From 074b8bc6248260245140ff8a1b9beb9a246ef6ad Mon Sep 17 00:00:00 2001 From: Petr Novak Date: Tue, 1 Oct 2024 13:10:12 +0200 Subject: [PATCH] added handling of tab in sequence name --- README.md | 4 +++- changelog.md | 5 +++++ utils/detect_putative_ltr.R | 2 +- version.py | 2 +- 4 files changed, 10 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 399bf0c..d737e63 100644 --- 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 index aacad35..63efaa2 100644 --- 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 index c104fe8..21f2eed 100755 --- 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 index 28cfdcd..7a2396f 100644 --- a/version.py +++ b/version.py @@ -1 +1 @@ -__version__ = '0.4.0.1' +__version__ = '0.4.0.2'