rename_species.py

#!/usr/bin/env python
from os import path
from glob import iglob
import re
trans = {'AGO':'DAR', 'CAZ':'GUN', 'CF':'CF', 'F':'CF', 
'CRU':'POR', 'ESP':'HOO', 'LG':'ABI', 'LP':'VIC', 
'LT':'VIC', 'PBL':'PBL', 'PBR':'PBR', 'PZ':'EPH', 
'SCR':'CHA', 'VA':'VAN', 'VD':'MIC'}

for fi in iglob('consensus/*.fa'):
    in_file = open(fi)
    out_name = re.sub('\.fa$', '', path.basename(fi)) + '_species.fa'
    out_file = open(path.join('consensus',out_name), 'w')

    for l in in_file:
        if l.startswith('>'):
                mat = re.match('>([A-Z]+)([_\d]*)', l)
                matches = mat.groups()
                out_file.write(''.join([l.rstrip(), '_', trans[matches[0]], '\n']))
        else:
            out_file.write(l)
    out_file.close()
    in_file.close()