extraCols=extraCols)
 			# create splice site decorator file
 			makeSpliceDecorator(bedObj, donor, acc, decFile)
 			bedObj.write(outfile)
 	decFile.close()
 	print('maxScore', maxScore)
 
 
 if __name__ == "__main__":
 	main()