Merge pull request #128 from qiyunzhu/test

renamed normalize as frac

.github/workflows/main.yml

@@ -2,34 +2,33 @@ name: main CI
 
 on:
   push:
-    branches: [ $default-branch ]
+    branches: [ master ]
   pull_request:
-    branches: [ $default-branch ]
+    branches: [ master ]
 
 jobs:
   build:
     runs-on: ${{ matrix.os }}-latest
     strategy:
       max-parallel: 5
       matrix:
-        os: ['ubuntu', 'macos']
-        python-version: ['3.6', '3.8']
+        os: ['ubuntu']
+        python-version: ['3.6']
 
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
+      - name: Set up Conda
+        uses: s-weigand/setup-conda@v1
         with:
+          update-conda: true
           python-version: ${{ matrix.python-version }}
-
-      - name: Set up Conda
-        run: echo $CONDA/bin >> $GITHUB_PATH
+          conda-channels: anaconda, conda-forge
 
       - name: Install dependencies
-        run: conda install -c conda-forge --file ci/conda_requirements.txt 
+        run: conda install --file ci/conda_requirements.txt 
 
       - name: Install CI packages
-        run: conda install -c conda-forge flake8 coveralls
+        run: conda install flake8 coveralls
 
       - name: Install program
         run: pip install -e .
@@ -40,7 +39,7 @@ jobs:
       - name: Run unit tests
         run: coverage run -m unittest
 
-      - name: Coveralls GitHub Action
-        uses: coverallsapp/github-action@v1.1.2
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
+      - name: Coveralls
+        run: coveralls --service=github
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

README.md

@@ -1,8 +1,7 @@
 # Woltka
 
 [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
-[![Build Status](https://travis-ci.org/qiyunzhu/woltka.svg?branch=master)](https://travis-ci.org/qiyunzhu/woltka)
-[![Workflow](https://github.com/qiyunzhu/woltka/actions/workflows/main.yml/badge.svg)](https://github.com/qiyunzhu/woltka/actions)
+[![CI Status](https://github.com/qiyunzhu/woltka/actions/workflows/main.yml/badge.svg)](https://github.com/qiyunzhu/woltka/actions)
 [![Coverage Status](https://coveralls.io/repos/github/qiyunzhu/woltka/badge.svg?branch=master)](https://coveralls.io/github/qiyunzhu/woltka?branch=master)
 
 **Woltka** (Web of Life Toolkit App), is a bioinformatics package for shotgun metagenome data analysis. It takes full advantage of, and it not limited by, the [WoL](https://biocore.github.io/wol/) reference phylogeny. It bridges first-pass sequence aligners with advanced analytical platforms (such as QIIME 2). Highlights of this program include:

doc/cli.md

@@ -126,7 +126,7 @@ Option | Description
 `--input`, `-i` (required) | Path to input profile.
 `--map`, `-m` (required) | Path to mapping of source features to target features.
 `--output`, `-o` (required) | Path to output profile.
-`--normalize`, `-z` | Count each target feature as 1 / _k_ (_k_ is the number of targets mapped to a source). Otherwise, count as one.
+`--frac`, `-f` | Count each target feature as 1 / _k_ (_k_ is the number of targets mapped to a source). Otherwise, count as one.
 `--names`, `-n` | Path to mapping of target features to names. The names will be appended to the collapsed profile as a metadata column.
 
 

doc/collapse.md

@@ -57,7 +57,7 @@ source4 <tab> target3
 
 ### Normalization
 
-By default, if one source feature is simultaneously mapped to _k_ targets, each target will be counted once. With the `--normalize` or `-z` flag added to the command, each target will be counted 1 / _k_ times.
+By default, if one source feature is simultaneously mapped to _k_ targets, each target will be counted once. With the `--frac` or `-f` flag added to the command, each target will be counted 1 / _k_ times.
 
 Whether to enable normalization depends on the nature and aim of your analysis. For example, one gene is involved in two pathways (which isn't uncommon), should each pathway be counted once, or half time?
 

doc/metacyc.md

@@ -86,7 +86,7 @@ woltka tools collapse -i pathway.biom -m metacyc/pathway-to-super_pathway.txt -n
 woltka tools collapse -i super_pathway.biom -m metacyc/pathway_type.txt -n metacyc/all_class_name.txt -o pathway_type.biom
 ```
 
-The collapse command supports **many-to-many** mapping. For example, if one reaction is found in three pathways, each pathway will be counted **once**. In some instances (e.g., to retain compositionality of the profile), one may consider adding the `--normalize` flag, which will instruct the program to count each pathway 1 / 3 times ([see details](collapse.md)).
+The collapse command supports **many-to-many** mapping. For example, if one reaction is found in three pathways, each pathway will be counted **once**. In some instances (e.g., to retain compositionality of the profile), one may consider adding the `--frac` flag, which will instruct the program to count each pathway 1 / 3 times ([see details](collapse.md)).
 
 
 ## Pathway coverage

doc/wol.md

@@ -220,8 +220,7 @@ So on so forth. See [here](metacyc.md) for a graph of all available collapsing d
 
 `classify` only supports a tree structure, in which one child unit has exactly one parent unit. This is typical in taxonomic classification. If multiple parents are present, all but the first parent will be discarded. In contrast, `collapse` supports **one-to-multiple** mappings, therefore it is more suitable when this is the norm instead of exception, especially in functional classification (where one gene can be involved in multiple metabolic pathways).
 
-`classify` always ensures the **compositionality** of the feature table, in which the frequencies match the numbers of aligned sequences. `collapse` however does not by default. In a one-to-multiple mapping, all parents will be counted once. But one can add `--normalize` to the `collapse` command to normalize the counts by the number of parents so that the compositionality is retained.
-
+`classify` always ensures the **compositionality** of the feature table, in which the frequencies match the numbers of aligned sequences. `collapse` however does not by default. In a one-to-multiple mapping, all parents will be counted once. But one can add `--frac` to the `collapse` command to normalize the counts by the number of parents so that the compositionality is retained.
 
 ## Stratified taxonomic / functional classification
 

woltka/cli.py

@@ -266,7 +266,7 @@ def merge_cmd(ctx, **kwargs):
     type=click.Path(writable=True, dir_okay=False),
     help='Path to output profile.')
 @click.option(
-    '--normalize', '-z', is_flag=True,
+    '--frac', '-f', is_flag=True,
     help=('Count each target feature as 1/k (k is the number of targets '
           'mapped to a source). Otherwise, count as one.'))
 @click.option(

woltka/tests/test_cli.py

@@ -236,7 +236,7 @@ def test_collapse_cmd(self):
                   '--map',    map_fp,
                   '--output', output_fp,
                   '--names',  names_fp,
-                  '--normalize']
+                  '--frac']
         res = self.runner.invoke(collapse_cmd, params)
         self.assertEqual(res.exit_code, 0)
         self.assertEqual(res.output.splitlines()[-1],

woltka/tests/test_tools.py

@@ -189,7 +189,7 @@ def test_collapse_wf(self):
         # wrong mapping file
         map_fp = join(self.datdir, 'tree.nwk')
         with self.assertRaises(SystemExit) as ctx:
-            collapse_wf(input_fp, map_fp, output_fp, normalize=True)
+            collapse_wf(input_fp, map_fp, output_fp, frac=True)
         errmsg = 'No source-target relationship is found in tree.nwk.'
         self.assertEqual(str(ctx.exception), errmsg)
 

woltka/tools.py

@@ -192,11 +192,11 @@ def _read_profile(fp):
     click.echo('Merged profile written.')
 
 
-def collapse_wf(input_fp:   str,
-                map_fp:     str,
-                output_fp:  str,
-                normalize: bool = False,
-                names_fp:   str = None):
+def collapse_wf(input_fp:  str,
+                map_fp:    str,
+                output_fp: str,
+                frac:     bool = False,
+                names_fp:  str = None):
     """Workflow for collapsing a profile based on many-to-many mapping.
 
     Raises
@@ -225,7 +225,7 @@ def collapse_wf(input_fp:   str,
 
     # collapse profile by mapping
     click.echo('Collapsing profile...', nl=False)
-    table = collapse_table(table, mapping, normalize)
+    table = collapse_table(table, mapping, frac)
     click.echo(' Done.')
     n = table_shape(table)[0]
     click.echo(f'Number of features after collapsing: {n}.')