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=1.3.1Environment activation:
source activate prophyleCompile all programs
make -C srcCustom taxonomic trees
Use bin/build_taxonomic_tree.py to build custom taxonomic trees starting from your database’s fasta indexes and taxonomy files (library/Taxonomy for more information). Taxonomic identifiers are assigned to the sequences first, and then the tree is built using ETE Toolkit and saved with newick format 1. Necessary node attributes are:
name: unique node name
taxid: unique taxonomic identifier
seqname: names of the sequences sharing the same taxid, separated by @
fastapath: paths of the sequences’ fasta files, separated by @ (relative paths from their library directory)
infasta_offset: positions where each sequence starts inside the corresponding fasta files, separated by @
base_len: length of each sequence, separated by @
seqname, infasta_offset and base_len can be found in samtools’ fasta index. Other optional attributes are sci_name, named_lineage, lineage, rank (more info here).
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