added handling of tab in sequence name

kavonrtep · Oct 1, 2024 · 074b8bc · 074b8bc
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diff --git a/README.md b/README.md
@@ -40,6 +40,8 @@ https://anaconda.org/petrnovak/dante_ltr/badges/version.svg)](https://anaconda.o
 ```shell
 conda create -n dante_ltr -c bioconda -c conda-forge -c petrnovak dante_ltr
 ```
+**Important version information** DANTE_LTR versions up to 0.3.5.3 are compatible with REXdb Viridiplante database version 3.0. Versions 4.0.1 are compatible with REXdb Viridiplante database version 3.0 and 4.0. REXdb Viridiplantae v 4.0 include additional LTR-RT lineages characterized non-angiosperm species. Updated REXdb and used classification system can be found https://github.com/repeatexplorer/rexdb.  
+
 
 [![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/kavonrtep/dante_ltr)
 
@@ -51,7 +53,7 @@ Detailed tutorial on how to use DANTE and DANTE_LTR on Galaxy server is [here](h
 
 #### Installation of both DANTE and DANTE_LTR using conda into single environment:
 ```shell
-conda create -n dante_ltr -c bioconda -c conda-forge -c petrnovak dante_ltr dante
+conda create -n dante_ltr -c bioconda -c conda-forge -c petrnovak dante_ltr=0.4.0.1 dante=0.2.0
 conda activate dante_ltr
 ```
 #### Download example data:

diff --git a/changelog.md b/changelog.md
@@ -1,3 +1,8 @@
+## 0.4.0.1 (2024-09-20)
+
+*  fix in installation instruction 
+*  updated to REXdb Viridiplantae 4.0 
+
 ## 0.3.5.1 (2024-04-18)
 
 *  Improved HTML report 

diff --git a/utils/detect_putative_ltr.R b/utils/detect_putative_ltr.R
@@ -126,7 +126,7 @@ s <- readDNAStringSet(opt$reference_sequence)  # genome assembly
 cat("done\n")
 
 # clean sequence names:
-names(s) <- gsub(" .+", "", names(s))
+names(s) <- gsub("\\s.+", "", names(s))
 
 # verify that seqlevels in g match seqlevels in s:
 if (!all(seqlevels(g) %in% seqlevels(s))){

diff --git a/version.py b/version.py
@@ -1 +1 @@
-__version__ = '0.4.0.1'
+__version__ = '0.4.0.2'