Libraries to help process Metataxonomy data, specifically NCBI gid, accession_numbers, and taxon ID.

I have taken all the scripts I have written and created libraries for my own use. And why not share?

• I use these libraries to parse alignments against metagenome databases, for example results from IMSA-A (my project on github).

• Accepts alignment files blast format6 (BLAST) or sam (BWA, BOWTIE2, etc) or psl (BLAT).
• Generates useful alignment statistics for all file types; enables comparative analyses.
• Use Genbank IDs (gid) or NCBI Accession numbers. Note that NCBI has deprecated the use of gid.

• Uses local data files improving speed over Eutils.
• Convert taxon ID to other taxons in the lineage
• Create cladograms

• Split a fasta file into chunks (by line count)
• (more)
• List of helpful bash tricks

• Written for Python 2.7.
• I recommend using Anaconda when running on Windows.
• ETE2 (etetoolkit.org) :: for making cladograms only. I use ete2-2.2.1072-py2.7.egg, which is years out of date. (Because I didn't need new features)

Project creation 2018-01-24 README.md drafted