diff bigwigtobed.python.txt @ 0:2fbbc1be6655 draft

planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bigwigtobed.python.txt	Mon Jul 01 00:53:01 2024 +0000
@@ -0,0 +1,131 @@
+#raw
+"""
+Ross Lazarus June 2024 for VGP 
+Bigwigs are great, but hard to reliably "see" small low coverage or small very high coverage regions.
+Colouring in JB2 tracks will need a new plugin, so this code will find bigwig regions above and below a chosen percentile point.
+0.99 and 0.01 work well in testing with a minimum span of 10 bp.
+Multiple bigwigs **with the same reference** can be combined - bed segments will be named appropriately
+Combining multiple references works but is silly because only display will rely on one reference so others will not be shown...
+Tricksy numpy method from http://gregoryzynda.com/python/numpy/contiguous/interval/2019/11/29/contiguous-regions.html
+takes about 95 seconds for a 17MB test wiggle
+JBrowse2 bed normally displays ignore the score, so could provide separate low/high bed file outputs as an option.
+Update june 30 2024: wrote a 'no-build' plugin for beds to display red/blue if >0/<0 so those are used for scores
+Bed interval naming must be short for JB2 but needs input bigwig name and (lo or hi).
+"""
+import argparse
+import numpy as np
+import pybigtools
+import sys
+from pathlib import Path
+class findOut():
+    def __init__(self, args):
+        self.bwnames=args.bigwig
+        self.bwlabels=args.bigwiglabels
+        self.bedwin=args.minwin
+        self.qlo=args.qlo
+        self.qhi=args.qhi
+        self.bedouthilo=args.bedouthilo
+        self.bedouthi=args.bedouthi
+        self.bedoutlo=args.bedoutlo
+        self.tableout = args.tableout
+        self.bedwin = args.minwin
+        self.qhi = args.qhi
+        self.qlo = args.qlo
+        self.makeBed()
+    def processVals(self, bw, isTop):
+        # http://gregoryzynda.com/python/numpy/contiguous/interval/2019/11/29/contiguous-regions.html
+        if isTop:
+            bwex = np.r_[False, bw >= self.bwtop, False] # extend with 0s
+        else:
+            bwex = np.r_[False, bw <= self.bwbot, False]
+        bwexd = np.diff(bwex)
+        bwexdnz = bwexd.nonzero()[0]
+        bwregions = np.reshape(bwexdnz, (-1,2))
+        return bwregions
+    def writeBed(self, bed, bedfname):
+        """
+        potentially multiple
+        """
+        bed.sort()
+        beds = ['%s\t%d\t%d\t%s\t%d' % x for x in bed]
+        with open(bedfname, "w") as bedf:
+            bedf.write('\n'.join(beds))
+            bedf.write('\n')
+        print('Wrote %d bed regions to %s' % (len(bed), bedfname))
+    def makeBed(self):
+        bedhi = []
+        bedlo = []
+        bwlabels = self.bwlabels
+        bwnames = self.bwnames
+        print('bwnames=', bwnames, "bwlabs=", bwlabels)
+        for i, bwname in enumerate(bwnames):
+            bwlabel = bwlabels[i].replace(" ",'')
+            p = Path('in.bw')
+            p.symlink_to( bwname ) # required by pybigtools (!)
+            bwf = pybigtools.open('in.bw')
+            chrlist = bwf.chroms()
+            chrs = list(chrlist.keys())
+            chrs.sort()
+            restab = ["contig\tn\tmean\tstd\tmin\tmax\tqtop\tqbot"]
+            for chr in chrs:
+                bw = bwf.values(chr)
+                bw = bw[~np.isnan(bw)] # some have NaN if parts of a contig not covered
+                if self.qhi is not None:
+                    self.bwtop = np.quantile(bw, self.qhi)
+                    bwhi = self.processVals(bw, isTop=True)
+                    for i, seg in enumerate(bwhi):
+                        if seg[1] - seg[0] >= self.bedwin:
+                            bedhi.append((chr, seg[0], seg[1], '%s_hi' % (bwlabel), 1))
+                if self.qlo is not None:
+                    self.bwbot = np.quantile(bw, self.qlo)
+                    bwlo = self.processVals(bw, isTop=False)            
+                    for i, seg in enumerate(bwlo):
+                        if seg[1] - seg[0] >= self.bedwin:
+                            bedlo.append((chr, seg[0], seg[1], '%s_lo' % (bwlabel), -1))
+                bwmean = np.mean(bw)
+                bwstd = np.std(bw)
+                bwmax = np.max(bw)
+                nrow = np.size(bw)
+                bwmin = np.min(bw)
+                restab.append('%s\t%d\t%f\t%f\t%f\t%f\t%f\t%f' % (chr,nrow,bwmean,bwstd,bwmin,bwmax,self.bwtop,self.bwbot))        
+        print('\n'.join(restab), '\n')
+        if self.tableout:
+            with open(self.tableout) as t:
+                t.write('\n'.join(restab))
+                t.write('\n')
+        if self.bedoutlo:
+            if self.qlo:
+                self.writeBed(bedlo, self.bedoutlo)
+        if self.bedouthi:
+            if self.qhi:
+                self.writeBed(bedhi, self.bedouthi)
+        if self.bedouthilo:
+            allbed = bedlo + bedhi
+            self.writeBed(allbed, self.bedouthilo)
+        return restab
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    a = parser.add_argument
+    a('-m', '--minwin',default=10, type=int)
+    a('-l', '--qlo',default=None, type=float)
+    a('-i', '--qhi',default=None, type=float)
+    a('-w', '--bigwig', nargs='+')
+    a('-n', '--bigwiglabels', nargs='+')
+    a('-o', '--bedouthilo', default=None, help="optional high and low combined bed")
+    a('-u', '--bedouthi', default=None, help="optional high only bed")
+    a('-b', '--bedoutlo', default=None, help="optional low only bed")
+    a('-t', '--tableout', default=None)
+    args = parser.parse_args()
+    print('args=', args)
+    if not (args.bedouthilo or args.bedouthi or args.bedoutlo):
+        sys.stderr.write("bigwig_outlier_bed.py cannot usefully run - need a bed output choice - must be one of low only, high only or both combined")
+        sys.exit(2)
+    if not (args.qlo or args.qhi):
+        sys.stderr.write("bigwig_outlier_bed.py cannot usefully run - need one or both of quantile cutpoints qhi and qlo")
+        sys.exit(2)
+    restab = findOut(args)
+    if args.tableout:
+        with open(args.tableout, 'w') as tout:
+            tout.write('\n'.join(restab))
+            tout.write('\n')
+#end raw