<commit_before>## Datasnakes-Scripts

This package is a collection of the scripts related to an Orthologs Project. 

## Description

The subdirectories here are used as modules in the Python3 package that we are developing.

## Installation

In development but working.  To test you'll want to create a virtual environment so that cleanup is easy.
Using _virtualenv_ with python3 insures that _python_ invokes py3.5 and _python3_ invokes py36.  Invoke python36.

```bash
$ mkdir dev
$ cd dev
$ virtualenv PackageTest --python=python3
$ source activate PackageTest
$ cd PackageTest
$ pip install cookiecutter
$ git clone -b RAG-Review http;//github.com/datasnakes/Datasnakes-Scripts
$ cd Datasnakes-Scripts
$ python3 tester.py
```
## Usage

After installation, you'll be able to easily import each module via:

```python
from Orthologs import biosql, blast, ftp, genbank, phylogenetics
```


## Contributors
* <NAME> | Github: [@grabear](https://github.com/grabear) | Email: [:email:](mailto:<EMAIL>)
* <NAME> | Github: [@sdhutchins](https://github.com/sdhutchins) | Twitter: [@MavenNBA](https://twitter.com/MavenNBA/) | Email: [:email:](mailto:<EMAIL>)<commit_msg>Incorporated Naming Conventions<commit_after># Datasnakes-Scripts

This package is a collection of the scripts related to an Orthologs Project. 

# Description

The subdirectories here are used as modules in the Python3 package that we are developing.

# Installation

In development but working.  To test you'll want to create a virtual environment so that cleanup is easy.
Using _virtualenv_ with python3 insures that _python_ invokes py3.5 and _python3_ invokes py36.  Invoke python36.

```bash
$ mkdir dev
$ cd dev
$ virtualenv PackageTest --python=python3
$ source activate PackageTest
$ cd PackageTest
$ pip install cookiecutter
$ git clone -b RAG-Review http;//github.com/datasnakes/Datasnakes-Scripts
$ cd Datasnakes-Scripts
$ python3 tester.py
```
# Usage

After installation, you'll be able to easily import each module via:

```python
from Orthologs import biosql, blast, ftp, genbank, phylogenetics
```
#  Naming Conventions and Paths
## _by class_
### CompGenAnalysis(ProjectMana) _comp_gen.py_
#### User Generated Files
* taxon_file
    * path = _project_index_ / Path(taxon_file)
    * name = "_projectname_\_tax.txt"
* paml_file
    * path = _project_index_ / Path(paml_file)
    * name = "_projectname_\_paml.txt"
    * TODO-ROB:  Deprecate this file
* acc_file
    * path _project_index_ / Path(acc_file)
    * name = "_projectname_\_acc.csv"

#### Programmatically Generated Files
* log_files
    * 1
    * 2
* my_gene_file
    * path = _project_data / Path(my_gene_file)
    * name = "_projectname_\_mygene.csv"
* post_blast_analysis_file
    * path _project_index_ / Path(pba_file)
    * name = "_projectname_\_pba.xlsx"

### BLASTAnalysis(CompGenAnalysis)  _ncbi_blast.py_
#### User Generated Files
* template_file
    * path = _project_index_ / Path(template_file)
    * name = "_projectname_\_temp.csv"

#### Programmatically Generated Files
* log_files
    * TODO-ROB Add loggers
    * accession/time logger
    * post blast analysis logger
* building_file
    * path = _project_raw_data_ / Path(builder_file)
    * name = "_projectname_\_building.csv"
* building_time_file
    * path = _project_raw_data_ / Path(builder_time_file)
    * name = "_projectname_\_building_time.csv"

### BLASTn(BT) _blastn.py_
#### User Generated Files
* template file
    * path = _project_index_ / Path(template file)
    * name = "_users_file_name_.csv"

#### Programmatically Generated Files
* gi list binary files
    * path = _project_index_ / Path(binary_files)
    * names = "_TAXID_\_gi"
* blast xml files
    * path = _project_raw_data_ / Path(gene) / Path(blast xml files)
    * name = "_gene_\__organism_.xml
* master accession file
    * path = _project_data_ / Path(MAF)
    * name = "_projectname_\_MAF.csv"
    * ___Note___:  _Only exists if the BLAST finishes all the genes._

## _by location_

# Contributors
* <NAME> | Github: [@grabear](https://github.com/grabear) | Email: [:email:](mailto:<EMAIL>)
* <NAME> | Github: [@sdhutchins](https://github.com/sdhutchins) | Twitter: [@MavenNBA](https://twitter.com/MavenNBA/) | Email: [:email:](mailto:<EMAIL>)
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