add requirements files and update README.md

A .pre-commit-config.yaml file is also included

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+repos:
+-   repo: https://github.com/ambv/black
+    rev: stable
+    hooks:
+    - id: black
+      language_version: python3.6
+-   repo: https://github.com/asottile/blacken-docs
+    rev: v0.3.0
+    hooks:
+    -   id: blacken-docs
+        additional_dependencies: [black==18.9b0]
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v1.2.3
+    hooks:
+    - id: flake8
+    - id: check-case-conflict
+    - id: check-docstring-first
+    - id: check-json
+    - id: check-merge-conflict
+    - id: check-yaml

README.md

@@ -1,17 +1,26 @@
 # README.md (find_differential_primers)
 
 ## Overview
-This repository contains code for finding discriminatory primers among genomes or other biological sequences of interest. 
+
+This repository contains code for finding discriminatory primers among genomes or other biological sequences of interest.
 
 ## DEPENDENCIES:
+
 The following dependencies have been confirmed to work for running the 'find_differential_primers.py' pipeline, though any later version (and in some cases, some earlier versions) should work:
 
-* **[Biopython](http://biopython.org/wiki/Download)**: (forthcoming) v1.63 - but **NOTE** you may need to clone the current Biopython repo from <https://github.com/biopython/biopython> (see below).
-* **[bx-python](https://bitbucket.org/james_taylor/bx-python/src)**: current Hg (Mercurial) version works as of June 19, 2013
-* **[EMBOSS](http://emboss.sourceforge.net/download/)** (for ePrimer3): v6.4.0, v6.6.0
-* **[primer3](http://primer3.sourceforge.net/releases.php)**: v1.1.4 **NOTE:** primer3 version2 does not play nice with EMBOSS ePrimer3 (see e.g. [this](https://code.google.com/p/msatcommander/issues/detail?id=29), [this](https://bugs.launchpad.net/ubuntu/+source/emboss/+bug/978257) and [this](http://stackoverflow.com/questions/9866113/why-am-i-getting-this-error-in-my-primer3-eprimer3-mac-osx-build))
-* **[prodigal](https://code.google.com/p/prodigal/)**  : v1.20
-* **[BLAST+](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)**: v2.2.22+, v2.2.28+, v2.2.29+
+- **[Biopython](http://biopython.org/wiki/Download)**: (forthcoming) v1.63 - but **NOTE** you may need to clone the current Biopython repo from <https://github.com/biopython/biopython> (see below).
+- **[bx-python](https://bitbucket.org/james_taylor/bx-python/src)**: current Hg (Mercurial) version works as of June 19, 2013
+- **[EMBOSS](http://emboss.sourceforge.net/download/)** (for ePrimer3): v6.4.0, v6.6.0
+- **[primer3](http://primer3.sourceforge.net/releases.php)**: v1.1.4 **NOTE:** primer3 version2 does not play nice with EMBOSS ePrimer3 (see e.g. [this](https://code.google.com/p/msatcommander/issues/detail?id=29), [this](https://bugs.launchpad.net/ubuntu/+source/emboss/+bug/978257) and [this](http://stackoverflow.com/questions/9866113/why-am-i-getting-this-error-in-my-primer3-eprimer3-mac-osx-build))
+- **[prodigal](https://code.google.com/p/prodigal/)**  : v1.20
+- **[BLAST+](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)**: v2.2.22+, v2.2.28+, v2.2.29+
+
+If you are installing `find_differential_primers` in a `conda` environment, then you can install all these tools with the commands:
+
+```bash
+conda install --file requirements-thirdparty.txt
+conda install --file requirements.txt
+```
 
 ### NOTE ON EMBOSS/PRIMER3/BIOPYTHON DEPENDENCIES
 
@@ -20,51 +29,51 @@ There is a point of fragility in choice of EMBOSS, primer3, and Biopython versio
 1. primer3 versions newer than v1.1.4 do not work with EMBOSS. This locks us, for now, into a 2008 version of primer3. As I chose to use the EMBOSS tools, I am taking their lead on this - when EMBOSS ePrimer3 changes to v2+, so will this script.
 2. EMBOSS' ePrimer3 interface is not stable between version numbers. In particular, v6.5.0 changes the -otm flag to -opttm. This means that Biopython version v1.63 or lower does not use the appropriate option for EMBOSS v6.5.0. If you are using an EMBOSS version older than v6.5.0 then Biopython 1.63 should be fine. If you are using EMBOSS v6.5.0+, then note that the appropriate change has been committed at the `git` repository at <https://github.com/biopython/biopython> (as of Dec 2013), and for now you should install Biopython from the bleeding edge source. It is anticipated that this change will appear in Biopython v1.64.
 
+If you are using the `conda install --file requirements-thirdparty.txt` approach noted above, the versions installed should be compatible with each other.
+
 #### Acceptable combinations:
 
-* EMBOSS v6.5.0+/Biopython cloned from GitHub repository/Primer3 v1.1.4 **should work**
-* EMBOSS pre-v6.5.0/Biopython pre-v1.63/Primer3 v1.1.4 **should work**
-* Primer3 v2+: **will not work**
+- EMBOSS v6.5.0+/Biopython cloned from GitHub repository/Primer3 v1.1.4 **should work**
+- EMBOSS pre-v6.5.0/Biopython pre-v1.63/Primer3 v1.1.4 **should work**
+- Primer3 v2+: **will not work**
 
-# INSTALLATION
+## INSTALLATION
 
-If you have downloaded v0.1.0 or greater, and the dependencies above are satisfied, then installation should be as simple as cloning the repository:
+If you have downloaded v0.1.0 or greater, and the dependencies above are satisfied, then installation should be as simple as cloning the repository as followis:
 
+```bash
+git clone https://github.com/widdowquinn/find_differential_primers
+cd find_differential_primers
 ```
-$ git clone https://github.com/widdowquinn/find_differential_primers
-$ cd find_differential_primers
-```
-
 
-then issuing:
+then issuing the installation command:
 
-```
-$ python setup.py install
+```bash
+python setup.py install
 ```
 
 (or whatever variant you wish, e.g. for a home directory-local installation) from the top directory in the repository, with root permissions, if necessary.
 
-# BASIC USE:
+## BASIC USE:
 
-1. Collect all biological sequences to be distinguished into a convenient location (e.g. in same directory; this is not essential, but it simplifies things if using a `Makefile`). 
+1. Collect all biological sequences to be distinguished into a convenient location (e.g. in same directory; this is not essential, but it simplifies things if using a `Makefile`).
 2. Construct a config file similar to the example given in `O104_primers_5.conf` or `test.conf`. This will describe each sequence by name, the classes to which it belongs, and (at least) the location of the FASTA file containing the sequence (or sequences - `find_differential_primers.py` will stitch sequences with the spacer `NNNNNCATTCCATTCATTAATTAATTAATGAATGAATGNNNNN`, if necessary).
 3. If you need a BLAST database of negative screening examples, construct this with `makeblastdb` (part of **BLAST+**).
 4. Run the `find_differential_primers.py` script, with suitable command-line options.
 
 These steps are encapsulated in the accompanying `makefile` in `samples/makefile`. This file can be modified to point to your input sequence file of interest, and run by issuing `make` at the command-line. See documentation in the `makefile` for more details.
 
-
-# TEST:
+## TEST:
 
 Change directory to `tests`, and run the script with the `test.conf` config file using default settings:
 
-```
-$ ../find_differential_primers/find_differential_primers.py -i test.conf -v
+```bash
+find_differential_primers.py -i test.conf -v
 ```
 
 This should run to completion, and produce the output indicated below:
 
-```
+```bash
 $ tree differential_primer_results/
 differential_primer_results/
 ├── Erwinia_family-specific_amplicons.fas
@@ -122,7 +131,7 @@ $ wc differential_primer_results/*
       18      24     936 differential_primer_results/wasabiae_family-specific_amplicons.fas
       52     166    1626 differential_primer_results/wasabiae_family-specific_primers.eprimer3
     1330    3726   50434 total
-$ cat differential_primer_results/differential_primer_results.tab 
+$ cat differential_primer_results/differential_primer_results.tab
 # Summary information table
 # Generated by find_differential_primers
 # Columns in the table:
@@ -138,7 +147,7 @@ Pca_PC1	Pectobacterium,carotovorum	6	1	sequences/NC_012917.fna	sequences/NC_0129
 Pwa_WPP163	Pectobacterium,wasabiae	6	2	sequences/NC_013421.fna	sequences/NC_013421.prodigalout	sequences/NC_013421.eprimer3
 Pca_PCC21	Pectobacterium,carotovorum	7	0	sequences/NC_018525.fna	sequences/NC_018525.prodigalout	sequences/NC_018525.eprimer3
 Eta_1_99	Erwinia,tasmaniensis	17	0	sequences/NC_010694.fna	sequences/NC_010694.prodigalout	sequences/NC_010694.eprimer3
-$ cat differential_primer_results/differential_primer_results-families.tab 
+$ cat differential_primer_results/differential_primer_results-families.tab
 # Summary information table
 # Generated by find_differential_primers
 # Columns in the table:
@@ -156,23 +165,26 @@ tasmaniensis	17	differential_primer_results/tasmaniensis_family-specific_primers
 
 Once you have run the tests once, you can use the `test_nocalc.conf` file to re-run the prediction/classification without having to execute `Prodigal`, `ePrimer3` or `PrimerSearch`, by running:
 
-```
-$ ../find_differential_primers/find_differential_primers.py -i test_nocalc.conf -v --noprimersearch --noprodigal --noprimer3
+```bash
+find_differential_primers.py -i test_nocalc.conf -v --noprimersearch --noprodigal --noprimer3
 ```
 
 ## FURTHER INFORMATION:
+
 Please read the comments contained within the top of each '*.py' file as well as the Supporting Information (['Methods S1' document](doi:10.1371/journal.pone.0034498.s006)) of [doi:10.1371/journal.pone.0034498](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0034498).
 
 ## CONTRIBUTORS
-* [Leighton Pritchard](https://github.com/widdowquinn)
-* [Benjamin Leopold](https://github.com/cometsong)
-* [Michael Robeson](https://github.com/mikerobeson)
+
+- [Leighton Pritchard](https://github.com/widdowquinn)
+- [Benjamin Leopold](https://github.com/cometsong)
+- [Michael Robeson](https://github.com/mikerobeson)
 
 ## CITATIONS
+
 Please refer to the following for methodological details:
 
-* Pritchard L _et al._ (2012) "Alignment-Free 
+- Pritchard L _et al._ (2012) "Alignment-Free
 Design of Highly Discriminatory Diagnostic Primer Sets for _Escherichia coli_ O104:H4 Outbreak Strains." _PLoS ONE_ **7**(4): e34498. [doi:10.1371/journal.pone.0034498](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0034498) - _Method description and application to human bacterial pathogens, sub-serotype resolution_
-* Pritchard L _et al._ (2013) "Detection of phytopathogens of the genus _Dickeya_ using a PCR primer 
+- Pritchard L _et al._ (2013) "Detection of phytopathogens of the genus _Dickeya_ using a PCR primer
 prediction pipeline for draft bacterial genome sequences." _Plant Pathology_, **62**, 587-596
 [doi:10.1111/j.1365-3059.2012.02678.x](http://onlinelibrary.wiley.com/doi/10.1111/j.1365-3059.2012.02678.x/full) - _Application to plant pathogens, species-level resolution_

requirements-dev.txt

@@ -0,0 +1,4 @@
+bandit
+black
+flake8
+pylint

requirements-pip.txt

@@ -0,0 +1 @@
+pre-commit

requirements-thirdparty.txt

@@ -0,0 +1,4 @@
+prodigal
+blast
+emboss
+primer3=1.1.4

requirements.txt

@@ -0,0 +1,2 @@
+biopython
+bx-python