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test fix
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Eric Kofman committed Dec 10, 2024
1 parent 5748850 commit c4b3d0c
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Showing 4 changed files with 23 additions and 27 deletions.
2 changes: 0 additions & 2 deletions examples/sc_subset_CT/depth_commands_source_cells.txt
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This file was deleted.

4 changes: 2 additions & 2 deletions src/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1109,10 +1109,10 @@ def delete_intermediate_files(output_folder):
'combined_source_cells_split_by_suffix',
'matrix_outputs',
'all_edit_info.tsv',
'concat_command.sh', 'depth_commands_source_cells.sh', 'combined.bed', 'merge_command.sh',
'concat_command.sh', 'depth_commands_source_cells.sh', 'depth_commands_source_cells.txt', 'combined.bed', 'merge_command.sh',
'final_edit_info_no_coverage.tsv', 'final_edit_info_no_coverage_sorted.tsv',
'depths_source_cells.txt', 'depth_modified.tsv', 'final_edit_info.tsv', 'final_filtered_edit_info.tsv',
'combined_all_cells.bed', 'depth_commands_all_cells.sh', 'depths_all_cells.txt', 'combined_source_cells.bed'
'combined_all_cells.bed', 'depth_commands_all_cells.sh', 'depth_commands_all_cells.txt', 'depths_all_cells.txt', 'combined_source_cells.bed'
]
for object in to_delete:
object_path = '{}/{}'.format(output_folder, object)
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42 changes: 20 additions & 22 deletions tests/integration_tests.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 2,
"id": "63b5feff-aa8a-417c-8c93-9b9d74e5dee9",
"metadata": {},
"outputs": [],
Expand All @@ -23,7 +23,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 3,
"id": "f6012705-9d34-4997-8681-c7bbcc4f008b",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -2889,7 +2889,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 4,
"id": "f5c3ed3e-13dd-4399-924e-3d1ac17ce387",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -2998,25 +2998,23 @@
"\n",
"\n",
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n",
"Checking results for long_read_sc_test\n",
"\tExpecting: {'contig': '6', 'barcode': 'ENSMUST00000203816-AACGTGTTGGAGAGGG-16-G', 'position': 115807969, 'num_rows': 1, 'count': 1, 'coverage': 1, 'conversion': 'A>C', 'strand_conversion': 'T>G', 'strand': '-', 'feature_name': 'Rpl32'}\n",
"\n",
"\t >>> long_read_sc_test passed! <<<\n",
"\n",
"\tExpecting: {'contig': '6', 'barcode': 'ENSMUST00000081840-AAGTCGTACCAGGCTC-40-C', 'position': 115805653, 'num_rows': 1, 'count': 1, 'coverage': 1, 'conversion': 'G>A', 'strand_conversion': 'C>T', 'strand': '-', 'feature_name': 'Rpl32'}\n",
"\n",
"\t >>> long_read_sc_test passed! <<<\n",
"\n",
"\tExpecting: {'contig': '6', 'barcode': 'ENSMUST00000081840-AACGTGTTGGAGAGGG-40-G', 'position': 115807015, 'num_rows': 1, 'count': 1, 'coverage': 8, 'conversion': 'C>T', 'strand_conversion': 'G>A', 'strand': '-', 'feature_name': 'Rpl32'}\n",
"\n",
"\t >>> long_read_sc_test passed! <<<\n",
"\n",
"Checking that analyzing a single-cell dataset in 'bulk' mode (i.e. not specificying the 'CB' barcode) yields the exact same positions and base changes, but with counts and coverages aggregated rather than at a single-cell resolution\n",
"grouped_sc_rows: 62, bulk_rows: 62\n",
"\n",
"\t >>> single-cell and bulk on same dataset comparison passed! <<<\n",
"\n",
"There were 0 failures\n"
"Checking results for long_read_sc_test\n"
]
},
{
"ename": "FileNotFoundError",
"evalue": "[Errno 2] No such file or directory: 'singlecell_tests/long_read_sc_test/final_filtered_site_info_annotated.tsv'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[4], line 267\u001b[0m\n\u001b[1;32m 265\u001b[0m folder \u001b[38;5;241m=\u001b[39m info\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mfolder\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 266\u001b[0m final_filtered_site_info_annotated \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m/\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m/final_filtered_site_info_annotated.tsv\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mformat(folder, test_name)\n\u001b[0;32m--> 267\u001b[0m final_filtered_site_info_annotated_df \u001b[38;5;241m=\u001b[39m \u001b[43mpd\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mread_csv\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfinal_filtered_site_info_annotated\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msep\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;130;43;01m\\t\u001b[39;49;00m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindex_col\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 269\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtotal_edit_sites\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m info:\n\u001b[1;32m 270\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n",
"File \u001b[0;32m~/miniconda3/envs/marine_environment/lib/python3.8/site-packages/pandas/io/parsers/readers.py:912\u001b[0m, in \u001b[0;36mread_csv\u001b[0;34m(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, date_format, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, encoding_errors, dialect, on_bad_lines, delim_whitespace, low_memory, memory_map, float_precision, storage_options, dtype_backend)\u001b[0m\n\u001b[1;32m 899\u001b[0m kwds_defaults \u001b[38;5;241m=\u001b[39m _refine_defaults_read(\n\u001b[1;32m 900\u001b[0m dialect,\n\u001b[1;32m 901\u001b[0m delimiter,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 908\u001b[0m dtype_backend\u001b[38;5;241m=\u001b[39mdtype_backend,\n\u001b[1;32m 909\u001b[0m )\n\u001b[1;32m 910\u001b[0m kwds\u001b[38;5;241m.\u001b[39mupdate(kwds_defaults)\n\u001b[0;32m--> 912\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_read\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfilepath_or_buffer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mkwds\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda3/envs/marine_environment/lib/python3.8/site-packages/pandas/io/parsers/readers.py:577\u001b[0m, in \u001b[0;36m_read\u001b[0;34m(filepath_or_buffer, kwds)\u001b[0m\n\u001b[1;32m 574\u001b[0m _validate_names(kwds\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mnames\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m))\n\u001b[1;32m 576\u001b[0m \u001b[38;5;66;03m# Create the parser.\u001b[39;00m\n\u001b[0;32m--> 577\u001b[0m parser \u001b[38;5;241m=\u001b[39m \u001b[43mTextFileReader\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfilepath_or_buffer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwds\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 579\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m chunksize \u001b[38;5;129;01mor\u001b[39;00m iterator:\n\u001b[1;32m 580\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m parser\n",
"File \u001b[0;32m~/miniconda3/envs/marine_environment/lib/python3.8/site-packages/pandas/io/parsers/readers.py:1407\u001b[0m, in \u001b[0;36mTextFileReader.__init__\u001b[0;34m(self, f, engine, **kwds)\u001b[0m\n\u001b[1;32m 1404\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39moptions[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mhas_index_names\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m kwds[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mhas_index_names\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[1;32m 1406\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhandles: IOHandles \u001b[38;5;241m|\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[0;32m-> 1407\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_engine \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_make_engine\u001b[49m\u001b[43m(\u001b[49m\u001b[43mf\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mengine\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda3/envs/marine_environment/lib/python3.8/site-packages/pandas/io/parsers/readers.py:1661\u001b[0m, in \u001b[0;36mTextFileReader._make_engine\u001b[0;34m(self, f, engine)\u001b[0m\n\u001b[1;32m 1659\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mb\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m mode:\n\u001b[1;32m 1660\u001b[0m mode \u001b[38;5;241m+\u001b[39m\u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mb\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m-> 1661\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhandles \u001b[38;5;241m=\u001b[39m \u001b[43mget_handle\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1662\u001b[0m \u001b[43m \u001b[49m\u001b[43mf\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1663\u001b[0m \u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1664\u001b[0m \u001b[43m \u001b[49m\u001b[43mencoding\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43moptions\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mencoding\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1665\u001b[0m \u001b[43m \u001b[49m\u001b[43mcompression\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43moptions\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcompression\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1666\u001b[0m \u001b[43m \u001b[49m\u001b[43mmemory_map\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43moptions\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mmemory_map\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1667\u001b[0m \u001b[43m \u001b[49m\u001b[43mis_text\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mis_text\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1668\u001b[0m \u001b[43m \u001b[49m\u001b[43merrors\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43moptions\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mencoding_errors\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstrict\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1669\u001b[0m \u001b[43m \u001b[49m\u001b[43mstorage_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43moptions\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstorage_options\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1670\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1671\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhandles \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 1672\u001b[0m f \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhandles\u001b[38;5;241m.\u001b[39mhandle\n",
"File \u001b[0;32m~/miniconda3/envs/marine_environment/lib/python3.8/site-packages/pandas/io/common.py:859\u001b[0m, in \u001b[0;36mget_handle\u001b[0;34m(path_or_buf, mode, encoding, compression, memory_map, is_text, errors, storage_options)\u001b[0m\n\u001b[1;32m 854\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(handle, \u001b[38;5;28mstr\u001b[39m):\n\u001b[1;32m 855\u001b[0m \u001b[38;5;66;03m# Check whether the filename is to be opened in binary mode.\u001b[39;00m\n\u001b[1;32m 856\u001b[0m \u001b[38;5;66;03m# Binary mode does not support 'encoding' and 'newline'.\u001b[39;00m\n\u001b[1;32m 857\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m ioargs\u001b[38;5;241m.\u001b[39mencoding \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mb\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m ioargs\u001b[38;5;241m.\u001b[39mmode:\n\u001b[1;32m 858\u001b[0m \u001b[38;5;66;03m# Encoding\u001b[39;00m\n\u001b[0;32m--> 859\u001b[0m handle \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mopen\u001b[39;49m\u001b[43m(\u001b[49m\n\u001b[1;32m 860\u001b[0m \u001b[43m \u001b[49m\u001b[43mhandle\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 861\u001b[0m \u001b[43m \u001b[49m\u001b[43mioargs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 862\u001b[0m \u001b[43m \u001b[49m\u001b[43mencoding\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mioargs\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mencoding\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 863\u001b[0m \u001b[43m \u001b[49m\u001b[43merrors\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43merrors\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 864\u001b[0m \u001b[43m \u001b[49m\u001b[43mnewline\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 865\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 866\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 867\u001b[0m \u001b[38;5;66;03m# Binary mode\u001b[39;00m\n\u001b[1;32m 868\u001b[0m handle \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mopen\u001b[39m(handle, ioargs\u001b[38;5;241m.\u001b[39mmode)\n",
"\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: 'singlecell_tests/long_read_sc_test/final_filtered_site_info_annotated.tsv'"
]
}
],
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2 changes: 1 addition & 1 deletion tests/singlecell_tests/scripts/long_read_sc_test.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ $MARINE/tests/singlecell_tests/long_read_sc_test \
0 \
--cores \
16 \
--barcode_whitelist_file $MARINE/examples/data/sc_lr_barcodes.tsv.gz \
--barcode_whitelist_file $MARINE/examples/data/sc_lr_barcodes.tsv \
--strandedness 2 \
--barcode_tag "IB" \
--contigs "6" \
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