Usage¶
How to run bold_retriever¶
You have to choose one of the databases available from BOLD http://www.boldsystems.org/index.php/resources/api?type=idengine and enter it as argument:
- COX1_SPECIES
- COX1
- COX1_SPECIES_PUBLIC
- COX1_L640bp
For example:
python bold_retriever.py -f ZA2013-0565.fasta -db COX1_SPECIES
The output should look like this:
bold_id seq_id similarity collection_country division taxon class order family
FIDIP558-11 TE-14-27_FHYP_av 0.9884 Finland animal Diptera Insecta Diptera None
GBDP6413-09 TE-14-27_FHYP_av 0.9242 None animal Ornithomya anchineura Insecta Diptera Hippoboscidae
GBDP2916-07 TE-14-27_FHYP_av 0.922 None animal Stenepteryx hirundinis Insecta Diptera Hippoboscidae
GBDP2919-07 TE-14-27_FHYP_av 0.9149 None animal Ornithomya biloba Insecta Diptera Hippoboscidae
GBDP2908-07 TE-14-27_FHYP_av 0.9078 None animal Ornithoctona sp. P-20 Insecta Diptera Hippoboscidae
GBDP2918-07 TE-14-27_FHYP_av 0.9076 None animal Ornithomya chloropus Insecta Diptera Hippoboscidae
GBDP2935-07 TE-14-27_FHYP_av 0.8936 None animal Crataerina pallida Insecta Diptera Hippoboscidae
GBMIN26225-13 TE-14-27_FHYP_av 0.8889 None animal Lucilia sericata Insecta Diptera Calliphoridae
GBDP5820-09 TE-14-27_FHYP_av 0.8833 None animal Coenosia tigrina Insecta Diptera Muscidae
GBMIN26204-13 TE-14-27_FHYP_av 0.883 None animal Lucilia cuprina Insecta Diptera Calliphoridae
GBMIN18768-13 TE-14-27_FHYP_av 0.8823 Brazil animal Ornithoctona erythrocephala Insecta Diptera Hippoboscidae
As an alternative you can use bold_retriever as a Python module¶
To use Bold Retriever in a project:
>>> from Bio import SeqIO
>>> from bold_retriever import bold_retriever as br
>>> # database from BOLD
>>> db = "COX1_SPECIES"
>>> all_ids = []
>>> for seq_record in SeqIO.parse("tests/ionx13.fas", "fasta"):
... my_ids = br.request_id(seq_record.seq, seq_record.id, db)
Psocoptera 0.9796
Selenops mexicanus 0.8933
Austrophorocera Janzen03 0.8736
Austrophorocera Janzen04 0.8667
Lepidoptera 0.8667
Proechimys simonsi 0.8667
Diptera 0.8667
Scathophaga stercoraria 0.8667
Culex quinquefasciatus 0.8667
Folsomia fimetaria L1 0.8652
Lepidopsocidae sp. RS-2001 0.8639
lepidopsocid RS-2001 0.8639
Selenops micropalpus 0.859
Geocoris pallidipennis 0.8586
Selenops sp. 2 SCC-2009 0.8571
Mermessus trilobatus 0.8571
Drosophila neotestacea 0.8571
Hemiptera 0.8556
Miromantis mirandula 0.8537
Houghia gracilis 0.8533
Adoxophyes nr. marmarygodes 0.8533
Trichoptera 0.8533
Araneae 0.8533
Hydroporus morio 0.8533
Rodentia 0.8533
In that case the output will be contained in the variable my_ids and will look like this:
[{'bold_id': 'FIPSO166-14',
'collection_country': 'Finland',
'id': 'ionx13',
'seq': 'AATTTGAGCTGGTATACTTGGGACTAGTTTAAGAATCTTAATTCGACTTGAGTTAGGCCAACCAGGTTTATTtttAGAAGATGACCAAACATATAATGTTATCGTTACCGCTCACGCTTTTATTATAATTttttttATAGTAATACCAATATA',
'similarity': '0.9796',
'tax_id': 'Psocoptera'},
{'bold_id': 'GBCH4611-10',
'collection_country': 'None',
'id': 'ionx13',
'seq': 'AATTTGAGCTGGTATACTTGGGACTAGTTTAAGAATCTTAATTCGACTTGAGTTAGGCCAACCAGGTTTATTtttAGAAGATGACCAAACATATAATGTTATCGTTACCGCTCACGCTTTTATTATAATTttttttATAGTAATACCAATATA',
'similarity': '0.8933',
'tax_id': 'Selenops mexicanus'},
{'bold_id': 'ASTAQ477-06',
'collection_country': 'Costa Rica',
'id': 'ionx13',
'seq': 'AATTTGAGCTGGTATACTTGGGACTAGTTTAAGAATCTTAATTCGACTTGAGTTAGGCCAACCAGGTTTATTtttAGAAGATGACCAAACATATAATGTTATCGTTACCGCTCACGCTTTTATTATAATTttttttATAGTAATACCAATATA',
'similarity': '0.8736',
'tax_id': 'Austrophorocera Janzen03'},
{'bold_id': 'ASTAR353-07',
'collection_country': 'Costa Rica',
'id': 'ionx13',
'seq': 'AATTTGAGCTGGTATACTTGGGACTAGTTTAAGAATCTTAATTCGACTTGAGTTAGGCCAACCAGGTTTATTtttAGAAGATGACCAAACATATAATGTTATCGTTACCGCTCACGCTTTTATTATAATTttttttATAGTAATACCAATATA',
'similarity': '0.8667',
'tax_id': 'Austrophorocera Janzen04'}]