DeeNuRP

De-novo Reference Package Pipeline

Under development.

Installation

The Easy Way

Install Python 2.7
run bin/bootstrap.sh
run source deenurp-env/bin/activate

the deenurp executable should now be on your $PATH

The Hard Way

First, install binary dependencies:

Python 2.7
- pip, for installing python dependencies (http://www.pip-installer.org/)
- Python packages:
  - Run pip install PACKAGE for every PACKAGE listed in requirements.txt, e.g. cat requirements.txt | xargs -n 1 pip install
uclust 1.1
Infernal version 1.1, (http://infernal.janelia.org/)
pplacer suite (http://matsen.fhcrc.org/pplacer)
FastTree 2 (http://www.microbesonline.org/fasttree/#Install)

Optional (for filter-outliers and pairwise-distances):

vsearch (https://github.com/torognes/vsearch)
muscle (http://www.drive5.com/muscle/)

Finally, install:

python setup.py install

UCLUST, pplacer, FastTree, Infernal, and R are all distributed with the QIIME Virtual Machine, which may be a great way to get started.

De-novo reference set creation

Similarity-search based reference sequence selection

Running

The deenurp package under the current directory provides to subcommands, accessed via the script deenurp.py, or the command deenurp if installed.

Subcommands fall into two general categories:

Building a set of reference sequences for use in refpkg building
Selecting sequences for a specific reference package

Creating a sequence set for refpkg building

deenurp filter-outliers

Removes outlier sequences from a reference database

deenurp expand-named

Expands poorly-represented names in a sequence file by similarity search

deenurp cluster-refs

Cluster reference sequences, first by tax-id at a specified rank (default: species), then by similarity for unnamed sequences or sequences not classified to the desired rank. Serves as input to search-sequences.

Selecting sequences for a reference package

deenurp hrefpkg-build

Builds a set of hierarchical reference packages.

deenurp search-sequences

Searches a set of sequences against a FASTA file containing possible reference sequences.

This subcommand does searches sequences against a reference FASTA file, saving the results and some metadata to a sqlite database for use in select-references

deenurp select-references

Given the output of search-sequences, select-references attempts to find a good set of reference sequences.

For each reference cluster with a minimal amount of sequences having best hits to the cluster, (see cluster-refs), selects a set number of sequences to serve as references.

deenurp fill-lonely

Taxa who are the sole descendent of their parent can complicate taxonomic classification.

The fill-lonely subcommand finds some company for these lonely taxa.

deenurp add-reps

Fetches sequences from a sequence file which match the taxtable for a reference set at a given rank. Useful for adding type strains.

deenurp tax2tree

Runs the tax2tree program on a reference package, updating the seq_info file.

Sequences whose lineage changes are relabeled. The prior tax_id is added to the seq_info file in the reference package.

File	Mode	Size
bin
deenurp
docs
tests
.gitignore	-rw-r--r--	129 bytes
.travis.yml	-rw-r--r--	947 bytes
CHANGES.rst	-rw-r--r--	2.0 KB
DEVELOPING.rst	-rw-r--r--	952 bytes
LICENSE.txt	-rw-r--r--	34.3 KB
MANIFEST.in	-rw-r--r--	95 bytes
README.rst	-rw-r--r--	3.6 KB
deenurp.py	-rwxr-xr-x	74 bytes
distribute_setup.py	-rw-r--r--	16.9 KB
requirements.txt	-rw-r--r--	325 bytes
setup.py	-rw-r--r--	1.9 KB
version.py	-rw-r--r--	1.6 KB

README.rst