Merge pull request #6 from moshi4/develop

Bump to v0.3.0
moshi4 · Mar 8, 2024 · aa26e90 · aa26e90
2 parents 20d069c + 16ef6b4
commit aa26e90
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diff --git a/README.md b/README.md
@@ -20,6 +20,11 @@ pybarrnap is a python implementation of [barrnap](https://github.com/tseemann/ba
 It provides a CLI compatible with barrnap and also provides a python API for running rRNA prediction and retrieving predicted rRNA.
 pybarrnap depends only on the python library and not on the external command-line tools nhmmer and bedtools.
 
+> [!NOTE]
+> Barrnap v0.9 uses the HMM profile database created from older releases of Rfam(11.0) and SILVA(128).
+> On the other hand, pybarrnap uses the HMM profile database created from the Rfam(14.10) latest release as of 2024/03.
+> Therefore, there will be some differences in results between Barrnap v0.9 and pybarrnap.
+
 ## Installation
 
 `Python 3.8 or later` is required for installation.
@@ -121,9 +126,9 @@ for rec in result.get_rrna_seq_records():
 
 ## LICENSE
 
-pybarrnap uses Barrnap v0.9 HMM profile database created from Rfam and SILVA.
+pybarrnap was reimplemented in python based on the perl implementation of Barrnap v0.9.
+HMM profile database for pybarrnap was created from Rfam(14.10) using a modified version of the database build script provided in Barrnap v0.9.
 
 - pybarrnap: [GPLv3](https://github.com/moshi4/pybarrnap/blob/main/LICENSE)  
-- Barrnap: [GPLv3](https://github.com/moshi4/pybarrnap/blob/main/src/pybarrnap/db/LICENSE.Barrnap)
-- Rfam: [CC0](https://github.com/moshi4/pybarrnap/blob/main/src/pybarrnap/db/LICENSE.Rfam)
-- SILVA: [Free for academic use](https://github.com/moshi4/pybarrnap/blob/main/src/pybarrnap/db/LICENSE.SILVA)
+- Barrnap([v0.9](https://github.com/tseemann/barrnap/tree/0.9)): [GPLv3](https://github.com/moshi4/pybarrnap/blob/main/src/pybarrnap/db/LICENSE.Barrnap)
+- Rfam([14.10](https://ftp.ebi.ac.uk/pub/databases/Rfam/14.10/)): [CC0](https://github.com/moshi4/pybarrnap/blob/main/src/pybarrnap/db/LICENSE.Rfam)
diff --git a/dbbuild/12S.mito.aln b/dbbuild/12S.mito.aln
diff --git a/dbbuild/16S.mito.aln b/dbbuild/16S.mito.aln
diff --git a/dbbuild/README.md b/dbbuild/README.md
@@ -0,0 +1,35 @@
+`build_HMMs.sh` script automatically builds the HMM profile database from the following data resources.
+This is a modified version of the database build [script](https://github.com/tseemann/barrnap/blob/0.9/build/build_HMMs.sh) provided in Barrnap v0.9.
+pybarrnap uses only [Rfam](https://rfam.org/) to create the HMM profile database and does not use [SILVA](https://www.arb-silva.de/), which is used in Barrnap v0.9.
+
+```diff
+Bacteria (70S)  
+        LSU 50S
+                5S      RF00001
+-               23S     SILVA-LSU-Bac (Barrnap v0.9)
++               23S     RF02541 (pybarrnap)
+        SSU 30S
+                16S     RF00177
+
+Archaea (70S)   
+        LSU 50S
+                5S      RF00001
+                5.8S    RF00002
+-               23S     SILVA-LSU-Arc (Barrnap v0.9)
++               23S     RF02540 (pybarrnap)
+        SSU 30S
+                16S     RF01959
+
+Eukaryote (80S)   
+        LSU 60S
+                5S      RF00001
+                5.8S    RF00002
+-               28S     SILVA-LSU-Euk (Barrnap v0.9)
++               28S     RF02543 (pybarrnap)
+        SSU 40S
+                18S     RF01960
+
+Metazoan Mito
+                12S     RefSeq (MT-RNR1, s-rRNA, rns)
+                16S     RefSeq (MT-RNR2, l-rRNA, rnl)      
+```
diff --git a/dbbuild/build_HMMs.sh b/dbbuild/build_HMMs.sh
@@ -0,0 +1,74 @@
+#!/bin/bash
+
+CPUS=$(grep -c bogomips /proc/cpuinfo)
+DB_OUTDIR="./db"
+
+# Download RFAM annotated seed alignments
+RFAM="Rfam.seed"
+RFAMURL="ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/${RFAM}.gz"
+if [ ! -r "$RFAM" ]; then
+  echo Downloading: $RFAM
+  wget $RFAMURL -q --show-progress
+  gunzip ${RFAM}.gz
+else
+  echo Using existing file: $RFAM
+fi
+
+# Retrieve target accession rRNA MSA
+echo Retrieve target accession MSA from MSA database...
+
+echo Indexing $RFAM
+esl-afetch --index $RFAM
+
+echo "Bacteria (5S=RF00001, 16S=RF00177, 23S=RF02541)"
+esl-afetch $RFAM RF00001 >5S.bac.aln
+esl-afetch $RFAM RF00177 >16S.bac.aln
+esl-afetch $RFAM RF02541 >23S.bac.aln
+
+echo "Archaea (5S=RF00001, 5.8S=RF00002, 16S=RF01959, 23S=RF02540)"
+esl-afetch $RFAM RF00001 >5S.arc.aln
+esl-afetch $RFAM RF00002 >5_8S.arc.aln
+esl-afetch $RFAM RF01959 >16S.arc.aln
+esl-afetch $RFAM RF02540 >23S.arc.aln
+
+echo "Eukaryote (5S=RF00001, 5.8S=RF00002, 18S=RF01960, 28S=RF02543)"
+esl-afetch $RFAM RF00001 >5S.euk.aln
+esl-afetch $RFAM RF00002 >5_8S.euk.aln
+esl-afetch $RFAM RF01960 >18S.euk.aln
+esl-afetch $RFAM RF02543 >28S.euk.aln
+
+# Check metazoan mitochondria alignment file exists
+FILE="12S.mito.aln"
+if [ ! -r "$FILE" ]; then
+  echo "Missing included $FILE file."
+  exit 1
+fi
+FILE="16S.mito.aln"
+if [ ! -r "$FILE" ]; then
+  echo "Missing included $FILE file."
+  exit 1
+fi
+
+# Build HMM profile
+mkdir -p $DB_OUTDIR
+for KINGDOM in arc bac euk mito; do
+  for TYPE in 5S 5_8S 12S 16S 23S 18S 28S; do
+    ID="${TYPE}.${KINGDOM}"
+    if [ -s "${ID}.aln" ]; then
+      echo "*** $ID ***"
+      hmmbuild --cpu $CPUS --rna -n ${TYPE}_rRNA ${ID}.hmm ${ID}.aln
+    fi
+  done
+  cat *.${KINGDOM}.hmm >${DB_OUTDIR}/${KINGDOM}.hmm
+done
+
+# Remove unnecessary files
+rm -f ${RFAM}.ssi
+for KINGDOM in arc bac euk; do
+  rm -f *.${KINGDOM}.aln *.${KINGDOM}.hmm
+done
+rm -f *.mito.hmm
+
+# Show HMM profile files
+echo -e "\nFinished building HMM profiles:"
+ls -1 ${DB_OUTDIR}/*.hmm
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybarrnap"
-version = "0.2.0"
+version = "0.3.0"
 description = "Python implementation of barrnap (Bacterial ribosomal RNA predictor)"
 authors = ["moshi4"]
 license = "GPL-3.0-only"

diff --git a/src/pybarrnap/__init__.py b/src/pybarrnap/__init__.py
@@ -1,6 +1,6 @@
 from pybarrnap.barrnap import Barrnap
 
-__version__ = "0.2.0"
+__version__ = "0.3.0"
 
 __all__ = [
     "Barrnap",

diff --git a/src/pybarrnap/db/LICENSE.Rfam b/src/pybarrnap/db/LICENSE.Rfam
@@ -1,10 +1,51 @@
-Rfam version 11.0 was produced at the Wellcome Trust Sanger
-Institute. Rfam is based on a sequence database called Rfamseq, which
-is derived from WGS and STD data classes from EMBL release 110.
+Rfam version 14.8 was produced at the European Bioinformatics Institute.
+Rfam is based on a sequence database called Rfamseq. The genome-centric
+version of Rfam is built from a collection of reference genomes,
+which are provided by Uniprot proteomes.
 
 Rfam is freely available under the Creative Commons Zero ("CC0")
 licence. (http://creativecommons.org/publicdomain/zero/1.0/)
 
-Rfam is powered by the Infernal package written by Eric Nawrockie at
-the Howard Hughes Janelia Farm Research Campus
-(http://www.hhmi.org/janelia/labs.html).
+Rfam is powered by the Infernal package (http://eddylab.org/infernal/).
+The current lead developer of Infernal is Eric Nawrocki,
+at the National Center for Biotechnology Information (NCBI,
+nawrocke@ncbi.nlm.nih.gov).
+
+
+If you make use of Rfam in your work we ask that you cite the
+following publications:
+
+I. Kalvari, J. Argasinska, N. Quinones-Olvera, E.P. Nawrocki, E. Rivas,
+S.R. Eddy, A. Bateman, R.D. Finn and A.I. Petrov
+Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
+Nucleic Acids Res. 2017 Sep;
+
+E.P. Nawrocki, S.W. Burge, A. Bateman, J. Daub, R.Y. Eberhardt, S.R. Eddy,
+E.W. Floden, P.P. Gardner, T.A. Jones, J.T. and R.D. Finn
+Rfam 12.0: updates to the RNA families database
+Nucleic Acids Res. 2014 Nov;
+
+Burge SW, Daub J, Eberhardt R, Tate JG, Barquist L, Nawrocki E, Eddy S, Gardner
+PP, Bateman A
+Rfam 11.0: 10 years of RNA families.
+Nucleic Acids Res. 2012 Nov;
+
+Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S,
+Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A
+Rfam: updates to the RNA families database.
+Nucleic Acids Res. 2008 Oct;
+
+Daub J, Gardner PP, Tate J, Ramskˆld D, Manske M, Scott WG,
+Weinberg Z, Griffiths-Jones S, Bateman A
+The RNA WikiProject: Community annotation of RNA families.
+RNA. 2008 Dec; 14:(12)2462-2464
+
+Rfam: annotating non-coding RNAs in complete genomes
+Sam Griffiths-Jones, Simon Moxon, Mhairi Marshall, Ajay Khanna,
+Sean R. Eddy and Alex Bateman
+Nucleic Acids Res. 2005 33:D121-D124
+
+Rfam: an RNA family database.
+Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna
+and Sean R. Eddy.
+Nucleic Acids Res. 2003 31:439-441
diff --git a/src/pybarrnap/db/LICENSE.SILVA b/src/pybarrnap/db/LICENSE.SILVA