Naming issue in CDS Search

[lecorguille]

@casteljade reportes that there is a naming issue within the Fasta generated by CDS Search that make issue with CodeML. The dN/dS aren't calculated.

https://github.com/abims-sbr/adaptsearch/blob/dev/scripts/05_CDS_search/S03_remove_site_with_not_enough_species_represented.py#L173-L183

Still under investigation, I'm trying a dummy fasta_name[0:3]

 # nuc
    if filtered_bash_nuc != {} and new_leng_nuc >= MIN_LENGTH_FINAL_ALIGNMENT_NUC:
        good+=1
        OUTnuc=open("%s/%s" %(path_OUT2, new_name), "w")
        for fasta_name in filtered_bash_nuc.keys():
            seq_nuc = filtered_bash_nuc[fasta_name]
            OUTnuc.write("%s\n" %fasta_name[0:3])
            OUTnuc.write("%s\n" %seq_nuc)

W&S