Mercurial > repos > fubar > microsatbed

changeset 16:ee773bbde3c3 draft

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planemo upload for repository https://github.com/fubar2/microsatbed commit d952bc313f408735456747c3d33e09a3170c8f59-dirty
author fubar
date Wed, 17 Jul 2024 05:08:00 +0000
parents 4af0486b8513
children 264d79548d19
files find_str.py microsatbed.xml
diffstat 2 files changed, 8 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/find_str.py	Wed Jul 17 04:28:28 2024 +0000
+++ b/find_str.py	Wed Jul 17 05:08:00 2024 +0000
@@ -27,12 +27,12 @@
             ssrs = pytrf.STRFinder(
                 name,
                 seq,
-                args.minreps,
-                args.minreps,
-                args.minreps,
-                args.minreps,
-                args.minreps,
-                args.minreps,
+                2,
+                1,
+                2,
+                2,
+                2,
+                2,
             )
         else:
             ssrs = pytrf.STRFinder(
@@ -55,7 +55,7 @@
                 ssr.length,
             )
             # pytrf reports a 1 based start position so start-1 fixes the bed interval lengths
-            if args.specific and ssr.motif in specific:
+            if args.specific and ssr.motif in specific and ssr.repeat >= args.minreps:
                 bed.append(row)
             elif args.mono and len(ssr.motif) == 1:
                 bed.append(row)
--- a/microsatbed.xml	Wed Jul 17 04:28:28 2024 +0000
+++ b/microsatbed.xml	Wed Jul 17 05:08:00 2024 +0000
@@ -1,4 +1,4 @@
-<tool name="STR to bed" id="microsatbed" version="1.3.0" profile="22.05">
+<tool name="STR to bed" id="microsatbed" version="1.3.0a" profile="22.05">
   <description>Short Tandem Repeats to bed features from fasta</description>
   <requirements>
     <requirement version="3.12.3" type="package">python</requirement>