From 11c20aca5133f0a02f11cb6e899bdc00a226b641 Mon Sep 17 00:00:00 2001
From: Matt Shirley <mdshw5@gmail.com>
Date: Mon, 12 Jan 2015 15:25:13 -0500
Subject: [PATCH] Remove bedmask script #38. Add tests to close #35.

---
 pyfaidx/bedmask.py               | 29 -----------------------------
 tests/test_feature_split_char.py | 29 +++++++++++++++++++++++++++++
 2 files changed, 29 insertions(+), 29 deletions(-)
 delete mode 100644 pyfaidx/bedmask.py
 create mode 100644 tests/test_feature_split_char.py

diff --git a/pyfaidx/bedmask.py b/pyfaidx/bedmask.py
deleted file mode 100644
index b1a4a6a..0000000
--- a/pyfaidx/bedmask.py
+++ /dev/null
@@ -1,29 +0,0 @@
-import argparse
-from pyfaidx import Fasta, bed_split
-
-
-def mask_sequence(args):
-    assert len(args.default_seq) == 1
-    fasta = Fasta(args.fasta, mutable=True)
-    for line in args.bed:
-        rname, start, end = bed_split(line)
-        if args.action == 'replace':
-            fasta[rname][start:end] = (end - start) * args.default_seq
-        elif args.action == 'lowercase':
-            fasta[rname][start:end] = fasta[rname][start:end].lowercase()
-
-
-def main():
-    parser = argparse.ArgumentParser(description="Mask regions in BED file "
-                                                 "from FASTA file")
-    parser.add_argument('fasta', type=str, help='FASTA file')
-    parser.add_argument('bed', type=argparse.FileType('r'), help="bed file of regions to mask")
-    parser.add_argument('--default_seq', type=str, default='N',
-                        help='default base for missing positions. default: %(default)s')
-    parser.add_argument('-a', '--action', type=str, default='replace', choices=['replace', 'lowercase'],
-                        help="masking action. default: %(default)s")
-    args = parser.parse_args()
-    mask_sequence(args)
-
-if __name__ == "__main__":
-    main()
diff --git a/tests/test_feature_split_char.py b/tests/test_feature_split_char.py
new file mode 100644
index 0000000..9ce8c73
--- /dev/null
+++ b/tests/test_feature_split_char.py
@@ -0,0 +1,29 @@
+import os
+from pyfaidx import Faidx, Fasta
+from nose.tools import raises
+
+path = os.path.dirname(__file__)
+os.chdir(path)
+
+
+class TestFeatureSplitChar:
+    def __init__(self):
+        self.fasta = os.path.join(path, 'data/genes.fasta')
+        self.faidx = Faidx(self.fasta, split_char='.')
+        self.genes = Fasta(self.fasta, split_char='.')
+
+    def test_keys(self):
+        expect = ['3', 'AB821309', 'KF435149', 'KF435150', 'NM_000465', 'NM_001282543', 'NM_001282545', 'NM_001282548', 'NM_001282549', 'NR_104212', 'NR_104215', 'NR_104216', 'XM_005249642', 'XM_005249643', 'XM_005249644', 'XM_005249645', 'XM_005265507', 'XM_005265508', 'XR_241079', 'XR_241080', 'XR_241081']
+        result = sorted(self.genes.keys())
+        assert result == expect
+
+    def test_key_function_by_dictionary_get_key(self):
+        expect = 'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'
+        result = self.genes['KF435150'][100-1:150]
+        assert str(result) == expect
+
+    def test_key_function_by_fetch(self):
+        expect = 'TTGAAGATTTTGCATGCAGCAGGTGCGCAAGGTGAAATGTTCACTGTTAAA'
+        result = self.faidx.fetch('KF435150',
+                             100, 150)
+        assert str(result) == expect