Small improvements for a better galaxy support

deeptools · Dec 25, 2017 · 5af8806 · 5af8806
1 parent 05a32f1
commit 5af8806
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Showing 5 changed files with 41 additions and 5 deletions.
diff --git a/hicexplorer/HiCMatrix.py b/hicexplorer/HiCMatrix.py
@@ -70,7 +70,7 @@ def __init__(self, matrixFile=None, file_format=None, skiprows=None, chrnameList
                     file_format = 'h5'
                 elif matrixFile.endswith('.gz'):
                     file_format = 'dekker'
-                elif matrixFile.endswith('.cool'):
+                elif matrixFile.endswith('.cool') or cooler.io.is_cooler(matrixFile):
                     file_format = 'cool'
                 # by default assume that the matrix file_format is hd5
                 else:

diff --git a/hicexplorer/hicPlotMatrix.py b/hicexplorer/hicPlotMatrix.py
@@ -13,6 +13,7 @@
 from past.builtins import zip
 from future.utils import itervalues
 
+import cooler
 import argparse
 import matplotlib
 matplotlib.use('Agg')
@@ -380,7 +381,10 @@ def getRegion(args, ma):
             exit("Chromosome name {} in --region not in matrix".format(change_chrom_names(chrom)))
 
     args.region = [chrom, region_start, region_end]
-    if args.matrix.endswith(".cool"):
+    is_cooler = False
+    if args.matrix.endswith('.cool') or cooler.io.is_cooler(args.matrix):
+        is_cooler = True
+    if is_cooler:
         idx1, start_pos1 = zip(*[(idx, x[1]) for idx, x in enumerate(ma.cut_intervals) if x[0] == chrom and
                                  ((x[1] >= region_start and x[2] < region_end) or
                                   (x[1] < region_end and x[2] < region_end and x[2] > region_start) or
@@ -398,7 +402,7 @@ def getRegion(args, ma):
                 chrom2 = toBytes(chrom)
             if chrom2 not in list(ma.interval_trees):
                 exit("Chromosome name {} in --region2 not in matrix".format(change_chrom_names(chrom2)))
-        if args.matrix.endswith(".cool"):
+        if is_cooler:
             idx2, start_pos2 = zip(*[(idx, x[1]) for idx, x in enumerate(ma.cut_intervals) if x[0] == chrom2 and
                                      ((x[1] >= region_start2 and x[2] < region_end2) or
                                       (x[1] < region_end2 and x[2] < region_end2 and x[2] > region_start2) or
@@ -431,8 +435,10 @@ def main(args=None):
     if args.region and args.region2 and args.pca:
         log.error("Inter-chromosomal pca is not supported.")
         exit(1)
-
-    if args.matrix.endswith('.cool') and not args.region2:
+    is_cooler = False
+    if args.matrix.endswith('.cool') or cooler.io.is_cooler(args.matrix):
+        is_cooler = True
+    if is_cooler and not args.region2:
         log.debug("Retrieve data from cooler format and use its benefits.")
         regionsToRetrieve = None
         if args.region:

diff --git a/hicexplorer/test/test_data/Li_et_al_2015 b/hicexplorer/test/test_data/Li_et_al_2015
diff --git a/hicexplorer/test/test_data/small_test_matrix_50kb_res b/hicexplorer/test/test_data/small_test_matrix_50kb_res
diff --git a/hicexplorer/test/test_hicPlotMatrix.py b/hicexplorer/test/test_hicPlotMatrix.py
@@ -263,6 +263,21 @@ def test_hicPlotMatrix_cool_log_region1_region2():
         os.remove(outfile.name)
 
 
+@pytest.mark.skipif(LOW_MEMORY > memory,
+                    reason="Travis has too less memory to run it.")
+def test_hicPlotMatrix_cool_log_region1_region2_without_cool_suffix():
+
+    outfile = NamedTemporaryFile(suffix='.png', prefix='hicexplorer_test_cool', delete=False)
+
+    args = "--matrix {0}/Li_et_al_2015 --region chrX:3000000-3500000 --region2 chrX:3100000-3600000 " \
+           "--outFileName  {1} --log ".format(ROOT, outfile.name).split()
+    hicexplorer.hicPlotMatrix.main(args)
+    res = compare_images(ROOT + "hicPlotMatrix" + '/Li_chrX30-35-chrX31-36_cool_log.png', outfile.name, tol=40)
+    assert res is None, res
+    if REMOVE_OUTPUT:
+        os.remove(outfile.name)
+
+
 @pytest.mark.skipif(LOW_MEMORY > memory,
                     reason="Travis has too less memory to run it.")
 def test_hicPlotMatrix_cool_log1p_region1_region2():
@@ -293,6 +308,21 @@ def test_hicPlotMatrix_perChr():
         os.remove(outfile.name)
 
 
+@pytest.mark.skipif(LOW_MEMORY > memory,
+                    reason="Travis has too less memory to run it.")
+def test_hicPlotMatrix_perChr_without_h5_suffix():
+
+    outfile = NamedTemporaryFile(suffix='.png', prefix='hicexplorer_test', delete=False)
+
+    args = "--matrix {0}/small_test_matrix_50kb_res --perChr  " \
+           "--outFileName  {1} ".format(ROOT, outfile.name).split()
+    hicexplorer.hicPlotMatrix.main(args)
+    res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_matrix_50kb_res_perChr.png', outfile.name, tol=40)
+    assert res is None, res
+    if REMOVE_OUTPUT:
+        os.remove(outfile.name)
+
+
 @pytest.mark.skipif(LOW_MEMORY > memory,
                     reason="Travis has too less memory to run it.")
 def test_hicPlotMatrix_cool_perChr_log():