Set version to 2.0.1

CHANGELOG.txt

@@ -1,3 +1,27 @@
+v2.0.1 (2022-08-23)
+- Accelerate fragment building for paired-end reads
+- Set color blind friendly colors for viz align plots
+v2.0.0 (2022-06-28)
+- Added multi-species analysis (changes the API)
+- Results of subcommands separated by species
+- Updated mapping statistics (e.g. count species-cross aligned reads)
+- Include or exclude species-cross aligned reads in read counts and/or normalization
+- Additional vizualisation for multi-species projects
+- Template fragment building for paired-end reads
+- Subcommands (for paired-end reads) use counts and/or normalization based on fragments or single reads
+- Filter reads by template length
+- Output folder creation only when calling the corresponding subcommands
+v1.0.5 (2021-10-12)
+- Fixed a bug of package creation, where the old build was not removed prior to cration
+v1.0.4 (2021-10-12)
+- Set biopython install requirements to v1.78
+- Bugfix wheel package
+v1.0.3 (2021-10-08)
+- Bugfix in gff3 parser
+v1.0.2 (2021-10-08)
+- Fixed segemehl tests
+- Gene quantification: Removed normalization by number of splits
+- Hotfix of calculating TMPs with zero values
 v1.0.1 (2020-07-11)
 - Hotfix of align error cause by realign arg still present
 v1.0.0 (2020-07-08)

CITATION.cff

@@ -0,0 +1,39 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it as below.
+authors:
+  - family-names: Förstner
+    given-names: Konrad Ulrich 
+    orcid: https://orcid.org/0000-0002-1481-2996
+  - family-names: Sauerwein
+    given-names: Till David 
+    orcid: https://orcid.org/0000-0001-5830-4208
+  - family-names: Bischler
+    given-names: Thorsten 
+    orcid: https://orcid.org/0000-0001-9288-9481
+  - family-names: Tobin
+    given-names: Diarmaid         
+title: "READemption"
+version: 2.0.1
+doi: https://zenodo.org/record/6772669
+date-released: 2022-08-23
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Förstner"
+    given-names: "Konrad U."
+    orcid: "https://orcid.org/0000-0002-1481-2996"
+  - family-names: "Vogel"
+    given-names: "Jörg"
+    orcid: "https://orcid.org/0000-0003-2220-1404"
+  - family-names: "Sharma"
+    given-names: "Cynthia M."
+    orcid: "https://orcid.org/0000-0002-2321-9705"    
+  doi: "10.1093/bioinformatics/btu533"
+  journal: "Bioinformatics"
+  month: 12
+  start: 3421
+  end: 3423
+  title: "READemption—a tool for the computational analysis of deep-sequencing–based transcriptome data"
+  issue: 23
+  volume: 30
+  year: 2014

bin/reademption

@@ -6,10 +6,10 @@ import argparse
 from reademptionlib.controller import Controller
 
 __author__ = "Konrad Foerstner <[email protected]>, Till Sauerwein <[email protected]>"
-__copyright__ = "2011-2020 by Konrad Foerstner <[email protected], , Till Sauerwein <[email protected]>"
+__copyright__ = "2011-2022 by Konrad Foerstner <[email protected], , Till Sauerwein <[email protected]>"
 __license__ = "ISC license"
 __email__ = "[email protected], [email protected]"
-__version__ = "1.0.1"
+__version__ = "2.0.1"
 
 
 def main():

docs/build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: b8a0a39fc8578a3122c23a91cf47a72c
+config: 583e472278924fbeadb4a0128b32f285
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_sources/installation.rst.txt

@@ -146,3 +146,48 @@ upgrade it to the newest version by running
 ::
 
   pip3 install --upgrade READemption
+
+
+Package version requirements and installation
+---------------------------------------------
+Create a python version 3.9 environment
+::
+    conda create --name py3.9_reademption python=3.9
+
+Activate the environment
+::
+    conda activate py3.9_reademption
+
+Install pysam
+::
+    conda install -c bioconda pysam=0.19.1
+
+
+Install segemehl
+::
+    conda install -c bioconda segemehl=0.3.4
+
+Install biopython (numpy 1.23 included)
+
+::
+    conda install biopython=1.79
+
+Install pandas
+
+::
+    conda install pandas=1.4.3
+
+Install seaborn
+
+::
+    conda install seaborn=0.11.2
+
+Install matplotlib
+
+::
+    conda install matplotlib=3.5.2
+
+Install pytest (only required for testing)
+
+::
+    conda install pytest

docs/build/html/_static/basic.css

@@ -222,7 +222,7 @@ table.modindextable td {
 /* -- general body styles --------------------------------------------------- */
 
 div.body {
-    min-width: 450px;
+    min-width: 360px;
     max-width: 800px;
 }
 
@@ -237,16 +237,6 @@ a.headerlink {
     visibility: hidden;
 }
 
-a.brackets:before,
-span.brackets > a:before{
-    content: "[";
-}
-
-a.brackets:after,
-span.brackets > a:after {
-    content: "]";
-}
-
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -334,13 +324,15 @@ aside.sidebar {
 p.sidebar-title {
     font-weight: bold;
 }
-
+nav.contents,
+aside.topic,
 div.admonition, div.topic, blockquote {
     clear: left;
 }
 
 /* -- topics ---------------------------------------------------------------- */
-
+nav.contents,
+aside.topic,
 div.topic {
     border: 1px solid #ccc;
     padding: 7px;
@@ -379,13 +371,17 @@ div.body p.centered {
 
 div.sidebar > :last-child,
 aside.sidebar > :last-child,
+nav.contents > :last-child,
+aside.topic > :last-child,
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
 }
 
 div.sidebar::after,
 aside.sidebar::after,
+nav.contents::after,
+aside.topic::after,
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -428,10 +424,6 @@ table.docutils td, table.docutils th {
     border-bottom: 1px solid #aaa;
 }
 
-table.footnote td, table.footnote th {
-    border: 0 !important;
-}
-
 th {
     text-align: left;
     padding-right: 5px;
@@ -614,20 +606,26 @@ ol.simple p,
 ul.simple p {
     margin-bottom: 0;
 }
-
-dl.footnote > dt,
-dl.citation > dt {
+aside.footnote > span,
+div.citation > span {
     float: left;
-    margin-right: 0.5em;
 }
-
-dl.footnote > dd,
-dl.citation > dd {
+aside.footnote > span:last-of-type,
+div.citation > span:last-of-type {
+  padding-right: 0.5em;
+}
+aside.footnote > p {
+  margin-left: 2em;
+}
+div.citation > p {
+  margin-left: 4em;
+}
+aside.footnote > p:last-of-type,
+div.citation > p:last-of-type {
     margin-bottom: 0em;
 }
-
-dl.footnote > dd:after,
-dl.citation > dd:after {
+aside.footnote > p:last-of-type:after,
+div.citation > p:last-of-type:after {
     content: "";
     clear: both;
 }
@@ -644,10 +642,6 @@ dl.field-list > dt {
     padding-right: 5px;
 }
 
-dl.field-list > dt:after {
-    content: ":";
-}
-
 dl.field-list > dd {
     padding-left: 0.5em;
     margin-top: 0em;