Accept Pathologic file as input.

[ArnaudBelcour]

To handle this format a file containing the taxon id for the corresponding species is needed.

Idea:

Folder_input
├── species_1
│   └── species_1.pf
├── species_2
│   └── species_2.gff
│   └── species_2.fasta
├── species_3
│   └── species_3.gbk
 pf_taxon_id.txt
..

[ArnaudBelcour]

Idea: pf_taxon_id.txt could contain taxon_id for Genbank or GFF (instead of looking into the Genbank or the GFF file).

[ArnaudBelcour]

Rename pf_taxon_id.txt into taxon_id.tsv.

[ArnaudBelcour]

With c46e76c8953d3212a701fa230260a679beca8f8a, it is possible to use taxon_id.tsv for Genbank and GFF files.

[ArnaudBelcour]

With 86453f9ab00c2ed77f4a1074b3bde4fceeaf126b, it is possible to force the use of taxon_id.tsv for GFF and Genbank files.

[ArnaudBelcour]

Added in #27.