Commit 5af8294b authored by Roman Sarrazin-Gendron's avatar Roman Sarrazin-Gendron
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Final paper supplementary version

parent 969ac9ad
......@@ -13,6 +13,7 @@ All scripts from this package can be found in src/pgmpy, updated from [github](
* regex
* GhostScript
* BioPython
* wrapt
## Software requirements
......@@ -22,8 +23,12 @@ All scripts from this package can be found in src/pgmpy, updated from [github](
# Installation
All the code and files required for the downloadable version of the software can be found in the git repository : http://jwgitlab.cs.mcgill.ca/sarrazin/rnabayespairing.git
We also have a webserver on which you can annotate sequences for module signal with our two main datasets: http://bayespairing.cs.mcgill.ca/
* Clone the git repository and execute the following commands:
* cd bayespairing
* cd rnabayespairing
* pip install .
This will install the dependencies and allow you to use some of the scripts outside of the directory.
......@@ -34,6 +39,9 @@ Three python scripts found in `/src` can be used to run `BayesPairing`.
# Predicting module likelihood from sequence
We provide a basic overview of the main functions of the software with the following examples, which use dummy sequences. For biologically relevant applications, please consult the python notebooks in the *test* directory
The main script for predicting the likelihood of a module in an input sequence is `parse_sequences.py`.
For manual:
......@@ -62,9 +70,9 @@ The following arguments can be used to call it. only -seq is required.
-m M number of folded candidates, must be larger than n
-n N number of outputted candidates
-seq SEQ sequences to parse, FASTA file
-ss SS facultative secondary structures, FASTA file
-ss SS facultative secondary structures in the commandline as a string. If your input comes within a fasta file, write "infile"
-d D Dataset, as a pickle. Default will be the dataset
presented in the paper
presented in the paper, rna3dmotif.
-mod MOD [MOD ...] If you only want to parse specific modules, list them.
ex -mod 1 4 12
-p P Number of times the Bayes Net should be sampled
......@@ -72,8 +80,9 @@ The following arguments can be used to call it. only -seq is required.
Default:25
-w W Window Length [50 to 300]. Default:200
-s S Step size between windows [10 to 200]. Default:100
-k K weight of the secondary structure analysis [0.8 to 2].
-sw SW weight of the secondary structure analysis [0.8 to 2].
Default:1
-o O The name of the output pickle file.
```
To test `parse_sequences.py`, you can try the following command, which will run 4 modules from the default dataset on two sequences in the example fasta file :
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