- RNA Folding project code for Robin Gutell's Lab
- Initial code created Spring 2014 and onward...
- Repository/source control initiated Fall 2015
- Contributors:
- Robin Gutell - Principle Investigator, Gutell Lab
- Jamie Cannone - Research Associate, Gutell Lab
- Ashton Berger - Fall 2015 BIO321G student researcher
- Vishal Patel - Fall 2015 BIO321G student researcher
- We should probably discuss and outline these...
- I think for right now, it's probably best for each individual to fork his/her own branch and make changes there. Once you feel you have a significant amount of work stored there, we can all meet, discuss the changes, and then incorporate the changes into the master branch.
* bin - directory housing run code
* src - package directory that houses various modules for calling within run code
* data - inputs for testing purposes and what not
* tests - will house code tests
- First, update your PYTHONPATH via the command line or else you will get ImportErrors:
- export PYTHONPATH=${PYTHONPATH}:/your/local/directory/with/copy/of/foldrr
- Next, install using the following command:
- python setup.py install
- Last, clean up your directory and start folding!
- python setup.py clean
- bin/python/
- bpseq_to_piesie.py
- Description:
- reads a .bpseq file and produces a .piesie file
- Inputs:
- .bpseq file
- Outputs:
- .piesie annotation file
- Usage example:
- python bin/python/piesie_annotation.py -i data/bpseq/rnasequence.bpseq -o data/piesie/rnasequence.piesie
- Description:
- fold_sequence.py
- Description:
- Currently requires a sequence (input as either a .fasta, a .txt file, or manually via the command line) and an energy file .energetics containing the energies of all the possible helices of the sequence. Outputs a tab-delimited .predicted file with corresponding PI hairpin loop predictions. Can also include the .piesie as an option to denote which sequences are the actual sequences.
- Inputs:
- .fasta file, .energetics file, .piesie file (OPTIONAL)
- Outputs:
- .predicted file
- Usage example:
- python bin/python/fold_sequence.py -s data/fasta/rnasequence.fasta -e data/energetics/rnasequence.energetics -p data/piesie/rnasequence.piesie
- Description:
- graph_helices.py
- Description:
- Given an input sequence via .fasta or manual entry, calculates all possible helices and plots them. Can also include .piesie as an option to include known structures in the plot.
- Inputs:
- .fasta file OR manually enter the sequence via the command line
- Outputs:
- an interactive graph of all of the possible helices for an RNA sequence
- Usage example:
- python bin/python/graph_helices.py sequence.fasta
- Description:
- predict_helices.py
- Description:
- Given an input .fasta or manually entered sequence, will generate a .energetics file which contains all possible helices for the sequence.
- Inputs:
- .fasta file OR manually enter the sequence via the command line
- Outputs:
- .energetics file
- Usage example:
- python bin/python/predict_helices.py rnasequence.fasta
- Description:
- seq_search.py
- Description:
- Searches GenBank records for RNA sequences and will return a .fasta of the sequence. Needs to be run interactively unless the Accession ID is already known.
- Inputs:
- accession number OR manually interact with the program via the command line
- Outputs:
- prints GenBank records to command line
- Usage example:
- python bin/python/seq_search.py
- Description:
- bpseq_to_piesie.py
- If you have any questions, please contact Vishal or Ashton.