Merge pull request #837 from uclahs-cds/czhu-fix-docs

Fix The Usage Section in Docs

.github/workflows/CICD-base.yaml

@@ -21,6 +21,6 @@ jobs:
 
       # Run CICD-base
       - name: CICD-base
-        uses: docker://blcdsdockerregistry/cicd-base:latest
+        uses: docker://ghcr.io/uclahs-cds/cicd-base:latest
         env:
           PYTHON_PYLINT_CONFIG_FILE: true

.pylintrc

@@ -60,86 +60,20 @@ confidence=
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use "--disable=all --enable=classes
 # --disable=W".
-disable=print-statement,
-        parameter-unpacking,
-        unpacking-in-except,
-        old-raise-syntax,
-        backtick,
-        long-suffix,
-        old-ne-operator,
-        old-octal-literal,
-        import-star-module-level,
-        non-ascii-bytes-literal,
-        raw-checker-failed,
+disable=raw-checker-failed,
         bad-inline-option,
         locally-disabled,
         file-ignored,
         suppressed-message,
         useless-suppression,
         deprecated-pragma,
         use-symbolic-message-instead,
-        apply-builtin,
-        basestring-builtin,
-        buffer-builtin,
-        cmp-builtin,
-        coerce-builtin,
-        execfile-builtin,
-        file-builtin,
-        long-builtin,
-        raw_input-builtin,
-        reduce-builtin,
-        standarderror-builtin,
-        unicode-builtin,
-        xrange-builtin,
-        coerce-method,
-        delslice-method,
-        getslice-method,
-        setslice-method,
-        no-absolute-import,
-        old-division,
-        dict-iter-method,
-        dict-view-method,
-        next-method-called,
-        metaclass-assignment,
-        indexing-exception,
-        raising-string,
-        reload-builtin,
-        oct-method,
-        hex-method,
-        nonzero-method,
-        cmp-method,
-        input-builtin,
-        round-builtin,
-        intern-builtin,
-        unichr-builtin,
-        map-builtin-not-iterating,
-        zip-builtin-not-iterating,
-        range-builtin-not-iterating,
-        filter-builtin-not-iterating,
-        using-cmp-argument,
-        eq-without-hash,
-        div-method,
-        idiv-method,
-        rdiv-method,
-        exception-message-attribute,
-        invalid-str-codec,
-        sys-max-int,
-        bad-python3-import,
-        deprecated-string-function,
-        deprecated-str-translate-call,
-        deprecated-itertools-function,
-        deprecated-types-field,
-        next-method-defined,
-        dict-items-not-iterating,
-        dict-keys-not-iterating,
-        dict-values-not-iterating,
-        deprecated-operator-function,
-        deprecated-urllib-function,
-        xreadlines-attribute,
-        deprecated-sys-function,
-        exception-escape,
-        comprehension-escape,
-        import-error
+        import-error,
+        superfluous-parens,
+        unnecessary-lambda-assignment,
+        unnecessary-dunder-call,
+        unspecified-encoding,
+        cyclic-import
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option

CHANGELOG.md

@@ -512,9 +512,9 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 - Enable `filterFasta` to filter by number of miscleavages per peptide. #382
 
-- Added CLI command `mergeFasta` to merge multiple variant peptide database Fasta files into one. This could be useful when working with multiplexed proteomic experiments such as TMT. [#380](https://github.com/uclahs-cds/private-moPepGen/issues/380)
+- Added CLI command `mergeFasta` to merge multiple variant peptide database Fasta files into one. This could be useful when working with multiplexed proteomic experiments such as TMT. [#380](https://github.com/uclahs-cds/package-moPepGen/issues/380)
 
-- Added CLI command `decoyFasta` to generate decoy database by shuffling or reversing each sequence. [#386](https://github.com/uclahs-cds/private-moPepGen/issues/386)
+- Added CLI command `decoyFasta` to generate decoy database by shuffling or reversing each sequence. [#386](https://github.com/uclahs-cds/package-moPepGen/issues/386)
 
 - Added parameter `--min-coverage-rna` to `parseREDItools` to filter by total RNA reads at a given position. #392
 
@@ -554,7 +554,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 - The command line arguments are standardized across all commands, for example '-i/--input-path' for inputs and '-o/--output-path' for outputs.
 
-- `generateIndex` is changed to use compressed text format to store genomic annotation, because for some reason that we are not sure, when loading the pickled genomic annotation, the memory usage is almost doubled. [#394](https://github.com/uclahs-cds/private-moPepGen/issues/394)
+- `generateIndex` is changed to use compressed text format to store genomic annotation, because for some reason that we are not sure, when loading the pickled genomic annotation, the memory usage is almost doubled. [#394](https://github.com/uclahs-cds/package-moPepGen/issues/394)
 
 ---
 

README.md

@@ -3,25 +3,25 @@
 <!-- badges: start -->
 
 [![Lifecycle:Maturing](https://img.shields.io/badge/Lifecycle-Maturing-007EC6)](https://img.shields.io/badge/Lifecycle-Maturing-007EC6)
-[![Tests](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/tests.yaml/badge.svg)](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/tests.yaml)
-[![Docker](https://img.shields.io/badge/docker-%230db7ed.svg?style=plastic&logo=docker&logoColor=white)](https://github.com/uclahs-cds/private-moPepGen/pkgs/container/mopepgen)
-[![Documentation](https://img.shields.io/static/v1?style=plastic&message=ReadTheDocs&color=2C4AA8&logo=ReadTheDocs&logoColor=FFFFFF&label=Documentation)](https://uclahs-cds.github.io/private-moPepGen/)
+[![Tests](https://github.com/uclahs-cds/package-moPepGen/actions/workflows/tests.yaml/badge.svg)](https://github.com/uclahs-cds/package-moPepGen/actions/workflows/tests.yaml)
+[![Docker](https://img.shields.io/badge/docker-%230db7ed.svg?style=plastic&logo=docker&logoColor=white)](https://github.com/uclahs-cds/package-moPepGen/pkgs/container/mopepgen)
+[![Documentation](https://img.shields.io/static/v1?style=plastic&message=ReadTheDocs&color=2C4AA8&logo=ReadTheDocs&logoColor=FFFFFF&label=Documentation)](https://uclahs-cds.github.io/package-moPepGen/)
 [![License](https://img.shields.io/badge/License-GPL_v2-blue)](./LICENSE.txt)
 
 <!-- badges: end -->
 
-moPepGen (multi-omics peptide generator) uses data from multiple -omics experiments and calls variant peptides as custom database for proteogenomics library search.
+moPepGen (multi-omics peptide generator) uses data from one or more omics experiments and calls variant peptides as custom databases for proteogenomic library search.
 
-moPepGen takes genomic variants such as single nucleotide variants (SNP or SNV), insertion/deletion (INDEL), gene fusion, and post transcriptional modifications such as RNA editing and alternative splicing, and detects variated peptides affected. 
+moPepGen takes genomic and transcriptomic variants such as single nucleotide variants (SNPs or SNVs), small insertions/deletions (indels), gene fusion, alternative splicing, RNA circularization and RNA editing events, and generates noncanonical peptides affected by the variants.
 
 ## Installation
 
-Install directly from github
+Install directly from GitHub
 
 ```shell
-pip install git+ssh://git@github.com/uclahs-cds/private-moPepGen.git
+pip install git+ssh://git@github.com/uclahs-cds/package-moPepGen.git
 ```
 
 ## Documentation
 
-See [here](https://uclahs-cds.github.io/private-moPepGen/index.html)
+See [here](https://uclahs-cds.github.io/package-moPepGen/index.html)

docs/README.md

@@ -1,14 +1,14 @@
 ## MKDocs
 
-Documentations are written in markdown and converted to html by [MKDocs](https://www.mkdocs.org/).
+Documentations are written in markdown and converted to HTML by [MKDocs](https://www.mkdocs.org/).
 
 ## Adding Pages
 
-To add a new documentation page, first create a '.md' file under this directory. Next go to the 'mkdocs.yml' file under the root directory of the repo, and add a key-value pair under `nav`, and after rendering, a link to the new added page will show up in the navbar.
+To add a new documentation page, first create a '.md' file under this directory. Next, go to the 'mkdocs.yml' file under the root directory of the repo, and add a key-value pair under `nav`, and after rendering, a link to the newly added page will show up in the navbar.
 
 ## Render locally
 
-The online documentation is rendered automatically by github actions, it is still useful to see the changes in real time. This can be done by running `mkdocs` locally. moPepGen, mkdocs and several dependencies need to be installed first.
+While the online documentation is rendered automatically by GitHub actions, it may be still useful to see the changes in real time. This can be done by running `mkdocs` locally. `moPepGen`, `mkdocs` and several dependencies need to be installed first.
 
 ```bash
 conda env create --name moPepGen python=3.8.11
@@ -17,7 +17,7 @@ pip install mkdocs==1.2.3 jinja2==3.0.0 mkdocstrings==0.16.2 mkdocs-macros-plugi
 pip install .
 ```
 
-Use the command below to start a development server and open http://127.0.0.1:8000/ to see the change in real time.
+Use the command below to start a development server and open http://127.0.0.1:8000/ to see the changes in real time.
 
 ```bash
 mkdocs serve

docs/call-alt-translation.md

@@ -25,12 +25,12 @@
 
 ## Alternative translation
 
-Alternative translation is when a different peptide is generated from the same transcript without any change of the genetic code from the genome.
+Alternative translation is when a different peptide is generated from the same transcript without any changes in the nucleotide sequence of the transcript.
 
 ### Selenocysteine Termination
 
-In eukaryotes, the UGA on some mRNAs can be decoded into selenocysteine instead of being recognized as a stop codon, and those proteins are called selenoproteins. However the decoding of UGA is regulated by complex signals including mRNA and sec-tRNA abundance, which could result two isoforms: one with UGA read through and one being truncated. Selenocysteine termination is used to represent the later situation. Selenocysteine terminations are not written into any GVF file but they are represented in the format of `SECT-<pos>` where `pos` is the position of the selenocysteine UGA being recognized as a stop codon in the **gene**.
+In eukaryotes, the UGA on some mRNAs can be decoded into selenocysteine instead of being recognized as a stop codon, and these proteins are called selenoproteins. However, the decoding of UGA is regulated by complex signals including mRNA and sec-tRNA abundance, which could result in two proteoforms: one with UGA read through and one with termination at the stop codon. Selenocysteine termination is used to represent the later situation. Selenocysteine terminations are not written into any GVF files but are represented in the format of `SECT-<pos>` where `pos` is the position of the selenocysteine UGA being recognized as a stop codon in the **gene**.
 
 ### Tryptophan > Phenylalanine Codon Reassignment
 
-Tryptophan > Phenylalanine substitutants, described in [Patasker, et al.](https://pubmed.ncbi.nlm.nih.gov/35264796/), happens when cellular tryptophan is depleted and phenylalanine is reassigned to tryptophan codons to have protein synthesis continue. The process largely exists in tumor cells. Similar to selenocysteine termination, W > F substitutants are also not written into GVFs, but is represented in the format of `W2F-<pos>`. Noted that the `pos` is at peptide coordinate (*i.e.,* zeroed at the beginning of the peptide).
+Tryptophan > Phenylalanine substitutants, described in [Patasker, et [al.](https://pubmed.ncbi.nlm.nih.gov/35264796/), happen when cellular tryptophan is depleted and phenylalanine is reassigned to tryptophan codons to continue protein synthesis. The process largely exists in tumor cells. Similar to selenocysteine termination, W > F substitutants are not written in GVFs, but are represented in the format of `W2F-<pos>`. Noted that the `pos` is a peptide coordinate (*i.e.,* zeroed at the beginning of the peptide).