Merge 05b1b23 into 0079197

.gitignore

@@ -5,6 +5,7 @@ dist
 *csv
 .idea
 *.py[cod]
+.mypy_cache
 _trial_temp*
 tests_eero
 benchmarks.R

.travis.yml

@@ -3,12 +3,12 @@
 language: python
 sudo: false
 python:
-  - "2.7"
+  - "3.6"
 
 # command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
 install: pip install -r requirements-test.txt
 
 # command to run tests, e.g. python setup.py test
-script: coverage run --source=bold_retriever `which trial` tests/
+script: coverage run setup.py test
 
 after_success: coveralls

LICENSE

@@ -1,12 +1,9 @@
-Copyright (c) 2014, Carlos Pena
-All rights reserved.
+MIT License
 
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+Copyright (c) 2018, Carlos Pena
 
-* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 
-* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
 
-* Neither the name of Bold Retriever nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Makefile

@@ -41,7 +41,7 @@ test-all:
 	tox
 
 coverage: clean-test
-	coverage run --source=bold_retriever `which trial` tests/
+	coverage run setup.py test
 	coverage report
 	coverage html
 

README.md

@@ -0,0 +1,20 @@
+# bold retriever
+
+bold_retriever is a Python application to identify specimens from COI sequences and BOLD SYSTEMS
+
+## Basic setup
+
+Install the requirements:
+```
+$ pip install -r requirements.txt
+```
+
+Run the application:
+```
+$ python -m bold_retriever --help
+```
+
+To run the tests:
+```
+    $ pytest
+```

README.rst

@@ -36,7 +36,7 @@ For example::
 
 * output::
 
-    seq_id  bold_id       similarity  division  class       order       family        species                collection_country
+    OtuID   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

bold_retriever.py

@@ -0,0 +1,136 @@
+from datetime import datetime, timedelta
+from typing import Dict, Optional
+from urllib.parse import urlencode
+
+from Bio import SeqIO
+import click
+import dataset
+import requests
+
+from engine import generate_output_content, parse_id_engine_xml
+
+
+DATABASE_URL = "sqlite:///bold.sqlite"
+DB = dataset.connect(DATABASE_URL)
+
+
+@click.command()
+@click.option('-f', '--filename', type=str, help='Fasta filename', required=True)
+@click.option('-db',
+              '--database',
+              type=click.Choice([
+                  'COX1_SPECIES', 'COX1', 'COX1_SPECIES_PUBLIC', 'COX1_L640bp',
+              ]),
+              help='Choose a BOLD database. Enter one option.',
+              required=True,
+              )
+def bold(filename, database):
+    "Send seqs to BOLD Systems API and retrieve results"
+    click.echo(filename +  " "  +  database)
+    output_filename = create_output_file(filename)
+    generate_jobs(output_filename, filename, database)
+
+
+def create_output_file(input_filename: str) -> str:
+    """Containing only column headers of the CSV file."""
+    output = "id,bold_id,sequencedescription,database,citation,taxonomicidentification,similarity,url,country,lat,lon,class,order,family,species,"
+    output += "collection_country\n"
+
+    output_filename = input_filename.strip() + "_output.csv"
+    print(f"Creating output file {output_filename}")
+    with open(output_filename, "w") as handle:
+        handle.write(output)
+    return output_filename
+
+
+def generate_jobs(output_filename: str, fasta_file: str, db: str):
+    print(f"Reading sequences from {fasta_file}")
+
+    for seq_record in SeqIO.parse(fasta_file, "fasta"):
+        print(f"* Reading seq {seq_record.name}")
+        response = id_engine(seq_record, db, output_filename)
+        seq_record_identifications = parse_id_engine_xml(response.text)
+
+        # add our seq id to the list of identifications
+        for seq_record_identification in seq_record_identifications:
+            seq_record_identification["OtuID"] = seq_record.id
+            taxonomy = get_taxonomy(seq_record_identification)
+            seq_record_identification.update(taxonomy)
+        generate_output_content(seq_record_identifications, output_filename, seq_record)
+
+
+def id_engine(seq_record, db, output_filename):
+    """Send a COI sequence to BOLD and retrieve its identification"""
+    print(f"* Processing sequence for {seq_record.id}")
+
+    domain = "http://boldsystems.org/index.php/Ids_xml"
+    payload = {'db': db, 'sequence': str(seq_record.seq)}
+    url = domain + '?' + urlencode(payload)
+
+    res = requests.get(url, headers={'User-Agent': 'bold_retriever'})
+    return res
+
+
+def get_taxonomy(seq_record: Dict[str, str]) -> Optional[Dict[str, str]]:
+    tax_id = get_tax_id(seq_record)
+    if tax_id:
+        taxonomy = get_higher_level_taxonomy(tax_id)
+        return taxonomy
+
+
+def get_tax_id(seq_record: Dict[str, str]):
+    tax_id = get_tax_id_from_db(seq_record)
+    if tax_id:
+        return tax_id
+
+    domain = "http://boldsystems.org/index.php/API_Tax/TaxonSearch?taxName="
+    url = domain + seq_record["taxonomicidentification"]
+    res = requests.get(url, headers={'User-Agent': 'bold_retriever'})
+    response_json = res.json()
+    try:
+        tax_id = response_json["top_matched_names"][0]["taxid"]
+    except (KeyError, IndexError):
+        tax_id = None
+
+    if tax_id:
+        table = DB["tax_ids"]
+        data = {
+            "taxon": seq_record["taxonomicidentification"],
+            "tax_id": tax_id,
+        }
+        table.insert(data)
+    return tax_id
+
+
+def get_tax_id_from_db(seq_record: Dict[str, str]) -> Optional[str]:
+    table = DB["tax_ids"]
+    element = table.find_one(taxon=seq_record["taxonomicidentification"])
+    if element:
+        return element["tax_id"]
+
+
+def get_higher_level_taxonomy(tax_id):
+    table = DB["taxonomy"]
+    element = table.find_one(tax_id=tax_id)
+    if element:
+        del element["id"]
+        return element
+
+    url = f"http://boldsystems.org/index.php/API_Tax/TaxonData?taxId={tax_id}&dataTypes=basic&includeTree=true"
+    res = requests.get(url, headers={'User-Agent': 'bold_retriever'})
+    response_json = res.json()
+    taxonomy = dict()
+
+    for id in response_json.keys():
+        category = response_json[id]
+        value = category["taxon"]
+        key = category["tax_rank"]
+        taxonomy[key] = value
+
+    taxonomy["tax_id"] = tax_id
+    table.insert(taxonomy)
+    return taxonomy
+
+
+if __name__ == '__main__':
+    bold()

docs/usage.rst

@@ -22,7 +22,7 @@ For example::
 
 The output should look like this::
 
-    seq_id            bold_id        similarity  division  class    order    family         species                      collection_country
+    OtuID             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