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:
seq_id bold_id similarity division class order family species collection_country
TE-14-27_FHYP_av FIDIP558-11 0.9884 animal Insecta Diptera None Diptera Finland
TE-14-27_FHYP_av GBDP6413-09 0.9242 animal Insecta Diptera Hippoboscidae Ornithomya anchineura None
TE-14-27_FHYP_av GBDP2916-07 0.922 animal Insecta Diptera Hippoboscidae Stenepteryx hirundinis None
TE-14-27_FHYP_av GBDP2919-07 0.9149 animal Insecta Diptera Hippoboscidae Ornithomya biloba None
TE-14-27_FHYP_av GBDP2908-07 0.9078 animal Insecta Diptera Hippoboscidae Ornithoctona sp. P-20 None
TE-14-27_FHYP_av GBDP2918-07 0.9076 animal Insecta Diptera Hippoboscidae Ornithomya chloropus None
TE-14-27_FHYP_av GBDP2935-07 0.8936 animal Insecta Diptera Hippoboscidae Crataerina pallida None
TE-14-27_FHYP_av GBMIN26225-13 0.8889 animal Insecta Diptera Calliphoridae Lucilia sericata None
TE-14-27_FHYP_av GBDP5820-09 0.8833 animal Insecta Diptera Muscidae Coenosia tigrina None
TE-14-27_FHYP_av GBMIN26204-13 0.883 animal Insecta Diptera Calliphoridae Lucilia cuprina None
TE-14-27_FHYP_av GBMIN18768-13 0.8823 animal Insecta Diptera Hippoboscidae Ornithoctona erythrocephala Brazil
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'}]