Merge pull request #14 from USDA-ARS-GBRU/1.8.1-EOL

1.8.1 eol

.github/workflows/python-package.yml

@@ -0,0 +1,57 @@
+name: Weekly Build and Test
+
+on:
+  push:
+    branches:
+      - 1.8.1-EOL
+  schedule:
+    - cron: "0 0 */7 * *"
+
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest   
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.8.13'
+    - run:   |
+         sudo apt update
+         sudo apt install gcc-10 g++-10
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Initiate conda channels
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: testenv
+        python-version: 3.8.13
+        channels: conda-forge,bioconda
+        allow-softlinks: true
+        channel-priority: flexible
+        show-channel-urls: true
+        use-only-tar-bz2: true
+
+    - name: Set up environment
+      run: |
+        wget https://data.qiime2.org/distro/core/qiime2-2022.8-py38-linux-conda.yml
+        conda env create -n qiime2-2022.8 --file qiime2-2022.8-py38-linux-conda.yml
+    - name: Install Dependencies
+      run: |
+        source activate qiime2-2022.8
+        conda install -y -c bioconda bbmap==38.69
+        pip install itsxpress==1.8.1
+        conda install biopython
+        pip install pyzstd
+        pip install pytest
+        pip install .
+    - name: Test with pytest
+      run: |
+        source activate qiime2-2022.8
+        pytest

README.rst

@@ -1,22 +1,37 @@
 Q2_ITSxpress: A Qiime2 plugin to rapidly trim the Internally transcribed spacer (ITS) region of FASTQ files
 ===========================================================================================================
-.. image:: https://travis-ci.org/USDA-ARS-GBRU/q2_itsxpress.svg?branch=master
-  :target: https://travis-ci.org/USDA-ARS-GBRU/q2_itsxpress
-
-.. image:: https://codecov.io/gh/USDA-ARS-GBRU/q2_itsxpress/branch/master/graph/badge.svg
-  :target: https://codecov.io/gh/USDA-ARS-GBRU/q2_itsxpress
-
-.. image:: https://api.codacy.com/project/badge/Grade/4d00341b4abc4e04a77cf5ca6674cd3c
-  :target: https://www.codacy.com/app/USDA-ARS-GBRU/q2_itsxpress?utm_source=github.com&utm_medium=referral&utm_content=USDA-ARS-GBRU/q2_itsxpress&utm_campaign=Badge_Grade
 
+.. image:: https://github.com/USDA-ARS-GBRU/q2_itsxpress/actions/workflows/python-package.yml/badge.svg
+   :target: https://github.com/USDA-ARS-GBRU/q2_itsxpress/actions/workflows/python-package.yml
+   :alt: Build Status
+
+.. image:: https://img.shields.io/github/v/release/USDA-ARS-GBRU/q2_itsxpress?style=social
+   :target: https://github.com/USDA-ARS-GBRU/q2_itsxpress/releases/latest
+   :alt: GitHub release (latest by date)
+
 .. image:: https://zenodo.org/badge/138209572.svg
    :target: https://zenodo.org/badge/latestdoi/138209572
 
 
+
+#####
+
+**This is the end of life version 1 of q2_itsxpress and the command line version of ITSxpress.
+The new version 2 of ITSxpress, has the Qiime2 plugin built in with command line version of ITSxpress. See 
+1.8.1-EOL branch of ITSxpress.**
+
+#####
+
+See ITSxpress 1.8.1-EOL branch here: ITSxpress-1.8.1-EOL_
+
+.. _`ITSxpress-1.8.1-EOL`: https://github.com/USDA-ARS-GBRU/itsxpress/tree/1.8.1-EOL
+
+
 Authors
 -------
 * Adam R. Rivers, US Department of Agriculture, Agricultural Research Service
 * Kyle C. Weber, US Department of Agriculture, Agricultural Research Service
+* Sveinn V. Einarsson, US Department of Agriculture, Agricultural Research Service
 
 Citation
 --------
@@ -36,8 +51,8 @@ length spacer regions. In amplicon sequencing studies it is common practice to
 trim off the conserved (SSU, 5,8S or LSU) regions. Bengtsson-Palme et al. (2013)
 published a software package ITSx_ to do this.
 
-Q2_ITSxpress extends this work by rapidly trimming FASTQ sequences within
-Qiime2.  Q2_ITSxpress is the Qiime2 plugin version of the stand alone command
+Q2-ITSxpress extends this work by rapidly trimming FASTQ sequences within
+Qiime2.  Q2-ITSxpress is the Qiime2 plugin version of the stand alone command
 line utility ITSxpress_. Q2_ITSxpress is designed to support the calling of
 exact sequence variants rather than OTUs. This newer method of sequence
 error-correction requires quality score data from each sequence, so each input
@@ -52,37 +67,49 @@ Requirements/Dependencies
 -------------------------
 
 * Qiime2 is required to run Q2-itsxpress (for stand alone software see ITSxpress_)
-* To install Qiime2 follow these instructions: https://docs.qiime2.org/2019.10/install/
+* To install Qiime2 follow these instructions: https://docs.qiime2.org/2022.8/install/
+* This end of life version 1 of q2-itsxpress and ITSxpress is **ONLY** compatible with Qiime2 version 2022.8. So make sure to follow the link above.
 
-Q2_itsxpress Installation
--------------------------
+* We are using mamba because it resolves packages better and faster, but conda can be substituted.
+	- Information on installing mamba or micromamba (either highly recommended) can be found here: `mamba installation guide`_
+
+.. _`mamba installation guide`: https://mamba.readthedocs.io/en/latest/installation.html
+
+Q2-itsxpress plugin installation
+--------------------------------
+1. Example on how to install and create new Qiime2-2022.8 environment.
+
+.. code-block:: bash
+
+  wget https://data.qiime2.org/distro/core/qiime2-2022.8-py38-osx-conda.yml
+  mamba env create -n qiime2-2022.8 --file qiime2-2022.8-py38-osx-conda.yml
 
-1. Activate the Qiime2 conda environment
+2. Activate the Qiime2 conda environment
 
 .. code-block:: bash
 
-  source activate qiime2-2019.10
+  mamba activate qiime2-2022.8
 
-2. Install Q2_itsxpress using BioConda_. Be sure to install Q2_itsxpres in the Qiime2 environment.
+3. Install Q2_itsxpress using BioConda_. Be sure to install itsxpress and q2_itsxpress in the Qiime2 environment using the following commands.
 
 .. code-block:: bash
 
-  conda install -c bioconda itsxpress
+  mamba install -c bioconda itsxpress==1.8.1
   pip install q2-itsxpress
 
-3. In your Qiime2 environment, refresh the plugins.
+4. In your Qiime2 environment, refresh the plugins.
 
 .. code-block:: bash
 
   qiime dev refresh-cache
 
-4. Check to see if the ITSxpress plugin is installed. You should see an output similar to the image below.
+5. Check to see if the ITSxpress plugin is installed. You should see an output similar to the image below.
 
 .. code-block:: bash
 
   qiime itsxpress
 
-.. image:: ../../screenshot.png
+.. image:: ./screenshot.png
 
 Usage
 -----

pyproject.toml

@@ -0,0 +1,49 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+
+[project]
+name = "q2_itsxpress"
+version = "1.8.1"
+description = "A QIIME2 plugin to trim ITS regions using ITSxpress"
+authors = [
+    {name = "Adam R. Rivers", email =  "adam.rivers@usda.gov"},
+    {name = "Sveinn V. Einarsson", email = "seinarsson@ufl.edu"}]
+maintainers = [
+    {name = "Adam R. Rivers", email =  "adam.rivers@usda.gov"},
+    {name = "Sveinn V. Einarsson", email = "seinarsson@ufl.edu"}]
+license = {file = "LICENSE.txt"}
+readme = "README.rst"
+keywords = ["Qiime2", "plugin", "Amplicon", "sequencing", "fungal", "ITS"]
+requires-python = ">=3.5"
+
+dependencies = [
+"qiime2",
+"itsxpress >=1.8.1",
+"pandas",
+]
+
+classifiers = [
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.5",
+    "Development Status :: 3 - Alpha"
+]
+
+
+[project.urls]
+repository = "http://github.com/usda-ars-gbru/q2_itsxpress"
+
+
+
+[project.optional-dependencies]
+tests = [
+"pytest"
+]
+
+[project.entry-points."qiime2.plugins"]
+q2_itsxpress="q2_itsxpress.plugin_setup:plugin"
+
+[tool.setuptools.package-data]
+q2_itsxpress = ["*.bib"]

q2_itsxpress/_itsxpress.py

@@ -1,7 +1,9 @@
 #!/usr/bin/env python
 """A python module to integrate ITSxpress into QIIME for the trimming of amplicon sequences.
 
-Authors: Adam Rivers and Kyle Weber, USDA Agricultural Research Service
+Authors: Adam Rivers, Kyle Weber, Sveinn V. Einarsson USDA Agricultural Research Service
+
+#####This is the end of life version 1 of the qiime2 plugin for ITSxpress. Please check Github page below to access version 2 of ITSxpress#####
 
 The internally transcribed spacer region is a region between the highly conserved small
 subunit (SSU) of rRNA and the large subunit (LSU) of the rRNA. The eukaryotic ITS contains
@@ -40,7 +42,7 @@ def _set_fastqs_and_check(fastq: str,
                           single_end: bool,
                           reversed_primers: bool,
                           threads: int) -> object:
-    """Checks and writes the fastqs as well as if they are paired end, interleaved and single end.
+    """Checks and writes the fastqs as well as if they are paired end and single end.
 
         Args:
             fastq (str): The path to the forward reads file.
@@ -68,22 +70,17 @@ def _set_fastqs_and_check(fastq: str,
 
         raise ValueError("There is a problem with the fastq file(s) you selected")
         # Create SeqSample objects and merge if needed.
-    if paired_end and interleaved:
-        sobj = itsxpress.SeqSamplePairedInterleaved(fastq=fastq,
-                                                    tempdir=None,
-                                                    reversed_primers=reversed_primers)
-        sobj._merge_reads(threads=threads)
-        return sobj
 
-    elif paired_end and not interleaved:
+
+    if paired_end:
         sobj = itsxpress.SeqSamplePairedNotInterleaved(fastq=fastq,
                                                        fastq2=fastq2,
                                                        tempdir=None,
                                                        reversed_primers=reversed_primers)
         sobj._merge_reads(threads=threads)
         return sobj
 
-    elif not paired_end and not interleaved:
+    elif not paired_end:
         sobj = itsxpress.SeqSampleNotPaired(fastq=fastq,
                                             tempdir=None)
         return sobj
@@ -198,7 +195,7 @@ def main(per_sample_sequences,
             fastq=sample.forward,
             fastq2=sample.reverse if paired_in else None,
             sample_id=sample.Index,
-            single_end=paired_out,
+            single_end=False if paired_in else True,
             reversed_primers=reversed_primers,
             threads=threads)
         # Deduplicate

q2_itsxpress/plugin_setup.py

@@ -17,12 +17,14 @@
                                      default_cluster_id)
 
 plugin = Plugin(
-    name='itsxpress',
-    version='1.8.0',
+    name='q2_itsxpress',
+    version='1.8.1',
     package='q2_itsxpress',
     website='https://github.com/USDA-ARS-GBRU/q2_itsxpress             '
             'ITSxpress: https://github.com/USDA-ARS-GBRU/itsxpress',
-    description='ITSxpress trims amplicon reads down to their ITS region. '
+    description='#####This is the end of life version 1 of ITSxpress. Please check Github for version 2'
+                'of ITSxpress.#####'
+                'ITSxpress trims amplicon reads down to their ITS region. '
                 'ITSxpress is designed to support the calling of exact sequence variants '
                 'rather than OTUs. This newer method of sequence error-correction requires '
                 'quality score data from each sequence, so each input sequence must be trimmed. '

tests/test_main.py

@@ -137,6 +137,7 @@ def test_trim_single_no_cluster():
     exp3 = getsizeof(TEST_DATA_SINGLEOUT)
     eq_(exp2, exp3)
 
+
 def test_trim_pair_no_hmmer():
     threads = 1
     taxa = "F"
@@ -149,7 +150,7 @@ def test_trim_pair_no_hmmer():
 
 class TrimTests(unittest.TestCase):
     def setUp(self):
-        self.plugin = qiime2.sdk.PluginManager().plugins['itsxpress']
+        self.plugin = qiime2.sdk.PluginManager().plugins['q2_itsxpress']
         self.trim_single_fn = self.plugin.methods['trim_single']
         self.trim_paired_fn = self.plugin.methods['trim_pair']
         self.trim_paired_unmerged_fn = \