Bold Retriever

This script accepts FASTA files containing COI sequences. It queries the BOLD database http://boldsystems.org/ in order to get the taxa identification based on the sequences.

Run this way

• clone repository:

  git clone https://github.com/carlosp420/bold_retriever.git
  

• install dependencies (python2.7):

  cd bold_retriever
  pip install -r requirements.txt
  

• run software

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

• output:

  seq_id  bold_id       similarity  division  class       order       family        species                collection_country
  OTU_99  FBNE064-11    1           animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius pini        Germany
  OTU_99  NEUFI079-11   1           animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius pini        Finland
  OTU_99  FBNE172-13    0.9937      animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius atrifrons   Germany
  OTU_99  FBNE162-13    0.9936      animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius contumax    Austria
  OTU_99  TTSOW138-09   0.9811      animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius ovalis      Canada
  OTU_99  CNPAH380-13   0.9811      animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius             Canada
  OTU_99  CNKOF1602-14  0.9811      animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius pinidumus   Canada
  OTU_99  NRAS173-11    0.9748      animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius conjunctus  Canada
  OTU_99  SSBAE2911-13  0.9748      animal    Collembola  None        None          Collembola             Canada
  OTU_99  CNPAQ117-13   0.9686      animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius humulinus   Canada
  

Speed

bold_retriever uses the library Twisted for performing asynchronous calls. This speeds up the total processing time.

Citation

The citation should be our MolEco paper:

Vesterinen, E. J., Ruokolainen, L., Wahlberg, N., Peña, C., Roslin, T., Laine, V. N., Vasko, V., Sääksjärvi, I. E., Norrdahl, K., and Lilley, T. M. (2016) What you need is what you eat? Prey selection by the bat Myotis daubentonii. Molecular Ecology, 25(7), 1581–1594. doi:10.1111/mec.13564

Full documentation

See the full documentation at http://bold-retriever.readthedocs.org