diff find_str.py @ 25:8d0b8a75350f draft

planemo upload for repository https://github.com/fubar2/microsatbed commit d952bc313f408735456747c3d33e09a3170c8f59-dirty

--- a/find_str.py	Fri Jul 19 05:20:35 2024 +0000
+++ b/find_str.py	Fri Jul 19 06:41:18 2024 +0000
@@ -21,7 +21,7 @@
     dw = [
         (name, (x * winwidth)+1, (x + 1) * winwidth, float(d[x]))
         for x in range(nwin + 1)
-        if  (x + 1) * winwidth <= chrlen
+        if  (x + 1) * winwidth <= chrlen - 1
     ]
     return dw
 
@@ -42,6 +42,8 @@
         specific = args.specific.upper().split(",")
     fa = Fastx(args.fasta, uppercase=True)
     for name, seq in fa:
+        chrlen = len(seq)
+        chrlens[name] = chrlen
         cbed = []
         for ssr in pytrf.STRFinder(
             name,
@@ -78,15 +80,12 @@
                 cbed.append(row)
         bed += cbed
         if args.bigwig:
-            chrlen = len(seq)
-            chrlens[name] = chrlen
             w = getDensity(name, cbed, chrlen, args.winwidth)
             wig += w
     if args.bigwig:
         wig.sort()
         bw = pybigtools.open("temp.bw", "w")
         bw.write(chrlens, wig)
-        bw.close()
         shutil.move("temp.bw", args.bed)
     else:
         bed.sort()