DEV: making the develop branch the default #7
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Partial download and install functions
[NEW] these are tsv files which contain a summary of the homology data.
There are no associated checksums, so we cannot do integrity checks
[NEW] other data are made available in an emf format, including
providing gene trees etc.. We allow the parser to be applied to these
by turning off format checking and by using callbacks for processing
data blocks.
[NEW] some files do not have checksums we can validate against, so we
provide a flag for these
[NEW] multiple sequence alignment format that is more efficient for parsing Current test very basic.
[NEW] not doing this step in parallel since overhead from pickling the large tables
is large, and the inflation in memory could cause problems on limited hardware.
As we filter the tables to only the genomes being analyses, the process
is fast enough.
[NEW] now include compara tree_names, this can be used to select
species instead of enumerating all names
[CHANGED] changed name of sample cfg file to sample.cfg
[NEW] add new properties for staging and installing genomes [CHANGED] use these attributes in download and install functions
[NEW] reports on what has been installed
[CHANGED] wakepy not robust on linux
[CHANGED] if no alignment specified, no point trying to
download one.
[CHANGED] move config related functions and classes to
new _config.py module.
[CHANGED] mainly to allow a threaded and unthreaded version,
as the latter is quite useful for debugging
[CHANGED] added download function for species trees and moved the
species_from_ensembl_tree function to species
[NEW] trees_for_aligns() matches based on splitting file paths at
the characters [_.- ]. As the names Ensembl gives the alignment directory
only partly corresponds to the names of the tree files associated
with the alignments, these mathes are incomplete. We select the tree with
the maximum number of matches from the name start.
[NEW] merges in a new collection of species names
[NEW] func tion takes the list of alignment names and returns
the corresponding species by identifying the alignment trees.
[NEW] use new capabilities to identify all the associated species
and add those to the Config object.
[NEW] this and associated functions are used to write meta-data
into the local install directory, or read that data from the
the local install directory.
[CHANGED] now specify the relationship type. Currently limited to
ortholog_one2one and ortholog_one2many
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