Merge pull request #56 from phac-nml/allele

Allele

.gitignore

@@ -84,6 +84,9 @@ ENV/
 
 # IDE
 .vscode/
+.idea/
+*.iml
+
 
 # Spyder project settings
 .spyderproject
@@ -110,3 +113,4 @@ output/
 validation/enterobase_90_50_with_blacklist.csv
 .coveragerc
 coverage_html_report/
+/.pytest_cache/

.travis.yml

@@ -1,27 +1,22 @@
 language: python
 python:
-  # We don't actually use the Travis Python, but this keeps it organized.
   - "3.6"
-install:
+before_install:
   - sudo apt-get update
-  # We do this conditionally because it saves us some downloading if the
-  # version is the same.
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    fi
+install:
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
   - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
+  - echo ". $HOME/miniconda/etc/profile.d/conda.sh" >> ~/.bashrc
+  - source ~/.bashrc
   - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
+  - conda update -y conda
   # Useful for debugging any issues with conda
   - conda info -a
   - conda config --add channels bioconda
-  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION samtools bowtie2 mash bcftools biopython nose blast pandas seqtk
-  - source activate test-environment
+  - conda config --add channels conda-forge
+  - conda create -q -n test-environment python=3.6 samtools>=1.7 pandas>=0.23 bowtie2>=2.3 mash>=2 bcftools>=1.7 biopython>=1.69 blast>=2.2.31 seqtk>=1.2 pytest>=3.6
+  - conda activate test-environment
   - python setup.py install
 
 script:
-  - nosetests
+  - pytest

README.md

@@ -1,14 +1,16 @@
+[![Master branch build status](https://api.travis-ci.org/phac-nml/ecoli_serotyping.svg?branch=master "Master Build Status")](https://travis-ci.org/phac-nml/ecoli_serotyping)
+
 # ECTyper (an easy typer)
-**ecyper** wraps a standalone serotyping module for _Escherichia coli_. 
-Supports _fasta_ and _fastq_ file formats.
+**ecyper** is a standalone serotyping module for _Escherichia coli_. It supports _fasta_ and _fastq_ file formats.
 
 # Dependencies:
 - python 3.6.3.*
+- pytest 3.6.*
 - pandas 0.21.0.*
 - samtools 1.5.*
 - bowtie2 2.3.0.*
-- mash 1.1.*
-- bcftools 1.6.*
+- mash 2.0.*
+- bcftools 1.8.*
 - biopython 1.69.*
 - blast 2.2.31 .*
 - seqtk 1.2.*
@@ -17,48 +19,58 @@ Supports _fasta_ and _fastq_ file formats.
 1. Get `miniconda` if you do not already have `miniconda` or `anaconda`:
     1. `wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh`
     1. `bash miniconda.sh -b -p $HOME/miniconda`
-    1. `export PATH="$HOME/miniconda/bin:$PATH"`
+    1. `echo ". $HOME/miniconda/etc/profile.d/conda.sh" >> ~/.bashrc`
+    1.  `source ~/.bashrc`
 2. Install ectyper  
     * Directly via `conda` 
     	1. `conda install -c bioconda ectyper` 
     * Through `github`
     	1. Install dependencies
-          `conda install pandas samtools bowtie2 mash bcftools biopython nose blast seqtk tqdm python=3.6`
+          `pandas samtools bowtie2 mash bcftools biopython pytest blast seqtk tqdm python=3.6`
     	1. Download git repository then unzip
           `wget https://github.com/phac-nml/ecoli_serotyping/archive/master.zip`
     	1. Install ectyper inside unzipped directory
           `python setup.py install`
 
 # Basic Usage
-1. Put all of your fasta/fastq files in one folder (concatenate paired files if you want the result to be considered a single entity)
+1. Put the fasta/fastq files for serotyping analyses in one folder (concatenate paired files if you would like them to be considered a single entity)
 1. `ectyper -i [file path]`
-1. View the results on the console or in `output/[datetime]/output.csv`
+1. View the results on the console or in `ectyper_[datetime]/output.csv`
 
 # Example Usage
 * `ectyper -i ecoliA.fasta`  for a single file
+* `ectyper -i ecoliA.fasta -o output_dir` for a single file, results stored in `output_dir`
 * `ectyper -i ecoliA.fasta,ecoliB.fastq,ecoliC.fna`	for multiple files  
 * `ectyper -i ecoli_folder`	for a folder
 
 # Advanced Usage
 ```
-usage: ectyper [-h] -i INPUT [-d PERCENTIDENTITY] [-l PERCENTLENGTH]
-               [--verify] [-s] [--detailed] [-o OUTPUT]
+usage: ectyper [-h] [-V] -i INPUT [-d PERCENTIDENTITY] [-l PERCENTLENGTH]
+               [--verify] [-o OUTPUT] [-r REFSEQ]
+
+ectyper v0.4.0 Prediction of Escherichia coli serotype from raw reads or
+assembled genome sequences
 
 optional arguments:
   -h, --help            show this help message and exit
+  -V, --version         show program's version number and exit
   -i INPUT, --input INPUT
                         Location of E. coli genome file(s). Can be a single
-                        file or a directory
+                        file, a comma-separated list of files, or a directory
   -d PERCENTIDENTITY, --percentIdentity PERCENTIDENTITY
-                        Percent identity required for an allele match [default 90]
+                        Percent identity required for an allele match [default
+                        90]
   -l PERCENTLENGTH, --percentLength PERCENTLENGTH
-                        Percent length required for an allele match [default 50]
+                        Percent length required for an allele match [default
+                        50]
   --verify              Enable E. coli species verification
-  -s, --species         Enable species identification when a non-E. coli
-                        genome is found Note: refseq downloading is required
-                        when running this option for the first time
-  --detailed            Enable detailed program output
   -o OUTPUT, --output OUTPUT
-                        Directory location of output files.
+                        Directory location of output files
+  -r REFSEQ, --refseq REFSEQ
+                        Location of pre-computed MASH RefSeq sketch. If
+                        provided, genomes identified as non-E. coli will have
+                        their species identified using MASH. For best results
+                        the pre-sketched RefSeq archive https://gembox.cbcb.um
+                        d.edu/mash/refseq.genomes.k21s1000.msh is recommended
 ```
-* The first time species identification is enabled you will need to wait for **ectyper** to download the reference sequences.
+