rnastructure howto install and use bootcamp examples ($179) · Snippets

PRELIMINARIES

WARNING above is completely untested. Needs testing on macos and maybe linuxbrew. You can setup brew on macos, and linux, and in windows usising something like WSL (Windows Sub-system-for-Linux) like WSL or WSL2 (or maybe even cygwin).

On linux, instead of brew you can do conda install rnastructure -c bioconda which as of Mar 2021 works only on linux and not macos (yet). See https://bioconda.github.io/recipes/rnastructure/README.html which also has docker info.

$ conda activate
$ conda install rnastructure -c bioconda
$ export DATAPATH="$CONDA_PREFIX/share/rnastructure/data_tables/" # survives `conda update rnastructure`

Most of the commands in RNAstructure suite (in bin or exe folder) require you set DATAPATH to point to the data_tables folder. If using brew it should maintain a symlink to it here:

$ ls -ld           $(brew --prefix)/share/rnastructure/data_tables/
$ export DATAPATH="$(brew --prefix)/share/rnastructure/data_tables/"

The symlink to it should get updated if you do brew switch rnafolder to switch between, say version 6.1 and 6.2.

We don't expect data_tables to change much, but there actually is one new file in the 6.2 version:

$ cd $(brew --prefix)/Cellar/rnastructure
diff -r 6.2/data_tables/ 6.1/data_tables/
Only in 6.2/data_tables/dists: DMSdist_nt.txt

EXAMPLE

Script adapted from https://rna.urmc.rochester.edu:81/mathews-lab/bootcamp/wikis/Shell-Scripting

#!/bin/bash
## this is demo-part.sh 

### === snip === this snip not be needed unless data_tables was not moved to ./share/rnastructure/
### If data_tables folder was left in same parent folder as exe (or bin) folder 
### brew install coreutils (to get realpath). Assuming RNAstructure.jar is in bin or exe folder...
# export HOMEBREW_PREFIX=$(brew --prefix)
# RNAJARFILE=$(realpath $HOMEBREW_PREFIX/bin/RNAstructure.jar)
# export DATAPATH="$(dirname $RNAJARFILE)//../data_tables"
### === end snip ===

### You may want to add the `export DATAPATH=...` line below to your ~/.bashrc  and/or ~/.zshrc

export DATAPATH="$(brew --prefix)/share/rnastructure/data_tables/"
echo "Note: DATAPATH size and location:"
du -sh $DATAPATH
 

echo "Adapted from https://rna.urmc.rochester.edu:81/mathews-lab/bootcamp/wikis/Shell-Scripting"

# This script runs a partition function, followed by the prediction of
# a maximum expected accuracy secondary structure

# Define a path to a sequence file for the input
seq_file="RD0500.seq"

# Define a path to a structure file for the output
ct_file="RD0500-demo.ct"

# Calculate the partition function, the output will be saved to foo.pfs
partition $seq_file foo.pfs

# Predict a secondary structure from the pfs file
MaxExpect foo.pfs $ct_file

To run above script...

bash-5.0$ cat RD0500.seq 
;
RD0500
GCCCGGGUGGUGUAGUGGCCCAUCAUACGACCCUGUCACGGUCGUGACGCGGGUUCgAAUCCCGCCUCGGGCGCCA1

bash-5.0$ ./demo-part.sh 
Note: DATAPATH size and location:
 14M	/usr/local/share/rnastructure/data_tables/
The script is from https://rna.urmc.rochester.edu:81/mathews-lab/bootcamp/wikis/Shell-Scripting
Initializing nucleic acids...done.
 92% [===============================================   ] \                     done.
Single strand partition function complete.
Initializing nucleic acids...done.
Calculating maximum expected accuracy structures...done.
Writing output ct file...done.
Calculation of maximum expected accuracy structures complete.

bash-5.0$ head RD0500-demo.ct 
   76  ENERGY = 6.2  RD0500
    1 G       0    2   72    1
    2 C       1    3   71    2
    3 C       2    4   70    3
    4 C       3    5   69    4
    5 G       4    6   68    5
    6 G       5    7   66    6
    7 G       6    8   65    7
    8 U       7    9   64    8
    9 G       8   10   63    9

TODO: add more info and examples here about python wrappers and/or functions to use RNAstructure like https://github.com/mmagnus/rna-tools/blob/master/rna_tools/rna_dot2ct.py (So you can write python scripts in addition to or instead of shell scripts ;-)

Self-tests can be run as follows.

$ make unit-tests
$ ./exe/unit-tests
Unit test results are shown below.
Tests are identified by line-number (in square brackets).
PASSED TEST[218] Expected==Actual=="Hello" [5 char*]
PASSED TEST[219] Expected==Actual=="Hello" [5 str]
### ... about 100 more lines of output ...
PASSED TEST[204] Expected==Actual=="" [0 str]
PASSED TEST[205] Expected==Actual=="" [0 str]
PASSED TEST[206] Expected==Actual=="ENERGY = 3.6" [12 str]
Done testing. Passed: 111 Failed: 0

Example below shows how to run tests for just the dot2ct utility with dot2ct-tests.sh (which I keep in /usr/local/bin/) dot2ct-tests.sh Or instead of using script, just do: cd tests; ./scripts/test-runner.sh --serial dot2ct

#!/usr/bin/env  bash
### dot2ct-tests.sh  runs tests of dot2ct utility
### see https://gitlab.oit.duke.edu/-/snippets/179
### TODO:  push dir before running and popdir when done.
export HOMEBREW_PREFIX=$(brew --prefix)
RNAJARFILE=$(realpath $HOMEBREW_PREFIX/bin/RNAstructure.jar)
# export DATAPATH="$(dirname $RNAJARFILE)//../data_tables"
RNAstructureHOME="$(dirname $RNAJARFILE)//../"
echo "RNAstructureHOME =$RNAstructureHOME"
echo "doing cd './tests/' subdir before running ./scripts/test-runner.sh"
cd $RNAstructureHOME/tests/
./scripts/test-runner.sh --serial dot2ct 
echo "For list of passed tests do:  tail  './!PASSED_TESTS.log' "
cat << EOF
If all tests passed then above file ends with lines similar to these:
2021-03-24 13:12:40     dot2ct_without_options
2021-03-24 13:12:40     dot2ct_all_structures
2021-03-24 13:12:40     dot2ct_single_structure
2021-03-24 13:12:40     dot2ct_format_multi
2021-03-24 13:12:40     dot2ct_format_simple
2021-03-24 13:12:40     dot2ct_format_side
2021-03-24 13:12:40     dot2ct_pseudoknot
EOF

Below is output, which is colorized with green for passed tests when run in typical terminal

bash-5.0$ dot2ct-tests.sh 
RNAstructureHOME =/usr/local/Cellar/rnastructure/6.2/bin//../
doing cd './tests/' subdir before running ./scripts/test-runner.sh
Running Test Script scripts/dot2ct.sh
Test Options: DumpErrors ShowOutput

Beginning 'dot2ct' tests...
  Building executables for dot2ct tests...
    Making dot2ct...
  Done Building executables (0 errors).
  Test dot2ct 'without_options' started...
Converting dot bracket file...Dot bracket file conversion complete.
  * Test Passed: dot2ct_without_options
  Test dot2ct 'all_structures' started...
Converting dot bracket file...Dot bracket file conversion complete.
  * Test Passed: dot2ct_all_structures
  Test dot2ct 'single_structure' started...
Converting dot bracket file...Dot bracket file conversion complete.
  * Test Passed: dot2ct_single_structure
  Test dot2ct 'format_multi' started...
Converting dot bracket file...Dot bracket file conversion complete.
  * Test Passed: dot2ct_format_multi
  Test dot2ct 'format_simple' started...
Converting dot bracket file...Dot bracket file conversion complete.
  * Test Passed: dot2ct_format_simple
  Test dot2ct 'format_side' started...
Converting dot bracket file...Found side label: 'ENERGY = -33.6  RA7680'
Found side label: 'ENERGY = -32.5  RA7680'
Found side label: 'ENERGY = -31.9  RA7680'
Found side label: 'ENERGY = -31.0  RA7680'
Dot bracket file conversion complete.
  * Test Passed: dot2ct_format_side
  Test dot2ct 'pseudoknot' started...
Converting dot bracket file...Dot bracket file conversion complete.
  * Test Passed: dot2ct_pseudoknot
Completed 'dot2ct' tests.

For list of passed tests do:  tail  './!PASSED_TESTS.log' 
If all tests passed then above file ends with lines similar to these:
2021-03-24 13:12:40     dot2ct_without_options
2021-03-24 13:12:40     dot2ct_all_structures
2021-03-24 13:12:40     dot2ct_single_structure
2021-03-24 13:12:40     dot2ct_format_multi
2021-03-24 13:12:40     dot2ct_format_simple
2021-03-24 13:12:40     dot2ct_format_side
2021-03-24 13:12:40     dot2ct_pseudoknot