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 @@ -1,125 +1,127 @@ #!/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, choices=['ccle', 'gtexv2', 'srav3h', 'tcgav2', 'srav1m'], help='one of ccle, gtexv2, srav3h, tcgav2, srav1m') args = parser.parse_args() junction_to_bed(args.bed, args.junctions, args.decorator, args.compilation) def makeSpliceDecorator(bedObj, donor, acc, outFH): '''Create decorators for splice consensus''' #chr1 1999 2000 green_circle 0 + 1999 2000 0,255,0,255 1 1 0 chr1:1000-2000:feature glyph 0,255,0,255 Circle #colorblind color scheme Paul Tol's Muted from # https://www.nceas.ucsb.edu/sites/default/files/2022-06/Colorblind%20Safe%20Color%20Schemes.pdf # dark blue = GT donor, AG acceptor (046,037,133), teal= GC donor (093,168,153), faded red = AG/AC (194,106,119) if bedObj.strand == '.': # do not decorate return # assign colors splice_map_donor = {'GT': '046,037,133','GC': '093,168,153','AT': '194,106,119'} splice_map_acc = {'AG': '046,037,133', 'AC': '194,106,119'} leftColor = splice_map_donor.get(donor, 'default') rightColor = splice_map_acc.get(acc, 'default') # correct for negative strand if bedObj.strand == '-': leftColor, rightColor = rightColor, leftColor # decorate the first and last two bases of each block leftChromStart = bedObj.chromStart leftChromEnd = leftChromStart + 2 leftBlocks = [BedBlock(bedObj.chromStart, bedObj.chromStart+2)] rightChromStart = bedObj.chromEnd - 2 rightChromEnd = bedObj.chromEnd rightBlocks = [BedBlock(bedObj.chromEnd-2, bedObj.chromEnd)] # format the target location (required for format) target='{}:{}-{}:{}'.format(bedObj.chrom, bedObj.chromStart, bedObj.chromEnd, bedObj.name) extraCols = [target, 'block', leftColor, 'Circle'] # create and write bed objects, one for each side leftObj = Bed(bedObj.chrom, leftChromStart, leftChromEnd, name='decl'+bedObj.name, strand=bedObj.strand, blocks=leftBlocks, numStdCols=12, itemRgb=leftColor, extraCols=extraCols) leftObj.write(outFH) extraCols = [target, 'block', rightColor, 'Circle'] rightObj = Bed(bedObj.chrom, rightChromStart, rightChromEnd, name='decr'+bedObj.name, strand=bedObj.strand, blocks=rightBlocks, numStdCols=12, itemRgb=rightColor, 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()