Installation instructions updated, hunter is now tested

tests/test_wolfpack.py

@@ -0,0 +1,43 @@
+#!/usr/bin/env python3.4
+import os
+import io
+import sys
+import unittest
+import tempfile
+
+virmet_dir = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+os.sys.path.insert(1, virmet_dir)
+mod = __import__('virmet')
+sys.modules["virmet"] = mod
+
+from virmet.wolfpack import hunter
+from virmet.common import run_child
+
+
+class TestHunter(unittest.TestCase):
+
+    def setUp(self):
+        self.tmpdir = tempfile.gettempdir()
+        self.reads = os.path.join(virmet_dir, 'VirMet', 'data', 'raw_reads.fastq.gz')
+
+    def test_hunter(self):
+        os.chdir(self.tmpdir)
+        s_dir = hunter(self.reads)
+        os.chdir(s_dir)
+        raw_reads = run_child('zcat', '%s | wc -l' % self.reads)
+        raw_reads = int(raw_reads.strip().split()[0]) / 4
+        with open('good.fastq') as f:
+            good_n = sum(1 for l in f) / 4
+        with open('bad.fastq') as f:
+            bad_n = sum(1 for l in f) / 4
+        with open('stats.tsv') as f:
+            stats = dict(l.strip().split() for l in f)
+        filtered_out = int(stats['low_entropy']) + int(stats['low_quality'])
+        self.assertEqual(bad_n, filtered_out)
+        self.assertEqual(good_n, int(stats['passing_filter']))
+        self.assertEqual(raw_reads, bad_n + good_n + int(stats['trimmed_too_short']))
+
+    def tearDown(self):
+        os.chdir(self.tmpdir)
+        for f in ['good.fastq', 'bad.fastq', 'prinseq.log', 'prinseq.err']:
+            os.remove(f)