Add pytest for alignment seive in sync with Planemo test

pydeeptools/deeptools/test/test_alignmentseive.py

@@ -0,0 +1,83 @@
+import deeptools.alignmentSieve as aln_seive
+
+import os.path
+from os import unlink
+
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+BAMFILE_IN = ROOT + "paired_chr2L.bam"
+CRAMFILE_IN = ROOT + "paired_chr2L.cram"
+FILTER_METRICS_FILE = ROOT + "alignmentSieve.txt"
+BED_OUT = ROOT + "alignmentSieve.bed"
+BAMFILE_OUT = ROOT + "alignmentSieve.bam"
+BAMFILE_OUT2 = ROOT + "alignmentSieve2.bam"
+BAMFILE_OUT3 = ROOT + "alignmentSieve3.bam"
+
+
+def test_minimum_mapping_quality_filter_metric():
+    """
+    Test minimal command line args for alignement sieve
+    """
+    outfile = '/tmp/test_bam.bam'
+    filter_metric_file = '/tmp/test_metrics.txt'
+    args = "--bam {} -o {} --minMappingQuality 10 --filterMetrics {}".format(BAMFILE_IN, outfile, filter_metric_file).split()
+    aln_seive.main(args)
+
+    _foo = open(filter_metric_file, "r")
+    resp = _foo.readlines()[2]
+    _foo.close()
+    expected = 'paired_chr2L.bam\t8440\t12644\n'
+    assert expected in resp, f"'{expected}' not found in '{resp}'"
+
+    bam_file_size = os.path.getsize(BAMFILE_OUT)
+    expected_file_size = os.path.getsize(outfile)
+    size_tolerance = 5000
+    size_difference = abs(bam_file_size - expected_file_size)
+    assert size_difference <= size_tolerance, "File size do not match"
+    unlink(outfile)
+    unlink(filter_metric_file)
+
+
+def test_with_bed_output_along_with_shifts():
+    """
+    Tests Alignment seive with shifts and output BED file
+    """
+    output_bed_file = "/tmp/aln_seive.bed"
+    args = "--bam {} -o {} --minMappingQuality 10 --BED --shift 1 -2 3 -4".format(BAMFILE_IN, output_bed_file).split()
+    aln_seive.main(args)
+    with open(output_bed_file, "r") as _foo:
+        result = len(_foo.readlines())
+    _expected = 4261
+    assert result == _expected, "No of lines in BED files differ"
+    unlink(output_bed_file)
+
+
+def test_with_bam_output_with_shifts():
+    """
+    Tests Alignment seive with shifts and output BAM file
+    """
+    output_bam_file = "/tmp/aln_seive.bam"
+    args = "--bam {} -o {} --minMappingQuality 10 --shift 1 -2 3 -4".format(BAMFILE_IN, output_bam_file).split()
+    aln_seive.main(args)
+
+    bam_file_size = os.path.getsize(BAMFILE_OUT2)
+    expected_file_size = os.path.getsize(output_bam_file)
+    size_tolerance = 5000
+    size_difference = abs(bam_file_size - expected_file_size)
+    assert size_difference <= size_tolerance, "File sizes do not match"
+    unlink(output_bam_file)
+
+
+def test_with_cram_output_with_shifts():
+    """
+    Tests Alignment seive with  CRAM input along with shifts
+    """
+    output_bam_file = "/tmp/aln_seive2.bam"
+    args = "--bam {} -o {} --minMappingQuality 10 --shift 1 -2 3 -4".format(BAMFILE_IN, output_bam_file).split()
+    aln_seive.main(args)
+
+    bam_file_size = os.path.getsize(BAMFILE_OUT3)
+    expected_file_size = os.path.getsize(output_bam_file)
+    size_tolerance = 5000
+    size_difference = abs(bam_file_size - expected_file_size)
+    assert size_difference <= size_tolerance, "File sizes do not match"
+    unlink(output_bam_file)