Fix a bug left by changes for #467: translate "INT" region to "IN".

Also link to DOI number on Zenodo's web site.

CONTRIBUTING.md

@@ -366,6 +366,13 @@ similar steps to setting up a development workstation. Follow these steps:
 18. Send an e-mail to users describing the major changes in the release.
 19. Close the milestone for this release, create one for the next release, and
     decide which issues you will include in that milestone.
+20. When the release is stable, check that it's included on the [Zenodo] page.
+    If you included more than one tag in the same release, the new tags have
+    not triggered Zenodo versions. Edit the release on GitHub, copy the
+    description text, update the release, then click the Delete button. Then
+    create a new release with the same description, and that will trigger a
+    Zenodo version.
 
 [release]: https://help.github.com/categories/85/articles
-[parse_args]: https://github.com/cfe-lab/MiCall/blame/master/micall_watcher.py
+[parse_args]: https://github.com/cfe-lab/MiCall/blame/master/micall_watcher.py
+[Zenodo]: https://doi.org/10.5281/zenodo.2644171

README.md

@@ -2,11 +2,15 @@
 ## Processing FASTQ data from an Illumina MiSeq ##
 [![Build Status]][travis]
 [![Code Coverage]][codecov]
+[![DOI]][zenodo]
+
 
 [Build Status]: https://travis-ci.org/cfe-lab/MiCall.svg?branch=master
 [travis]: https://travis-ci.org/cfe-lab/MiCall
 [Code Coverage]: https://codecov.io/github/cfe-lab/MiCall/coverage.svg?branch=master
 [codecov]: https://codecov.io/github/cfe-lab/MiCall?branch=master
+[DOI]: https://zenodo.org/badge/DOI/10.5281/zenodo.2644171.svg
+[zenodo]: https://doi.org/10.5281/zenodo.2644171
 
 Maps all the reads from a sample against a set of reference sequences, then
 stitches all the reads into consensus sequences and coverage maps.

micall/resistance/asi_algorithm.py

@@ -243,6 +243,8 @@ def load_yaml(self, rules_config, genotype):
             self.drugs[drug_code] = (drug['name'], drug_rules)
 
     def get_gene_positions(self, gene):
+        if gene == 'INT':
+            gene = 'IN'
         positions = set([])
         for drug_class in self.gene_def[gene]:
             for drug_code in self.drug_class[drug_class]:

micall/tests/test_asi_algorithm.py

@@ -435,7 +435,7 @@ def test_negative_positions(self):
 
         self.assertEqual(expected_positions, positions)
 
-    def test(self):
+    def test_multiple_positions(self):
         drugs = """\
           <DRUG>
             <NAME>ABC</NAME>
@@ -457,6 +457,58 @@ def test(self):
 
         self.assertEqual(expected_positions, positions)
 
+    def test_integrase_position(self):
+        xml = """\
+            <ALGORITHM>
+              <ALGNAME>HIVDB</ALGNAME>
+              <ALGVERSION>fake</ALGVERSION>
+              <ALGDATE>2017-03-02</ALGDATE>
+              <DEFINITIONS>
+                <GENE_DEFINITION>
+                  <NAME>IN</NAME>
+                  <DRUGCLASSLIST>INSTI</DRUGCLASSLIST>
+                </GENE_DEFINITION>
+                <LEVEL_DEFINITION>
+                  <ORDER>1</ORDER>
+                  <ORIGINAL>Susceptible</ORIGINAL>
+                  <SIR>S</SIR>
+                </LEVEL_DEFINITION>
+                <LEVEL_DEFINITION>
+                  <ORDER>5</ORDER>
+                  <ORIGINAL>High-Level Resistance</ORIGINAL>
+                  <SIR>R</SIR>
+                </LEVEL_DEFINITION>
+                <DRUGCLASS>
+                  <NAME>INSTI</NAME>
+                  <DRUGLIST>BIC</DRUGLIST>
+                </DRUGCLASS>
+                <GLOBALRANGE><![CDATA[(-INF TO 9 => 1,  10 TO INF => 5)]]></GLOBALRANGE>
+                <COMMENT_DEFINITIONS>
+                </COMMENT_DEFINITIONS>
+              </DEFINITIONS>
+              <DRUG>
+                <NAME>BIC</NAME>
+                <FULLNAME>bictegravir</FULLNAME>
+                <RULE>
+                  <CONDITION><![CDATA[SCORE FROM(51Y => 10)]]></CONDITION>
+                  <ACTIONS>
+                    <SCORERANGE>
+                      <USE_GLOBALRANGE/>
+                    </SCORERANGE>
+                  </ACTIONS>
+                </RULE>
+              </DRUG>
+              <MUTATION_COMMENTS>
+              </MUTATION_COMMENTS>
+            </ALGORITHM>
+        """
+        asi = AsiAlgorithm(StringIO(xml))
+        expected_positions = {51}
+
+        positions = asi.get_gene_positions('INT')
+
+        self.assertEqual(expected_positions, positions)
+
     def test_custom_score_range(self):
         drugs = """\
   <DRUG>