Merge pull request #1040 from taylorpaisie/tkp-rdp

RDP classifier

Program_Licenses.md

@@ -145,6 +145,7 @@ The licenses of the open-source software that is contained in these Docker image
 | raven | MIT | https://github.com/lbcb-sci/raven/blob/master/LICENSE |
 | RAxML | GNU GPLv3 | https://github.com/stamatak/standard-RAxML/blob/master/gpl-3.0.txt |
 | RAxML-NG | GNU AGPLv3| https://github.com/amkozlov/raxml-ng/blob/master/LICENSE.txt |
+| RAxML-NG | GNU GPLv2 | https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html |
 | ResFinder | Apache 2.0 | https://bitbucket.org/genomicepidemiology/resfinder/src/master/ |
 | Roary | GNU GPLv3 | https://github.com/sanger-pathogens/Roary/blob/master/GPL-LICENSE |
 | SalmID| MIT | https://github.com/hcdenbakker/SalmID/blob/master/LICENSE |

README.md

@@ -251,6 +251,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [raven](https://hub.docker.com/r/staphb/raven/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/raven)](https://hub.docker.com/r/staphb/raven) | <ul><li>1.5.1</li><li>1.8.1</li><li>[1.8.3](./raven/1.8.3)</li></ul> | https://github.com/lbcb-sci/raven |
 | [RAxML](https://hub.docker.com/r/staphb/raxml/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/raxml)](https://hub.docker.com/r/staphb/raxml) | <ul><li>8.2.12</li><li>[8.2.13](./raxml/8.2.13/)</li></ul> | https://github.com/stamatak/standard-RAxML |
 | [RAxML-NG](https://hub.docker.com/r/staphb/raxml-ng/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/raxml-ng)](https://hub.docker.com/r/staphb/raxml-ng) | <ul><li>[1.2.2](./raxml-ng/1.2.2/)</li></ul> | https://github.com/amkozlov/raxml-ng |
+| [rdp](https://hub.docker.com/r/staphb/rdp) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/rdp)](https://hub.docker.com/r/staphb/rdp) | <ul><li>[2.14](./rdp/0.4.0/)</li></ul> | https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.14.zip/download |
 | [ResFinder](https://hub.docker.com/r/staphb/resfinder/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/resfinder)](https://hub.docker.com/r/staphb/resfinder) | <ul><li>[4.1.1](./resfinder/4.1.11/)</li><li>[4.5.0](./resfinder/4.5.0/)</li></ul> | https://bitbucket.org/genomicepidemiology/resfinder/src/master/ |
 | [Roary](https://hub.docker.com/r/staphb/roary/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/roary)](https://hub.docker.com/r/staphb/roary) | <ul><li>3.12.0</li><li>3.13.0</li></ul> | https://github.com/sanger-pathogens/Roary |
 | [SalmID](https://hub.docker.com/r/staphb/salmid) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/salmid)](https://hub.docker.com/r/staphb/salmid) | <ul><li>0.1.23</li></ul> | https://github.com/hcdenbakker/SalmID |
@@ -367,3 +368,4 @@ Each Dockerfile lists the author(s)/maintainer(s) as a metadata `LABEL`, but the
   * [@nawrockie](https://github.com/nawrockie)
   * [@stephenturner](https://github.com/stephenturner)
   * [@soejun](https://github.com/soejun)
+  * [@taylorpaisie](https://github.com/taylorpaisie)

rdp/2.14/Dockerfile

@@ -0,0 +1,59 @@
+# set global variables
+ARG RDP_VER="2.14"
+
+# build Dockerfile
+FROM ubuntu:jammy as app
+ARG RDP_VER
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="RDP Classifier"
+LABEL software.version=${RDP_VER}
+LABEL description="The RDP Classifier is a naive Bayesian classifier which was developed to provide rapid taxonomic placement based on rRNA sequence data."
+LABEL website="https://github.com/rdpstaff/classifier"
+LABEL documentation="https://sourceforge.net/projects/rdp-classifier/"
+LABEL license.url="https://github.com/rdpstaff/classifier/blob/master/LICENSE"
+LABEL maintainer="Taylor K. Paisie"
+LABEL maintainer.email='[email protected]'
+
+ENV DEBIAN_FRONTEND=noninteractive 
+
+# Install dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    openjdk-11-jre \
+    wget \
+    unzip && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/* 
+
+# Install rdp_classifer
+RUN wget -q https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_${RDP_VER}.zip &&\
+    unzip rdp_classifier_${RDP_VER}.zip &&\
+    mv /rdp_classifier_${RDP_VER} /rdp_classifier &&\
+    chmod +x /rdp_classifier/dist/classifier.jar &&\
+    echo "#!/bin/bash" >> /rdp_classifier/dist/classifier &&\
+    echo "exec java -jar /rdp_classifier/dist/classifier.jar """"$""@"""" " >> /rdp_classifier/dist/classifier &&\
+    chmod +x /rdp_classifier/dist/classifier
+
+ENV PATH="${PATH}:/rdp_classifier/dist" LC_ALL=C
+
+CMD classifier
+
+RUN mkdir data/
+WORKDIR /data
+
+# Running RDP on test controls
+FROM app as test
+
+WORKDIR /test
+
+# running help to ensure executable is in path
+RUN classifier
+
+# testing on real files
+RUN apt-get update && apt-get install -y \
+    python3 \
+    wget
+
+RUN mkdir ../tests/
+COPY tests/ ../tests/
+RUN python3 -m unittest discover -v -s ../tests

rdp/2.14/README.md

@@ -0,0 +1,53 @@
+# RDP Classifier 
+
+Main tool: [RDP Classifier](https://sourceforge.net/projects/rdp-classifier/)
+
+Code repository: https://github.com/rdpstaff/classifier
+
+Basic information on how to use this tool:
+- executable: |
+```
+	classify      - classify one or multiple samples
+	crossvalidate - cross validate accuracy testing
+	libcompare    - compare two samples
+	loot          - leave one (sequence or taxon) out accuracy testing
+	merge-detail  - merge classification detail result files to create a taxon assignment counts file
+	merge-count   - merge multiple taxon assignment count files to into one count file
+	random-sample - random select a subset or subregion of sequences
+	rm-dupseq     - remove identical or any sequence contained by another sequence
+	rm-partialseq - remove partial sequences
+	taxa-sim      - calculate and plot the similarities within taxa
+	train         - retrain classifier
+```
+
+- help: classify # with no flags
+- version: NA
+- description: | 
+> The RDP Classifier is a naive Bayesian classifier which was developed to provide rapid taxonomic placement based on rRNA sequence data.
+
+
+Full documentation: https://sourceforge.net/projects/rdp-classifier/
+
+
+## Example analysis
+Get test data:
+```
+# Download test data
+wget -nv https://raw.githubusercontent.com/taylorpaisie/docker_containers/main/rdp/2.14/16S_rRNA_gene.Burkholderia_pseudomallei.2002721184.AY305776.1.fasta -O 16S_test.fa
+wget -nv https://raw.githubusercontent.com/taylorpaisie/docker_containers/main/rdp/2.14/18S_rRNA_gene.Homo_sapiens.T2T-CHM13v2.0.Chromosome13.fasta -O 18S_test.fa
+```
+
+Use RDP Classifier to get taxonomic assignments for bacterial and archaeal 16S rRNA sequences:
+```
+classifier classify -o taxa_16S_test.txt 16S_test.fa
+classifier classify -o taxa_18S_test.txt 18S_test.fa
+```
+
+## Output
+```
+head -2 taxa_16S_test.txt
+
+AY305776.1		Root	rootrank	1.0	Bacteria	domain	1.0	Pseudomonadota	phylum	1.0	Betaproteobacteria	class	1.0	Burkholderiales	order	1.0	Burkholderiaceae	family	1.0	Burkholderia	genus	1.0
+```
+
+

rdp/2.14/tests/scripts/run_controls.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+# Download test data
+wget -nv https://raw.githubusercontent.com/taylorpaisie/docker_containers/main/rdp/2.14/16S_rRNA_gene.Burkholderia_pseudomallei.2002721184.AY305776.1.fasta -O 16S_test.fa
+wget -nv https://raw.githubusercontent.com/taylorpaisie/docker_containers/main/rdp/2.14/18S_rRNA_gene.Homo_sapiens.T2T-CHM13v2.0.Chromosome13.fasta -O 18S_test.fa
+
+# Get taxonomic assignments for your data
+classifier classify -o taxa_16S_test.txt 16S_test.fa
+classifier classify -o taxa_18S_test.txt 18S_test.fa
+
+# run checksum on files
+sha256sum 16S_test.fa > 16S_checksum.txt
+sha256sum 18S_test.fa > 18S_checksum.txt
+
+
+
+

rdp/2.14/tests/test_controls.py

@@ -0,0 +1,31 @@
+import unittest
+import subprocess
+from subprocess import PIPE
+
+
+class TestControls(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        command = "bash /tests/scripts/run_controls.sh"
+        subprocess.run(command, shell=True, stdout=PIPE)
+
+
+    def test_rdp16S(self):
+        with open("16S_checksum.txt") as f:
+            rdp_checksum = f.readlines()[0].split(" ")[0]
+        self.assertEqual(
+            rdp_checksum,
+            "a38342a9ba63946ffb4324c7858f5cc43b873673cb08080437f7500dda351f65",
+        )
+
+    def test_rdp18S(self):
+        with open("18S_checksum.txt") as f:
+            rdp_checksum = f.readlines()[0].split(" ")[0]
+        self.assertEqual(
+            rdp_checksum,
+            "44bf9c60750ff3b804b3e3a56969dab982307a16faee63f0928b2f54e70b02f7",
+        )
+
+
+if __name__ == "__main__":
+    unittest.main()

rdp/2.14/tests/test_versions.py

@@ -0,0 +1,14 @@
+import unittest
+import subprocess
+import sys
+import re
+
+
+class TestVersion(unittest.TestCase):
+    def test_python(self):
+        version = f"{sys.version_info.major}.{sys.version_info.minor}"
+        self.assertEqual(version, "3.10")  # Update this with the expected Python version
+
+
+if __name__ == "__main__":
+    unittest.main()