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BreadCrumbs

BreadCrumbs is an unofficial collection of scripts and code intended to consolidate functions for tool development and contain scripts for command line access to commonly used functions. Breadcrumbs tends to include functionality associated with metagenomics analysis but you never know what you will find!

Dependencies:

NOTE: Python dependencies will be automatically installed, if needed, when installing BreadCrumbs. The R libraries are not automatically installed. Please install the required R libraries manually.

  1. Cogent https://pypi.python.org/pypi/cogent
  2. MatplotLib http://matplotlib.org/downloads.html
  3. Mercurial http://mercurial.selenic.com/ (optional for downloading)
  4. Numpy http://www.numpy.org/
  5. Python 2.x http://www.python.org/download/
  6. SciPy http://www.scipy.org/install.html
  7. biom support http://biom-format.org/
  8. blist https://pypi.python.org/pypi/blist/
  9. R http://www.r-project.org/
  10. R libraries including vegan, optparse, ggplot2, ggtree, RColorBrewer, and Biostrings

How to download

To download BreadCrumbs from BitBucket use the command:

hg clone https://bitbucket.org/biobakery/breadcrumbs

To update BreadCrumbs, in the BreadCrumbs directory use the 2 commands sequentially:

hg pull
hg update

Install:

To install please use the setup.py script in a terminal.

python setup.py install

Note to Mac users:

Before using the setup.py script you will need to install the following.

  1. GCC compiler Go to https://developer.apple.com/downloads/index.action Register for an Apple account you do not have one (it is free) In the Developer Tools category download "Command Line Tools for Xcode" Download and install.

  2. Fortran Compiler See Fortran section of http://www.scipy.org/scipylib/building/macosx.html

You may also need to run the command: (errors referencing the egg).

pip install setuptools --upgrade

Scripts:

Scripts are included to expose core functionality through the command line. Currently these scripts center on manipulating and visualizing abundance tables.
A quick description of the scripts include:

  • Hclust.py Flexible script to create a visualization of hierarchical clustering of abundance tables (or other matrices).

  • scriptBiplotTSV.R Allows one to plot a tsv file as a biplot using nonmetric multidimensional scaling.

  • scriptPlotFeature.py Allows one to plot a histogram, boxplot, or scatter plot of a bug or metadata in an abundance table. Will work on any row in a matrix.

  • scriptManipulateTable.py Allows one to perform common functions on an abundance table including, summing, normalizing, filtering, stratifying tables.

  • scriptPcoa.py Allows one to plot a principle covariance analysis (PCoA) plot of an abundance table.

  • scriptConvertBetweenBIOMAndPCL.py Allows one to convert between BIOM and PCL file formats.

  • strainphlan_ggtree.R Allows one to plot dendrograms from StrainPhlAn outputs.

  • strainphlan_ordination.R Allows one to plot an ordination from StrainPhlAn outputs.

Programming Classes:

Brief descriptions of classes are as follows. More detailed descriptions are given in the classes themselves.

  • AbundanceTable Data structure to contain and perform operations on an abundance table.

  • BoxPlot Wrapper to plot box plots.

  • CClade Helper object used in hierarchical summing and normalization

  • Cladogram Object that manipulated an early dendrogram visualization. Deprecated, should use the GraPhlan visualization tool on bitbucket instead.

  • CommandLine Collection of code to work with command line. Deprecated. Should use sfle calls.

  • ConstantsBreadCrumbs Contains generic constants.

  • ConstantsFiguresBreadCrumbs Contains constants associated with formatting figures.

  • KMedoids Code from MLPY which performs KMedoids sample selection.

  • MLPYDistanceAdaptor Used to allow custom distance matrices to be used by KMedoids.

  • Metric Difference functions associated with distance and diversity metrics.

  • PCoA Functionality surrounding the plotting of a PCoA

  • PlotMatrix Allows on to plot a matrix of numbers.

  • SVM Support Vector Machine associated scripts.

  • Utility Generic functions

  • UtilityMath Generic math related functions

  • ValidateData Collection of functions to validate data types when needed.

Demo input files:

  • fastunifrac_Ley_et_al_NRM_2_sample_id_map.txt Example Unifrac Id mapping file (source http://bmf2.colorado.edu/fastunifrac/tutorial.psp)

  • GreenGenesCore-May09.ref.tre Example Greengenes core set reference for Unifrac demo (source http://bmf2.colorado.edu/fastunifrac/tutorial.psp)

  • Test.pcl Example file / Test PCL file to run scripts on.

  • Test.biom Example file / Test BIOM file to run scripts on.

  • Test_no_metadata.pcl Example file / Test PCL file to run scripts on which does not have metadata.

  • Test_no_metadata.biom Example file / Test BIOM file to run scripts on which does not have metadata.

  • Test-biplot.tsv Example file / Test file for the scriptBiplotTSV.R

Contributing Authors:

Timothy Tickle, George Weingart, Nicola Segata, Randall Schwager, Curtis Huttenhower

Contact:

Please feel free to contact ttickle@hsph.harvard.edu with questions.