Mercurial > repos > petr-novak > re_utils

changeset 11:16150c85fb3a draft

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Uploaded
author petr-novak
date Tue, 04 Feb 2020 07:39:32 -0500
parents 768883847008
children 6b7d31026d1c
files RM_custom_search.py RM_custom_search.xml
diffstat 2 files changed, 5 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/RM_custom_search.py	Mon Feb 03 06:44:58 2020 -0500
+++ b/RM_custom_search.py	Tue Feb 04 07:39:32 2020 -0500
@@ -19,7 +19,10 @@
         # extract only dirCLXXXX/reads.fas
         seq_list = []
         for filein in z.namelist():
-            if filein.lower().startswith("seqclust/clustering/clusters/dir_cl") and filein.endswith("reads.fas"):
+            c1 = filein.lower().startswith("seqclust/clustering/clusters/dir_cl")
+            c2 = filein.endswith("reads.fas")
+            c3 = filein.endswith("reads.fasta")  # in newer RE2 versions
+            if c1 and (c2 or c3):
                 outdir = filein.split("/")[3]
                 outfile = outdir +"/reads.fas"
                 source = z.open(filein)
--- a/RM_custom_search.xml	Mon Feb 03 06:44:58 2020 -0500
+++ b/RM_custom_search.xml	Tue Feb 04 07:39:32 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="RMsearch" name="RepeatMasker custom search" version="1.0.1">
+<tool id="RMsearch" name="RepeatMasker custom search" version="1.0.2">
 
   <description>Scan clustering results using RepeatMasker against custom database of repeats</description>
   <requirements>