Metadata-Version: 2.0
Name: tsfm
Version: 0.9.4
Summary: tRNA structure function mapper
Home-page: https://github.com/tlawrence3/tsfm
Author: Travis J. Lawrence and David H. Ardell
Author-email: tlawrence3@ucmerced.edu
License: LGPLv3
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: ~=3.4
Requires-Dist: cython
Requires-Dist: mpmath
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: patsy
Requires-Dist: scipy
Requires-Dist: statsmodels

[![Travis](https://img.shields.io/travis/tlawrence3/tsfm.svg)]() [![PyPI](https://img.shields.io/pypi/format/tsfm.svg)]() [![PyPI](https://img.shields.io/pypi/pyversions/tsfm.svg)]() [![PyPI](https://img.shields.io/pypi/l/tsfm.svg)]()

# Example command
```shell
tsfm -vc struct_file.txt ferns/FERN Gnetidae/GNET -j
```
This example command assumes you have the below directory structure and follow this file naming convention (`otuName_function.aln`) for sequence alignment files in clustal format:
```shell
.
├── Gnetidae
│   ├── GNET_A.aln
│   ├── GNET_C.aln
│   ├── GNET_D.aln
│   ├── GNET_E.aln
│   ├── GNET_F.aln
│   ├── GNET_G.aln
│   ├── GNET_H.aln
│   ├── GNET_I.aln
│   ├── GNET_J.aln
│   ├── GNET_K.aln
│   ├── GNET_L.aln
│   ├── GNET_M.aln
│   ├── GNET_N.aln
│   ├── GNET_P.aln
│   ├── GNET_Q.aln
│   ├── GNET_R.aln
│   ├── GNET_S.aln
│   ├── GNET_T.aln
│   ├── GNET_V.aln
│   ├── GNET_W.aln
│   ├── GNET_X.aln
│   └── GNET_Y.aln
└── ferns
    ├── FERN_A.aln
    ├── FERN_C.aln
    ├── FERN_D.aln
    ├── FERN_E.aln
    ├── FERN_F.aln
    ├── FERN_G.aln
    ├── FERN_H.aln
    ├── FERN_I.aln
    ├── FERN_J.aln
    ├── FERN_K.aln
    ├── FERN_L.aln
    ├── FERN_M.aln
    ├── FERN_N.aln
    ├── FERN_P.aln
    ├── FERN_Q.aln
    ├── FERN_R.aln
    ├── FERN_S.aln
    ├── FERN_T.aln
    ├── FERN_V.aln
    ├── FERN_W.aln
    ├── FERN_X.aln
    └── FERN_Y.aln
```


