Added values to synonyms table

[bilalix]

Added common names and authority values to the synonyms table and created get_synonyms() to retrieve them. Fix #382

[cpommier]

Hi @jhcepas @fransua , any chance to see this merged in ete3? It is a little change that make the library very usefull. Thanks in advance.

[jhcepas]

yes. Sorry we didn't find time to work on requests for a long time. We are now working on a new release and this addon sounds good. @dengzq1234 could you review and merge if everything is ok? I think we migth need a unitest function before merge though.

[cpommier]

Thank you!

[Anoosha-Sehar]

Hi, I'm using ETE3 package for getting common names and scientific names for NCBI id's. Currently, I'm working on extracting synonyms. Is there any chance that you will update it with 'get_synonym'? That would be really helpful.

[chanind]

Until this is merged, I was able to manually create this as a separate method below:

def get_synonyms(ncbi, taxids):
    id2syn = {}
    # since they could be more than one synonym
    # we first create a dictionary filled with taxonID
    # and have an array of values/synonyms
    for tax in taxids:
        id2syn[tax] = []
    query = ",".join(['"%s"' % v for v in taxids])
    cmd = "select taxid, spname FROM synonym WHERE taxid IN (%s);" % query
    result = ncbi.db.execute(cmd)
    for tax, synonym in result.fetchall():
        if synonym:
            id2syn[tax].append(synonym)
    return id2syn

This works the same as this PR, except you need to pass the ncbi database object as the first parameter