# HG changeset patch
# User fubar
# Date 1721431979 0
# Node ID efc775ab30fe4c4ead53dbec9b28b761fbfb1252
# Parent  4cb6cc083620fe4cd6e37142c3aeccc0a9877677
planemo upload for repository https://github.com/fubar2/microsatbed commit d952bc313f408735456747c3d33e09a3170c8f59-dirty

diff -r 4cb6cc083620 -r efc775ab30fe dibed.bw
Binary file dibed.bw has changed
diff -r 4cb6cc083620 -r efc775ab30fe find_str.py
--- a/find_str.py	Fri Jul 19 22:32:44 2024 +0000
+++ b/find_str.py	Fri Jul 19 23:32:59 2024 +0000
@@ -2,7 +2,6 @@
 import shutil
 import subprocess
 
-import pybigtools
 import pytrf  # 1.3.0
 from pyfastx import Fastx  # 0.5.2
 
@@ -13,18 +12,22 @@
 
 
 def getDensity(name, bed, chrlen, winwidth):
+    """
+    pybigtools can write bigwigs and they are processed by other ucsc tools - but jb2 will not read them.
+    Swapped the conversion to use a bedgraph file processed by bedGraphToBigWig
+    """
     nwin = int(chrlen / winwidth)
     d = [0.0 for x in range(nwin + 1)]
     for b in bed:
         nt = b[5]
         bin = int(b[1] / winwidth)
         d[bin] += nt
-    dw = [
+    bedg = [
         (name, (x * winwidth), ((x + 1) * winwidth) - 1, float(d[x]))
         for x in range(nwin + 1)
         if (x + 1) * winwidth <= chrlen
     ]
-    return dw
+    return bedg
 
 
 def write_ssrs(args):
@@ -86,7 +89,6 @@
     if args.bigwig:
         wig.sort()
         bedg = ['%s %d %d %.3f' % x for x in wig]
-        # bedg.insert(0,'track type=bedGraph') https://genomebrowser.wustl.edu/goldenPath/help/bigWig.html
         with open("temp.bedg", "w") as bw:
             bw.write('\n'.join(bedg))
         chroms = ["%s\t%s" % (x, chrlens[x]) for x in chrlens.keys()]
@@ -94,8 +96,6 @@
             cl.write('\n'.join(chroms))
         cmd = ["bedGraphToBigWig", "temp.bedg", "temp.chromlen", "temp.bw" ]
         subprocess.run(cmd)
-        #bw = pybigtools.open("temp.bw", "w")
-        #bw.write(chrlens, wig)
         shutil.move("temp.bw", args.bed)
     else:
         bed.sort()
diff -r 4cb6cc083620 -r efc775ab30fe microsatbed.xml
--- a/microsatbed.xml	Fri Jul 19 22:32:44 2024 +0000
+++ b/microsatbed.xml	Fri Jul 19 23:32:59 2024 +0000
@@ -1,10 +1,9 @@
-<tool name="STR to bed" id="microsatbed" version="1.3.2.0" profile="22.05">
+<tool name="STR to bed" id="microsatbed" version="1.3.2" profile="22.05">
   <description>Short Tandem Repeats to bed features from fasta</description>
   <requirements>
     <requirement version="3.12.3" type="package">python</requirement>
     <requirement version="2.1.0" type="package">pyfastx</requirement>
     <requirement version="1.3.2" type="package">pytrf</requirement>
-    <requirement version="0.2.0" type="package">pybigtools</requirement>
     <requirement version="455" type="package">ucsc-bedgraphtobigwig</requirement>
      
   </requirements>
diff -r 4cb6cc083620 -r efc775ab30fe test.bw
Binary file test.bw has changed