annotate bigwig_outlier_bed.xml @ 3:6bedfd2a11f9 draft

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

<tool name="bigwig_outlier_bed" id="bigwigoutlierbed" version="0.01" profile="22.05">
  <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
  <!--Created by [e-mail] at 30/06/2024 19:44:14 using the Galaxy Tool Factory.-->
  <description>Writes high and low bigwig regions as features in a bed file</description>
  <edam_topics>
      <edam_topic>topic_0157</edam_topic>
      <edam_topic>topic_0092</edam_topic>
  </edam_topics>
  <edam_operations>
      <edam_operation>operation_0337</edam_operation>
  </edam_operations>  
  <requirements>
    <requirement type="package" version="3.12.3">python</requirement>
    <requirement type="package" version="2.0.0">numpy</requirement>
    <requirement type="package" version="0.1.4">pybigtools</requirement>
  </requirements>
  <version_command><![CDATA[python -c "import pybigtools; from importlib.metadata import version; print(version('pybigtools'))"]]></version_command>
  <command><![CDATA[python
'$runme'
--bigwig
'$bigwig'
--bedouthilo
'$bedouthilo'
--minwin
'$minwin'
--qhi
'$qhi'
--qlo
'$qlo'
#if $tableout == "set"
 --tableout
#end if
--bigwiglabels
'$bigwiglabels']]></command>
  <configfiles>
    <configfile name="runme"><![CDATA[#raw
"""
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 display will rely on one reference so features mapped to other references will not appear.

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]]></configfile>
  </configfiles>
  <inputs>
    <param name="bigwig" type="data" optional="false" label="Bigwig file(s) to process. " help="If more than one, MUST all use the same reference sequence to be displayable. Feature names will include the bigwig label." format="bigwig" multiple="true"/>
    <param name="minwin" type="integer" value="10" label="Minimum continuous bases to count as a high or low bed feature" help="Actual run length will be found and used for continuous features as long or longer."/>
    <param name="qhi" type="float" value="0.99" label="Quantile cutoff for a high region - 0.99 will cut off at or above the 99th percentile" help=""/>
    <param name="qlo" type="float" value="0.01" label="Quantile cutoff for a low region - 0.01 will cut off at or below the 1st percentile." help=""/>
    <param name="tableout" type="select" label="Write a table showing contig statistics for each bigwig" help="" display="radio">
      <option value="notset">Do not set this flag</option>
      <option value="set">Set this flag</option>
    </param>
    <param name="bigwiglabels" type="text" value="outbed" label="Label to use in bed feature names to indicate source bigwig contents - such as coverage" help=""/>
  </inputs>
  <outputs>
    <data name="bedouthilo" format="bed" label="Both high and low contiguous regions as long or longer than window length into one bed " hidden="false"/>
  </outputs>
  <tests>
    <test>
      <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/>
      <param name="bigwig" value="bigwig_sample"/>
      <param name="minwin" value="10"/>
      <param name="qhi" value="0.99"/>
      <param name="qlo" value="0.01"/>
      <param name="tableout" value="notset"/>
      <param name="bigwiglabels" value="outbed"/>
    </test>
  </tests>
  <help><![CDATA[
 **What it Does**
 
 Takes one or more bigwigs mapped to the same reference and finds all the minimum window sized or greater contiguous regions above or below an upper and lower quantile cutoff.
 A window size of 10 works well, and quantiles set at 0.01 and 0.99 will generally work well.
 
  ]]></help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/btae350</citation>
  </citations>
</tool>