Add pytest for r_computematrix (Rust computeMatrix) (#1433)

Salvaged from #1369: keeps only the computeMatrix test, which passes
against the current Rust bindings. The alignmentSieve, bamCompare and
bamCoverage tests from that PR were dropped because their Rust function
signatures have since changed (and alignmentSieve2 is not yet wired up
on 4.0.0).

Co-authored-by: gerikson <galina.erikson@gmail.com>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

Author: 3 people

pydeeptools/deeptools/test/test_r_computeMatrix.py

@@ -0,0 +1,109 @@
+import pytest
+from deeptools.computeMatrix2 import r_computematrix  # Adjust the import to your actual module
+import os.path
+import gzip
+import hashlib
+
+root = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+matrix = root + "computeMatrixOperations.mat.gz"
+bed = root + "computeMatrixOperations.bed"
+rbindMatrix1 = root + "somegenes.txt.gz"
+rbindMatrix2 = root + "othergenes.txt.gz"
+bigwig = root + "testA.bw"
+outnpz = root + "output.mat.npz.gz"
+
+def test_r_computematrix_referencePoint():
+    mode = "reference-point"
+    regionlis = [bed]
+    bwlis = [bigwig]
+    sampleslabel = ["sample1"]
+    upstream = 1000
+    downstream = 1000
+    unscaled5prime = 0
+    unscaled3prime = 0
+    regionbodylength = 0
+    binsize = 50
+    missingdatazero = False
+    metagene = False
+    txnid = ""
+    exonid = ""
+    txniddesignator = ""
+    scale = 1.0
+    nanafterend = False
+    skipzeros = False
+    minthresh = 0.0
+    maxthresh = 0.0
+    averagetypebins = "mean"
+    sortregions = "keep"
+    sortusing = "mean"
+    ortusingsamples = []
+    referencepoint = "TSS"
+    nproc = 1
+    verbose = False
+    ofile = outnpz
+
+    result = r_computematrix(
+        mode, regionlis, bwlis, sampleslabel, upstream, downstream, unscaled5prime, unscaled3prime,
+        regionbodylength, binsize, missingdatazero, metagene, txnid, exonid, txniddesignator, scale,
+        nanafterend, skipzeros, minthresh, maxthresh, averagetypebins, sortregions, sortusing,
+        ortusingsamples, referencepoint, nproc, verbose, ofile
+    )
+
+
+
+    with gzip.open(ofile, 'rb') as f:
+        file_content = f.read()
+        h = hashlib.md5(file_content).hexdigest()
+
+    expectedh = '4f1a2ce422d5b74fb6b75a81916929db'
+    assert h == expectedh
+
+    os.remove(ofile)
+
+def test_r_computematrix_scale():
+    mode = "scale-regions"
+    regionlis = [bed]
+    bwlis = [bigwig]
+    sampleslabel = ["sample1"]
+    upstream = 1000
+    downstream = 1000
+    unscaled5prime = 0
+    unscaled3prime = 0
+    regionbodylength = 0
+    binsize = 50
+    missingdatazero = False
+    metagene = False
+    txnid = ""
+    exonid = ""
+    txniddesignator = ""
+    scale = 1.0
+    nanafterend = False
+    skipzeros = False
+    minthresh = 0.0
+    maxthresh = 0.0
+    averagetypebins = "mean"
+    sortregions = "keep"
+    sortusing = "mean"
+    ortusingsamples = []
+    referencepoint = "TSS"
+    nproc = 1
+    verbose = False
+    ofile = outnpz
+
+    result = r_computematrix(
+        mode, regionlis, bwlis, sampleslabel, upstream, downstream, unscaled5prime, unscaled3prime,
+        regionbodylength, binsize, missingdatazero, metagene, txnid, exonid, txniddesignator, scale,
+        nanafterend, skipzeros, minthresh, maxthresh, averagetypebins, sortregions, sortusing,
+        ortusingsamples, referencepoint, nproc, verbose, ofile
+    )
+
+    with gzip.open(ofile, 'rb') as f:
+        file_content = f.read()
+        h = hashlib.md5(file_content).hexdigest()
+
+    
+    expectedh = '4f1a2ce422d5b74fb6b75a81916929db'
+    assert h == expectedh
+
+    os.remove(ofile)
+