aavilaherrera / simulate_tools Goto Github PK

These scripts are mainly wrappers for various tools used to run a sequence evolution simulator.

simulate_alignment.py generates simulated protein alignments of a fixed length along a given phylogeny, while maintaining domain constraints imposed by a given profile HMM. The intention is to simulate a sequence alignment that looks like a given observed alignment. A starting sequence (either inferred ancestral or randomly generated using the given alignment) is evolved with Revolver

Currently, the gapping pattern of the current alignment is overlayed onto the generated alignments.

Aram Avila-Herrera (Aram.Avila-Herrera at ucsf dot edu)

Dependencies

1. Revolver: http://www.cibiv.at/software/revolver/
2. HMMER3: http://hmmer.janelia.org/ (Make sure hmmfetch is in your path)
   • NOTE: Revolver requires version: Easel h3.0rc2 (March 2010)
3. ANCESCON: ftp://iole.swmed.edu/pub/ANCESCON/ Heads up, these are 32-bit binaries
4. numpy: http://www.numpy.org/

revolver alias: Alias revolver to make it easy to call from the commandline.

alias my_revolver_alias="java -cp /path/to/revolver/ revolver"
# Increase java's stack size for large alignments
# alias my_revolver_alias="java -Xss16m -cp /path/to/revolver/ revolver"

simulate_tools: Let simulate_tools scripts know where they're located by editing the __SRC_PATH and __REVOLVER variables in the runSimAli.sh helper script.

export __SRC_PATH="/path/to/simulate_tools"
export __REVOLVER="my_revolver_alias"

python ${__SRC_PATH}/src/simulate_alignment.py ${@}

• src/simulate_alignment.py -- master python script that ties everything together
• format/ -- scripts used to go between the various miscellaneous sequence formats
• simulate/ -- scripts that help run Revolver, ANCESCON, and HMMER3
• test/ -- a test directory with an example script test.sh

• This is currently a huge mess, but surprisingly works
• Increase the java stack size with -XssN for large alignments. For alignments with more than 1052 sequences set N greater than or equal to 16m (eg. -Xss16m).
• ANCESCON has a weird bug that doesn't like long path names.
  • A workaround involving symlinking requires absolute paths be used.
• ANCESCON is unusable with more than 250 sequences. An alternate starting sequence is generated from the alignment.
• Don't run multiple instances with the same job name at the same time...
• Be very careful about editing simulate_alignment.py to run Revolver in parallel, it will overwrite Revolver's out.fa or block.

• Package nicely
• Find replacement or source for ANCESCON