bold_retriever 0.2.2

It queries the BOLD database to get identification of taxa based on COI sequences

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:

  cd $USERAPPL
  git clone https://github.com/carlosp420/bold_retriever.git

• install dependencies:

  cd bold_retriever
  module load biopython-env
  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:

  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

Full documentation

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

History

• v0.2.2: Killed bug taxon search.

• v0.2.1: Killed bug in scraping web Public_BIN for species ID.

• v0.2.0: Scraping web Public_BIN for species ID.

• v0.1.9: Added request_id test and option to run fuction in debug mode.

• v0.1.8: Fixed bug for exception when BOLD sends empty list of taxon names.

• v0.1.7: Fixed bug for exception when BOLD sends empty list of taxon names.

• v0.1.6: Append taxon identification results to file as we get them.

• v0.1.5: Additionat tests coverage 92%

• v0.1.4: Fixed bug in taxon_search function

• v0.1.3: Coverage 75%

• v0.1.2: Pep8 and test coverage 69%

• v0.1.1: Packaged as Python module.

• v0.1.0: You can specify which BOLD datase should be used for BLAST of FASTA sequences.

• v0.0.7: Catching exception for NULL, list and text returned instead of XML from BOLD.

• v0.0.6: Catching exception for malformed XML from BOLD.

• v0.0.5: Catch exception when BOLD sends funny data such as {"481541":[]}.