Mercurial > repos > fubar > microsatbed
changeset 23:45f690db0eaf draft
planemo upload for repository https://github.com/fubar2/microsatbed commit d952bc313f408735456747c3d33e09a3170c8f59-dirty
| author | fubar |
|---|---|
| date | Wed, 17 Jul 2024 23:19:12 +0000 |
| parents | b5acf60b903d |
| children | 94c5f834c0cc |
| files | dibed.bw find_str.py microsatbed.xml |
| diffstat | 3 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- a/find_str.py Wed Jul 17 22:41:41 2024 +0000 +++ b/find_str.py Wed Jul 17 23:19:12 2024 +0000 @@ -11,14 +11,14 @@ Designed to build some of the microsatellite tracks from https://github.com/arangrhie/T2T-Polish/tree/master/pattern for the VGP. """ -def getDensity(name, bed, len, winwidth): - nwin = int(len / winwidth) +def getDensity(name, bed, chrlen, winwidth): + 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 = [(name,x*winwidth,(x+1)*winwidth,float(d[x])) for x in range(nwin+1) if (x+1)*winwidth <= len] + dw = [(name,x*winwidth,(x+1)*winwidth,float(d[x])) for x in range(nwin+1) if (x+1)*winwidth <= chrlen] return dw def write_ssrs(args):
--- a/microsatbed.xml Wed Jul 17 22:41:41 2024 +0000 +++ b/microsatbed.xml Wed Jul 17 23:19:12 2024 +0000 @@ -92,6 +92,7 @@ help="Bed features will be output for every motif of the selected length(s) with the minimum required repeats or more"> <option value="DI" selected="true">All dimers (AC,AG,AT,...)</option> <option value="TRI">All trimers (ACG,..)</option> + <option value="TETRA">All tetramers (ACGT,..)</option> <option value="PENTA">All pentamers (ACGTC,..)</option> <option value="HEXA">All hexamers (ACGTCG,..)</option> <option value="MONO">All monomers (A,C...). Warning! Can produce overwhelming numbers of bed features</option> @@ -102,6 +103,7 @@ help="Bed features will be output for every motif of the selected length(s) with the minimum required repeats or more"> <option value="DI" selected="true">All dimers (AC,AG,AT,...)</option> <option value="TRI">All trimers (ACG,..)</option> + <option value="TETRA">All tetramers (ACGT,..)</option> <option value="PENTA">All pentamers (ACGTC,..)</option> <option value="HEXA">All hexamers (ACGTCG,..)</option> <option value="MONO">All monomers (A,C...). Warning! Can produce overwhelming numbers of bed features</option>