Package: moca
MoCA: Tool for MOtif Conservation AnalysisLICENSEISCInstallationRequirementspybedtoolsbiopythonpandasscipystatsmodelspybigwigseabornMEME==4.10.2NOTE: MoCA also relies onfasta-shuffle-lettersthat was introduced in MEME4.11.0hence if you are using4.10.2make sure thefasta-shuffle-lettersis the updated one.For a sample script seetravis/install_meme.shUsing Condamocais most compatible with thecondaenvironment.$ conda config --add channels bioconda
$ conda install mocaUsing pip$ pip install mocaFor development$ git clone https://github.com:saketkc/moca.git
$ cd moca
$ conda env create -f environment.yml python=2.7
$ source activate mocadev
$ python setup.py installWorkflowMoCA makes use of PhyloP/PhastCons/GERP scores to assess the quality of a
motif, the hypothesis being a ‘true motif’ would evolve slower as compared
to its surrounding(flanking sequences).Usage$ moca
Usage: moca [OPTIONS] COMMAND [ARGS]...

  moca: Motif Conservation Analysis

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  find_motifs  Run meme to locate motifs and create...
  plot         Create stacked conservation plotsMotif analysis using MEMEMoCA can perform motif analysis for you given a bedfile containing
ChIP-Seq peaks.Genome builds and MEME binary locations are specified through a configuraton file.
A sample configuration file is available:tests/data/application.cfgand should be
self-explanatory.moca find_motifs$ moca find_motifs -h
Usage: moca find_motifs [OPTIONS]

  Run meme to locate motifs and create conservation stacked plots

Options:
  -i, --bedfile TEXT            Bed file input  [required]
  -o, --oc TEXT                 Output Directory  [required]
  -c, --configuration TEXT      Configuration file  [required]
  --slop-length INTEGER         Flanking sequence length  [required]
  --flank-motif INTEGER         Length of sequence flanking motif  [required]
  --n-motif INTEGER             Number of motifs
  -t, --cores INTEGER           Number of parallel MEME jobs  [required]
  -g, -gb, --genome-build TEXT  Key denoting genome build to use in
                                configuration file  [required]
  --show-progress               Print progress
  -h, --help                    Show this message and exit.moca plot$ moca plot -h
Usage: moca plot [OPTIONS]

  Create stacked conservation plots

Options:
  --meme-dir, --meme_dir TEXT     MEME output directory  [required]
  --centrimo-dir, --centrimo_dir TEXT
                                  Centrimo output directory  [required]
  --fimo-dir-sample, --fimo_dir_sample TEXT
                                  Sample fimo.txt  [required]
  --fimo-dir-control, --fimo_dir_control TEXT
                                  Control fimo.txt  [required]
  --name TEXT                     Plot title
  --flank-motif INTEGER           Length of sequence flanking motif
                                  [required]
  --motif INTEGER                 Motif number
  -o, --oc TEXT                   Output Directory  [required]
  -c, --configuration TEXT        Configuration file  [required]
  --show-progress                 Print progress
  -g, -gb, --genome-build TEXT    Key denoting genome build to use in
                                  configuration file  [required]
  -h, --help                      Show this message and exit.ExampleMost users will require using the command line version only:$ moca find_motifs -i encode_test_data/ENCFF002DAR.bed\
    -c tests/data/application.cfg -g hg19 --show-progressCreating plots if you already have run MEME and Centrimo:$ moca plot -c tests/data/application.cfg -g hg19\
    --meme-dir moca_output/meme_out\
    --centrimo-dir moca_output/centrimo_out\
    --fimo-dir-sample moca_output/meme_out/fimo_out_1\
    --fimo-dir-control moca_output/meme_out/fimo_random_1\
    --name ENCODEIDThere is also a structured API available,
however it might be missing examples and documentation at places.API Documentationhttp://saketkc.github.io/moca/Testsmocais mostly extensively tested. Seecode-coverage.Run tests locally$ ./runtests.shCreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.History0.4.1 (2017-02-16)Added $delta$ options for sample vs control ttestRemoved unused requirements: ipaddressFixed meme runner to plot0.3.3 (2016-10-03)Removed pycairo dependency0.2.9 (2016-05-31)Do not fail silently on MEME failingSupport –cores to support parallel threads0.2.8 (2016-05-30)Fixed MEME pipeline missing from mocacli0.2.7 (2016-05-30)Fixed bug where missing wig keys were not handled in mocacli0.2.4 (2016-05-29)Cleaned up unused scripts under scripts directoryAdd configuration file example0.2.3 (2016-05-29)Include package_dir in setup.pyInclude requirements.txt in MANIFEST0.2.0 (2016-05-29)First release on PyPI.