added new test to build matrix using RF and updated previous test

deeptools · Jun 27, 2017 · 6571f10 · 6571f10
1 parent 095560d
commit 6571f10
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Showing 18 changed files with 464,529 additions and 8 deletions.
diff --git a/hicexplorer/hicBuildMatrix.py b/hicexplorer/hicBuildMatrix.py
@@ -1059,7 +1059,7 @@ def main(args=None):
         args.restrictionSequence = args.restrictionSequence.upper()
         args.danglingSequence = args.danglingSequence.upper()
         dangling_sequences['pat_forw'] = args.danglingSequence
-        dangling_sequences['pat_rev'] = str(Seq(args.danglingSequence, generic_dna).reverse_complement())
+        dangling_sequences['pat_rev'] = str(Seq(args.danglingSequence, generic_dna).complement())
 
         sys.stderr.write("dangling sequences to check "
                          "are {}\n".format(dangling_sequences))

diff --git a/hicexplorer/test/test_buildMatrix.py b/hicexplorer/test/test_buildMatrix.py
@@ -2,13 +2,15 @@
 from hicexplorer import HiCMatrix as hm
 from tempfile import NamedTemporaryFile, mkdtemp
 import shutil
+import filecmp
 import os
 import numpy.testing as nt
 
 
 ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
 sam_R1 = ROOT + "small_test_R1_unsorted.bam"
 sam_R2 = ROOT + "small_test_R2_unsorted.bam"
+dpnii_file = ROOT + "DpnII.bed"
 
 
 def test_build_matrix():
@@ -23,10 +25,36 @@ def test_build_matrix():
     test = hm.hiCMatrix(ROOT + "small_test_matrix.h5")
     new = hm.hiCMatrix(outfile.name)
     nt.assert_equal(test.matrix.data, new.matrix.data)
-    assert test.cut_intervals == new.cut_intervals
+    nt.assert_equal(test.cut_intervals, new.cut_intervals)
 
     print set(os.listdir(ROOT + "QC/"))
+    filecmp(ROOT + "QC/QC.log", qc_folder + "/QC.log")
     assert set(os.listdir(ROOT + "QC/")) == set(os.listdir(qc_folder))
 
     os.unlink(outfile.name)
     shutil.rmtree(qc_folder)
+
+
+def test_build_matrix_rf():
+    outfile = NamedTemporaryFile(suffix='.h5', delete=False)
+    outfile.close()
+    qc_folder = mkdtemp(prefix="testQC_")
+    args = "-s {} {} -rs {} -o {}  --QCfolder {} " \
+           "--restrictionSequence GATC " \
+           "--danglingSequence GATC " \
+           "--minDistance 150 " \
+           "--maxDistance 1500".format(sam_R1, sam_R2, dpnii_file,
+                                       outfile.name,
+                                       qc_folder).split()
+    hicBuildMatrix.main(args)
+
+    test = hm.hiCMatrix(ROOT + "small_test_rf_matrix.h5")
+    new = hm.hiCMatrix(outfile.name)
+    nt.assert_equal(test.matrix.data, new.matrix.data)
+    nt.assert_equal(test.cut_intervals, new.cut_intervals)
+
+    print set(os.listdir(ROOT + "QC_rc/"))
+    assert set(os.listdir(ROOT + "QC_rc/")) == set(os.listdir(qc_folder))
+
+    os.unlink(outfile.name)
+    shutil.rmtree(qc_folder)