ProPhyle metagenomic classifier
Project description
Getting started
Prerequisities
GCC 4.8+
ZLib
Python 3 with ete3 library
SamTools
Recommended way of installation using Conda
Environment installation:
conda create -y --name prophyle \
-c etetoolkit -c bioconda \
python==3.4 ete3 bitarray \
parallel blast samtools=1.3.1
Environment activation:
source activate prophyle
Compile all programs
make -C src
Custom taxonomic trees
Use [bin/build_taxonomic_tree.py](bin/build_taxonomic_tree.py) to build custom taxonomic trees starting from your database’s fasta indexes and taxonomy files ([library/Taxonomy](library/Taxonomy) for more information). Taxonomic identifiers are assigned to the sequences first, and then the tree is built using [ETE Toolkit](http://etetoolkit.org/) and saved as newick format 1. Necessary node attributes are:
name: unique node name (format n[0-9]*)
taxid: unique taxonomic identifier
seqname: names of the sequences sharing the same taxid, separated by @
fastapath: paths of the sequences’ fasta files, separated by @ (absolute or relative from the main directory of the repository)
infasta_offset: positions where each sequence starts inside the corresponding fasta files, separated by @
base_len: length of each sequence, separated by @
Other optional attributes are sci_name, named_lineage, lineage, rank (more info [here](http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html#automatic-tree-annotation-using-ncbi-taxonomy)).
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for prophyle-0.1.0.9-cp35-cp35m-macosx_10_7_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 82272c67cf27165d27b581fb5cbc662fc3fe54b8a23fcc1ff1bb5ba060b1e628 |
|
MD5 | 82d1eb6217197cc62b3cfc1a0cf2fd20 |
|
BLAKE2b-256 | 2ea03ab5647b2699b22f29c508a499d9924e23673366858a215c4167d7640823 |