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gb_taxonomy_tools

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GenBank taxonomy processing tools

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## Use CMake to install ##

To build, use

`cmake ./`

`make install` (by default into /usr/local)

## Convert GID to TaxID ##

These are four simple utilities which perform the following manipulations and visualization tasks on GenBank 
taxonomic information.

`gid-taxid` : convert a list of GenBank IDs and associated counts into the list of tripets: genbank id, taxonomy id, count. 
It requires access to (quite large) mapping files maintained by GenBank <ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz>
which are tab separated lists of  `gid taxid count`, e.g. the input line `160338813  160` is output as `160338813  436308	160`

Try running it on as `$gid-taxid tests/data/test.gid path/to/gi_taxid_nucl.dmp`

The result should be as in tests/data/test.taxid

## Convert TaxID into full taxonomic rankings ##

`taxonomy-reader`: convert the output of `gid-taxid` (i.e. gid taxid count triplets) into a fully expanded 22 level 
taxonomy based on NCBI classification. The program requires access to the nodes.dmp and names.dmp files which match taxid
data to scientific names and define the taxonomic hierarchy <ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz>.

Try running
`$taxonomy-reader path/to/names.dmp path/to/nodes.dmp` and entering `160338813  436308	160` <enter> <ctrl-D> on the command line.

The output should be 
`160  436308	root	Archaea	n	n	n	Thaumarchaeota	n	n	n	n	n	Nitrosopumilales	n	n	Nitrosopumilaceae	n	n	n	Nitrosopumilus	n	Nitrosopumilus maritimus	n`

Typical usage involves piping the output file generated by `git-taxid` to `taxonomy-reader`, .e.g

`cat test/data/test.taxid | $taxonomy-reader path/to/names.dmp path/to/nodes.dmp > test/data/test.taxonomy`

##Convert taxonomic rankings into a tree and a text summary##

`taxonomy2tree` takes the output of `taxonomy-reader` and converts it to 2 outputs: a Newick tree file representing the 
hierarchical taxonomy and a summary file.

Try running
`$taxonomy2tree test/data/test.taxonomy 0 test/data/test.tree test/data/test_summary.txt 0`

The output tree uses the standard Newick format with "branch lengths" representing samples representing the given 
taxonomic group.

`((((((Nitrosopumilus maritimus:162)Nitrosopumilus:162)Nitrosopumilaceae:162)Nitrosopumilales:162,uncultured crenarchaeote 74A4:...`

The output summary file is simply a tab-separated count:

root  root	10401
    superkingdom	Archaea	295
    superkingdom	Bacteria	9469
    superkingdom	Eukaryota	553
    superkingdom	Viruses	16
    kingdom	Fungi	100
    kingdom	Metazoa	231
    kingdom	Viridiplantae	110
    subkingdom	Dikarya	97
    ...
  
## Convert the taxonomic tree into a PostScript image ##
  
`tree2ps` takes the Newick tree output of `taxonomy2tree` and converts it to a PostScript rendering subject to a variety of
conditions.

The program arguments are as follows

1. Newick tree file
2. The file to write PostScript to
3. Maximum taxonomic depth -- only show leaves this many or fewer steps away from the root. Use 0 or a negative number to show all levels.
4. font size (in points)
5. Maximum number of leaves -- display the tree up to the depth level (see 3) which has this many or fewer leaves.
6. Count duplicate tax ids -- this is used for coloring the tree; if set to 0, only count the number of leaves below each node, ignoring the counts associated with the leaves themselves.
                            
Try

`$tree2ps test/data/test.tree test/data/tree1.ps 5 8 0 1`

`$tree2ps test/data/test.tree test/data/tree2.ps 0 8 256 1`

`$tree2ps test/data/test.tree test/data/tree3.ps 0 8 256 0`

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