Metadata-Version: 2.1
Name: dcma
Version: 0.1.0
Summary: Deep Codon Mutation Analyser
Home-page: https://github.com/janjusti/dppa
Author: Jan Justi
Author-email: jan.ma.justi@gmail.com
License: MIT
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Description-Content-Type: text/markdown
Requires-Dist: tqdm (==4.31.1)
Requires-Dist: anytree (==2.6.0)
Requires-Dist: pandas (==0.24.2)
Requires-Dist: numpy (==1.16.3)
Requires-Dist: biopython (==1.73)
Requires-Dist: openpyxl (==2.6.2)
Requires-Dist: styleframe (==2.0.3)

Deep Codon Mutation Analyser (DCMA)
===================================

Installation
------------
```bash
pip install dcma --user
```

Usage
-----
CLI:

```bash
usage: run-dcma [-h] [--reportName REPORTNAME] [--reportPath REPORTPATH]
                [--searchKP SEARCHKP] [--debug]
                TARGET REPORTTYPE

Analyse all protein alignment .fasta files from a target.

positional arguments:
  TARGET                Target .fasta file to be analysed.
  REPORTTYPE            Output report file type.

optional arguments:
  -h, --help            show this help message and exit
  --reportName REPORTNAME
                        Output report custom file name.
  --reportPath REPORTPATH
                        Output report custom file path.
  --searchKP SEARCHKP   Custom keyphrase to detect searchable sequences.
  --debug               Turn debug messages on.
```

Python:

```python
import dcma.core as solver

target_path = 'example.fasta'
report_name = 'myrep'
report_type = 'xls'
report_path = 'results-folder' # optional

solver.set_debug_mode(True) # optional

# results[0] -> polarity results dataframe
# results[1] -> alerts dataframe
results = solver.run(target_path)

# option 1: export to the current folder
solver.export(results, report_type, report_name)
# option 2: export to custom folder
solver.export(results, report_type, report_name, report_path)
```

