[unit tests] update commands

tests/data_1/shotgun_test.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
 
-shorah shotgun -a 0.1 -w 201 -x 100000 -p 0.9 -c 0 \
+viloca run -a 0.1 -w 201 -x 100000 -p 0.9 -c 0 \
 -r HXB2:2469-3713 -R 42 -f test_ref.fasta -b test_aln.cram --out_format csv "$@"

tests/data_5/shotgun_prepare.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-shorah shotgun -a 0.1 -w 42 -x 100000 -p 0.9 -c 0 -r REF:43-273 -R 42 -b test_aln.cram -f ref.fasta
+viloca run -a 0.1 -w 42 -x 100000 -p 0.9 -c 0 -r REF:43-273 -R 42 -b test_aln.cram -f ref.fasta

tests/test_b2w.py

@@ -2,7 +2,7 @@
 import filecmp
 import os
 import glob
-from shorah import b2w, tiling
+from viloca import b2w, tiling
 import math
 import libshorah
 

tests/test_b2w_mapping.py

@@ -1,7 +1,7 @@
 from array import array
 import pytest
 from cigar import Cigar
-from shorah import b2w
+from viloca import b2w
 import hashlib
 
 class MockAlignedSegment:

tests/test_envp_post.py

@@ -1,5 +1,5 @@
 from unittest.mock import patch, mock_open
-from shorah import envp_post
+from viloca import envp_post
 
 DEFAULT_MOCK_DATA = "default mock data"
 

tests/test_pooled_post.py

@@ -1,5 +1,5 @@
 from unittest.mock import patch, mock_open
-from shorah import pooled_post
+from viloca import pooled_post
 import numpy as np
 
 DEFAULT_MOCK_DATA = "default mock data"
@@ -48,4 +48,4 @@ def open_side_effect(name):
 #                                      open("debug/w-HXB2-2938-3138.dbg"),
 #                                      open("support/w-HXB2-2938-3138.reads-support.fas"),
 #                                      open("corrected/w-HXB2-2938-3138.reads-cor.fas"),
-#                                      "shorah") # TODO
+#                                      "shorah") # TODO

tests/test_pooled_pre.py

@@ -1,6 +1,6 @@
 import pysam
 import os
-from shorah import pooled_pre
+from viloca import pooled_pre
 
 def test__annotate_alignment_file():
     out = "out.bam"
@@ -48,4 +48,4 @@ def test_pre_process_pooled():
     os.remove(out + ".bai")
 
     assert a[0] == a[1] != 0
-    assert a[2] == 0
+    assert a[2] == 0

tests/test_shorah_snv.py

@@ -1,5 +1,5 @@
 import pytest
-from shorah.shorah_snv import _compare_ref_to_read, SNP_id, SNV
+from viloca.shorah_snv import _compare_ref_to_read, SNP_id, SNV
 
 
 @pytest.mark.parametrize("ref, seq, spec", [
@@ -39,4 +39,4 @@ def test_compare_ref_to_read(ref, seq, spec):
 
     assert snp == spec
 
-    assert tot_snv == len(snp)
+    assert tot_snv == len(snp)

tests/test_tiling.py

@@ -1,4 +1,4 @@
-from shorah import tiling
+from viloca import tiling
 import pytest
 
 def test_equispaced():