RNA suffix array traversal through chromosomal multiple alignment files (MAF format) to fold and score (with both free-energy models and phylogenetic likelihood) all local and long-range RNA duplexes while allowing bulges and mismatches.
Full documentation is coming soon (Requires Julia v0.6.4), however comprehensive examples of API usage for EvoDuplexes package can be found in test/runtests.jl.
Executable can be run using evo-duplex.jl in /bin:
$ julia evo-duplex.jl -h
usage: evo-duplex.jl --tree TREE [--cons-regions CONS-REGIONS]
--gene-regions GENE-REGIONS --maf MAF
[--model-load MODEL-LOAD]
[--model-data MODEL-DATA] [--model-train]
[-o OUTPUT] [--cons-branch CONS-BRANCH]
[--sig-ratio SIG-RATIO] [--output-all]
[--max-distance MAX-DISTANCE]
[--max-duplex-length MAX-DUPLEX-LENGTH]
[--max-bulges MAX-BULGES]
[--max-mismatches MAX-MISMATCHES]
[--max-deltag MAX-DELTAG] [-h]
optional arguments:
--tree TREE Phylogenetic tree with neutral branch lengths
(in newick format)
--cons-regions CONS-REGIONS
BED file containing conserved regions
--gene-regions GENE-REGIONS
BED file containing gene units to allow
long-range folding within
--maf MAF Directory with MAF files named by chromosome
(chr1.maf.gz...) (default: "../maf")
--model-load MODEL-LOAD
Load pre-trained IsolationForest models,
.evt.jls
--model-data MODEL-DATA
Load training data from `.jlt` file, output
`.evt.jls` file
--model-train Train the IsolationForest models from scratch
using input regions, output `.evt.jls` file
-o, --output OUTPUT Output prefix (default: "evoduplex")
--cons-branch CONS-BRANCH
When conserved regions are given, use this
branch length multiplier (type: Float64,
default: 0.33)
--sig-ratio SIG-RATIO
Output the top fraction of outliers (type:
Float64, default: 0.05)
--output-all Output all folds regardless of prediction
status
--max-distance MAX-DISTANCE
Set a limit on the maximum distance between a
left/right arm of a duplex (type: Int64,
default: 2000)
--max-duplex-length MAX-DUPLEX-LENGTH
Set the maximum duplex length that will be
accessible from the suffix array (type: Int64,
default: 50)
--max-bulges MAX-BULGES
Set the maximum number of bulges to allow for
a duplex (type: Int64, default: 3)
--max-mismatches MAX-MISMATCHES
Set the maximum number of mismatches to allow
for a duplex (type: Int64, default: 3)
--max-deltag MAX-DELTAG
Set the maximum allowable deltaG value (type:
Float64, default: -8.0)
-h, --help show this help message and exit