py-cmdtabs 1.2.1__tar.gz → 1.2.2__tar.gz

{py_cmdtabs-1.2.1 → py_cmdtabs-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: py_cmdtabs
-Version: 1.2.1
+Version: 1.2.2
 Summary: Set of tools to facilitate parsing of tabulated files
 Home-page: https://github.com/seoanezonjic/py_cmdtabs
 Author: seoanezonjic
@@ -15,6 +15,7 @@ License-File: LICENSE.txt
 Requires-Dist: importlib-metadata; python_version < "3.8"
 Requires-Dist: openpyxl
 Requires-Dist: numpy
+Requires-Dist: pandas
 Provides-Extra: testing
 Requires-Dist: setuptools; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
@@ -71,3 +72,6 @@ py_cmdtabs includes tools that make it easier for its user to manipulate tabulat
 * Replace information: The standard_name_replacer.py script replaces values in a table based on a contributed value code.
 * Filter columns: The column_filter.py script filters columns from a tabulated file whose elements match a specified pattern.
 * Transform Excel format into tabular: the excel_to_tabular.py script transforms files with an .xlsx extension into tabular files and makes their handling easier.
+
+
+See https://github.com/seoanezonjic/py_cmdtabs

{py_cmdtabs-1.2.1 → py_cmdtabs-1.2.2}/README.rst

@@ -47,4 +47,7 @@ py_cmdtabs includes tools that make it easier for its user to manipulate tabulat
 * Obtain common information: the table_linker.py script allows you to save in the same output file the information extracted from a tabulated file, based on the identifiers of a second file.
 * Replace information: The standard_name_replacer.py script replaces values in a table based on a contributed value code.
 * Filter columns: The column_filter.py script filters columns from a tabulated file whose elements match a specified pattern.
-* Transform Excel format into tabular: the excel_to_tabular.py script transforms files with an .xlsx extension into tabular files and makes their handling easier.
+* Transform Excel format into tabular: the excel_to_tabular.py script transforms files with an .xlsx extension into tabular files and makes their handling easier.
+
+
+See https://github.com/seoanezonjic/py_cmdtabs

{py_cmdtabs-1.2.1 → py_cmdtabs-1.2.2}/setup.cfg

@@ -25,6 +25,7 @@ install_requires =
 	importlib-metadata; python_version<"3.8"
 	openpyxl
 	numpy
+	pandas
 
 [options.packages.find]
 where = src

{py_cmdtabs-1.2.1 → py_cmdtabs-1.2.2}/src/py_cmdtabs/cli_manager.py

@@ -339,6 +339,8 @@ def cmdtabs(args=None):
                         help="Sheet number to work with. Default 1")
     parser.add_argument("--file_type", dest="file_type", default='text',
                         help="Default text. Other options;excel")
+    parser.add_argument("--out_file_type", dest="out_file_type", default='text',
+                        help="Default text. Other options;excel")    
     parser.add_argument("--from", dest="frm", default=0, type=based_0,
                         help="Column in index file to take reference value. Default 1. Numeration is 1 based")
     parser.add_argument("--to", dest="to", default=1, type=based_0,
@@ -347,6 +349,8 @@ def cmdtabs(args=None):
                         help="Write table in latex code")
     parser.add_argument("--sample_attributes", dest="sample_attributes", default=[], type=list_str,
                         help="Define sample atributtes (comma separated list) to colapse a long table in a wide metric table")
+    parser.add_argument("--long_to_wide", dest="long_to_wide", default=False, action='store_true',
+                        help="To transform a long table in a wide table. The id column will be the column/s of sample attributes if specified, or the first column if not. The key columns will be the columns between the id column and the value column, that will be the last column of the table")
     parser.add_argument("--corrupted", dest="corrupted",
                         help="File where corrupted metrics are stored")
     parser.add_argument("--offset", dest="offset", default=[], type=list_str,
@@ -375,6 +379,8 @@ def cmdtabs(args=None):
                         help="Print row extraction statistics")                        
     parser.add_argument("--uniq", dest="uniq", default=False, action='store_true',
                         help="Make rows unique")
+    parser.add_argument("--sort_rows_by", dest="sort_rows_by", default=None,
+                        help="Sort rows of the table ([a]scending or [d]escending or custom) by given columns, like: 0,a;1,d;2,d score,a;name,d pats,pat1|pat2|pat3 pats,path_sort_file")
     opts = parser.parse_args(args)
     main_cmdtabs(opts)
 

{py_cmdtabs-1.2.1 → py_cmdtabs-1.2.2}/src/py_cmdtabs/cmdtabs.py

@@ -194,7 +194,7 @@ class CmdTabs:
 		aggregated_values = []
 		for aggregator in aggregation_modes.split(','):
 			aggregated_column_copy = aggregated_column.copy()
-			if aggregator != "concatenate": aggregated_column_copy = [float(item) for item in aggregated_column_copy]
+			if aggregator not in ["concatenate", "count"]: aggregated_column_copy = [float(item) for item in aggregated_column_copy]
 			agg_value = str(make_aggregation[aggregator](aggregated_column_copy))
 			aggregated_values.append(agg_value)
 		return "|".join(aggregated_values)
@@ -241,6 +241,16 @@ class CmdTabs:
 		corrupted_records.insert(0, allTags) # Add header
 		return table_output, corrupted_records
 	
+	def long_to_wide(table, id_col, key_col, value_col):
+		import pandas as pd
+		col_names = [ f"col{idx}" for idx in range(len(table[0]))]
+		df = pd.DataFrame(table, columns=col_names)
+		df_wide = df.pivot_table(index=df.columns[id_col].tolist(),
+						    columns=df.columns[key_col].tolist(), 
+							values=df.columns[value_col].tolist(), aggfunc='first').reset_index()
+		metric_names = [metric_name for metric_name in df_wide.columns.get_level_values(1) if metric_name != '']
+		return df_wide.values.tolist(), metric_names
+	
 	def name_replaces(tabular_input, sep, cols_to_replace, indexed_file_index, remove_uns=False):
 		translated_fields = []
 		untranslated_fields = []
@@ -451,7 +461,7 @@ class CmdTabs:
 
 	def get_table_from_excel(file, sheet_number):
 		import openpyxl
-		x = openpyxl.load_workbook(file)
+		x = openpyxl.load_workbook(file, data_only=True)
 		sheets = x.sheetnames # list excel sheets by name
 		ws = x[sheets[sheet_number]] #select sheet by index (so, we select by sheet order)
 		sheet = []
@@ -468,6 +478,15 @@ class CmdTabs:
 			
 		return sheet
 
+	def table_to_excel(table, output_file, sheet_name='Sheet1'):
+		import openpyxl
+		wb = openpyxl.Workbook()
+		ws = wb.active
+		ws.title = sheet_name
+		for row in table:
+			ws.append(row)
+		wb.save(output_file)
+
 	def get_groups(a_records, b_records): # inputs are list of string but should be nested lists. This is due to python don't allow to hash list in dicts.
 		a_rec = set(a_records)				# For this reason, the last lines convert in lists the strings of the original list to keep the format
 		b_rec = set(b_records)				# TODO: See to tranfor to tuples instead to string
@@ -524,16 +543,57 @@ class CmdTabs:
 		else:
 			final_table = latex_table
 		return final_table
-
-	def write_output_data(output_data, output_path=None, sep="\t"):
+	
+	def get_custom_sorts(cols, modes):
+		direct_transform = {}
+		inverse_transform = {}
+		for idx, mode in enumerate(modes):
+			if mode not in ["a", "d"]:
+				if os.path.exists(mode):
+					content = open(mode).read().split("\n")
+					direct_transform[cols[idx]] = {col: pos for pos,col in enumerate(content)}
+					inverse_transform[cols[idx]] = {pos: col for pos,col in enumerate(content)}
+				else:
+					direct_transform[cols[idx]] = {col: pos for pos,col in  enumerate(mode.split("|"))}
+					inverse_transform[cols[idx]] = {pos: col for pos,col in  enumerate(mode.split("|"))}
+		return direct_transform, inverse_transform
+
+
+	def sort_table(table, sort_rows_by, has_header):
+		import pandas
+		header = table[0] if has_header else []
+		sorted_table = [header] if has_header else [] 
+		start_idx = 1 if has_header else 0
+
+		cols_to_sort = sort_rows_by.split(';')
+		cols, modes = list(zip(*[col.split(',') for col in cols_to_sort]))
+		cols = [int(col_idx) if col_idx.isdigit() else header.index(col_idx) for col_idx in cols]
+		cols = [f"col_{col_idx}" for col_idx in cols]
+		direct_transform, inverse_transform = CmdTabs.get_custom_sorts(cols, modes)
+
+		df = pandas.DataFrame(table[start_idx:], columns=[f"col_{idx}" for idx in range(len(table[0]))])
+		for col, transform_dict in direct_transform.items(): df[col] = df[col].apply(lambda x: transform_dict[x])
+		df = df.apply(pandas.to_numeric, errors='ignore')
+		df.sort_values(by=cols, ascending=[False if mode == "d" else True for mode in modes], inplace=True) #if mode=="a" or mode=[custom_sort] then ascending is True
+		for col, inverse_transform_dict in inverse_transform.items(): df[col] = df[col].apply(lambda x: inverse_transform_dict[x])
+		df = df.astype(str)
+		sorted_table += df.values.tolist()
+		return sorted_table
+
+
+	def write_output_data(output_data, output_path=None, sep="\t", sort_rows_by=None, header=False, out_type='text'):
 		open_file = gzip.open if CmdTabs.compressed_output else open
+		if sort_rows_by is not None:
+			output_data = CmdTabs.sort_table(output_data, sort_rows_by, header)
 		if CmdTabs.transposed:
 			output_data = CmdTabs.transpose(output_data)
-			
 		if output_path != None:
-			with open_file(output_path, 'wt') as out_file:
-				for line in output_data:
-					out_file.write(sep.join([str(l) for l in line]) + "\n")
+			if out_type == 'excel':
+				CmdTabs.table_to_excel(output_data, output_path)
+			elif out_type == 'text':
+				with open_file(output_path, 'wt') as out_file:
+					for line in output_data:
+						out_file.write(sep.join([str(l) for l in line]) + "\n")
 		else:
 			if CmdTabs.compressed_output:
 				columns_joined = []

{py_cmdtabs-1.2.1 → py_cmdtabs-1.2.2}/src/py_cmdtabs/main_modules.py

@@ -254,12 +254,22 @@ def main_cmdtabs(opts):
   # STATS
   if opts.count_cols != None: table = CmdTabs.records_count(table, opts.count_cols) # [records_count]
   # TRANSFORMATIONS
-  if len(opts.sample_attributes) > 0: #[create_metric_table]
+  if len(opts.sample_attributes) > 0 and not opts.long_to_wide: #[create_metric_table]
     samples_tag = opts.sample_attributes.pop(0)
     metric_names, indexed_metrics = CmdTabs.index_metrics(table, opts.sample_attributes)
     table, corrupt_recs = CmdTabs.create_table(indexed_metrics, samples_tag, opts.sample_attributes, metric_names)
     if opts.corrupted != None and len(corrupt_recs) > 0: CmdTabs.write_output_data(corrupt_recs, opts.corrupted)
 
+  if opts.long_to_wide == True: 
+    id_col = list(range(len(opts.sample_attributes))) if len(opts.sample_attributes) > 0 else [0] # id col será el rango de las columnas de atributos si se han especificado, sino la primera columna
+    value_col = [len(table[0]) - 1]
+    key_cols = [len(table[0]) - 2]
+    table, metric_names = CmdTabs.long_to_wide(table, id_col, key_cols, value_col) # [long_to_wide]
+    header = opts.sample_attributes + metric_names
+    table = [header] + table
+    CmdTabs.write_output_data(table, opts.output_file, sep=output_sep)
+
+
   if opts.aggregate: table = CmdTabs.aggregate_column(table, opts.agg_col_index, opts.col_aggregate, opts.agg_sep, opts.agg_mode) # [aggregate_table]
 
   if opts.desaggregate: table = CmdTabs.desaggregate_column(table, opts.desagg_col, opts.desagg_sep) # [desaggregate_table]
@@ -291,7 +301,7 @@ def main_cmdtabs(opts):
     elif opts.sp_file_number > 0: # [subset] split by file number
       CmdTabs.split_by_nFiles(table, opts.sp_file_number, opts.output_file, file_name, header = header)
   else:
-    CmdTabs.write_output_data(table, opts.output_file, sep=output_sep)
+    CmdTabs.write_output_data(table, opts.output_file, sep=output_sep, sort_rows_by=opts.sort_rows_by, header=opts.header, out_type=opts.out_file_type)
   
 
 ########################################################

{py_cmdtabs-1.2.1 → py_cmdtabs-1.2.2}/src/py_cmdtabs.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: py_cmdtabs
-Version: 1.2.1
+Version: 1.2.2
 Summary: Set of tools to facilitate parsing of tabulated files
 Home-page: https://github.com/seoanezonjic/py_cmdtabs
 Author: seoanezonjic
@@ -15,6 +15,7 @@ License-File: LICENSE.txt
 Requires-Dist: importlib-metadata; python_version < "3.8"
 Requires-Dist: openpyxl
 Requires-Dist: numpy
+Requires-Dist: pandas
 Provides-Extra: testing
 Requires-Dist: setuptools; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
@@ -71,3 +72,6 @@ py_cmdtabs includes tools that make it easier for its user to manipulate tabulat
 * Replace information: The standard_name_replacer.py script replaces values in a table based on a contributed value code.
 * Filter columns: The column_filter.py script filters columns from a tabulated file whose elements match a specified pattern.
 * Transform Excel format into tabular: the excel_to_tabular.py script transforms files with an .xlsx extension into tabular files and makes their handling easier.
+
+
+See https://github.com/seoanezonjic/py_cmdtabs

{py_cmdtabs-1.2.1 → py_cmdtabs-1.2.2}/src/py_cmdtabs.egg-info/SOURCES.txt

@@ -30,6 +30,8 @@ src/py_cmdtabs.egg-info/dependency_links.txt
 src/py_cmdtabs.egg-info/entry_points.txt
 src/py_cmdtabs.egg-info/not-zip-safe
 src/py_cmdtabs.egg-info/requires.txt
+src/py_cmdtabs.egg-info/scm_file_list.json
+src/py_cmdtabs.egg-info/scm_version.json
 src/py_cmdtabs.egg-info/top_level.txt
 tests/__init__.py
 tests/conftest.py
@@ -45,6 +47,7 @@ tests/cli_example_report/launch.sh
 tests/cli_example_report/styles.css
 tests/cli_example_report/template.txt
 tests/cli_example_report/outputs/blackfiltered_long_table
+tests/cli_example_report/outputs/corrupted_table
 tests/cli_example_report/outputs/filtered_long_table
 tests/cli_example_report/outputs/ref_filtered_disease_cluster_ref_rnd
 tests/cli_example_report/outputs/wide_table
@@ -74,6 +77,7 @@ tests/cli_example_report/subtemplates/intersect_columns
 tests/cli_example_report/subtemplates/merge_tabular
 tests/cli_example_report/subtemplates/records_count
 tests/cli_example_report/subtemplates/show_n_exec
+tests/cli_example_report/subtemplates/sort_rows_by
 tests/cli_example_report/subtemplates/standard_name_replacer
 tests/cli_example_report/subtemplates/subset_table
 tests/cli_example_report/subtemplates/table_linker
@@ -97,7 +101,9 @@ tests/cli_example_report/tables/metrics_table
 tests/cli_example_report/tables/mondo_to_orpha
 tests/cli_example_report/tables/nets_to_filter
 tests/cli_example_report/tables/organization
+tests/cli_example_report/tables/pats_order
 tests/cli_example_report/tables/simple_table
+tests/cli_example_report/tables/table_to_sort_2cols_header
 tests/cli_example_report/tables/tracker
 tests/data_tests/agg_2index_2values.txt
 tests/data_tests/agg_data_3_columns.txt
@@ -121,7 +127,11 @@ tests/data_tests/ids2count_short
 tests/data_tests/metric_table
 tests/data_tests/mondo_genes
 tests/data_tests/mondo_genes.gz
+tests/data_tests/pats_order
 tests/data_tests/simple_table
+tests/data_tests/table_to_sort_2cols_header
+tests/data_tests/table_to_sort_header
+tests/data_tests/table_to_sort_noheader
 tests/data_tests/tracker
 tests/data_tests/ref_output_scripts/TEST_file
 tests/data_tests/ref_output_scripts/TEST_file_transposed
@@ -161,6 +171,13 @@ tests/data_tests/ref_output_scripts/mondo_genes_transposed.gz
 tests/data_tests/ref_output_scripts/replaced_name
 tests/data_tests/ref_output_scripts/replaced_name_untranslated
 tests/data_tests/ref_output_scripts/subset_table
+tests/data_tests/ref_output_scripts/table_to_sort_2cols_header
+tests/data_tests/ref_output_scripts/table_to_sort_header_by_cat
+tests/data_tests/ref_output_scripts/table_to_sort_header_by_pat
+tests/data_tests/ref_output_scripts/table_to_sort_header_by_score
+tests/data_tests/ref_output_scripts/table_to_sort_noheader_by_cat
+tests/data_tests/ref_output_scripts/table_to_sort_noheader_by_pat
+tests/data_tests/ref_output_scripts/table_to_sort_noheader_by_score
 tests/data_tests/ref_output_scripts/tag_table
 tests/data_tests/ref_output_scripts/tag_table_header
 tests/data_tests/ref_output_scripts/transposed_cluster_genes_dis_AGG

{py_cmdtabs-1.2.1 → py_cmdtabs-1.2.2}/src/py_cmdtabs.egg-info/requires.txt

@@ -1,5 +1,6 @@
 openpyxl
 numpy
+pandas
 
 [:python_version < "3.8"]
 importlib-metadata

py_cmdtabs-1.2.2/src/py_cmdtabs.egg-info/scm_file_list.json

@@ -0,0 +1,199 @@
+{
+  "files": [
+    ".readthedocs.yml",
+    "AUTHORS.rst",
+    "CHANGELOG.rst",
+    "CONTRIBUTING.rst",
+    "LICENSE.txt",
+    "README.rst",
+    "docs/Makefile",
+    "docs/_static/.gitignore",
+    "docs/authors.rst",
+    "docs/changelog.rst",
+    "docs/conf.py",
+    "docs/contributing.rst",
+    "docs/index.rst",
+    "docs/license.rst",
+    "docs/readme.rst",
+    "docs/requirements.txt",
+    "make_package.sh",
+    "pyproject.toml",
+    "requirements.txt",
+    "setup.cfg",
+    "setup.py",
+    "src/py_cmdtabs/__init__.py",
+    "src/py_cmdtabs/cli_manager.py",
+    "src/py_cmdtabs/cmdtabs.py",
+    "src/py_cmdtabs/main_modules.py",
+    "tests/__init__.py",
+    "tests/cli_example_report/Report.html",
+    "tests/cli_example_report/example",
+    "tests/cli_example_report/launch.sh",
+    "tests/cli_example_report/outputs/blackfiltered_long_table",
+    "tests/cli_example_report/outputs/corrupted_table",
+    "tests/cli_example_report/outputs/filtered_long_table",
+    "tests/cli_example_report/outputs/ref_filtered_disease_cluster_ref_rnd",
+    "tests/cli_example_report/outputs/subset_table/disease_cluster_ref_rnd_chunk0",
+    "tests/cli_example_report/outputs/subset_table/disease_cluster_ref_rnd_chunk1",
+    "tests/cli_example_report/outputs/subset_table/disease_cluster_ref_rnd_chunk2",
+    "tests/cli_example_report/outputs/subset_table2/disease_cluster_ref_rnd_chunk0",
+    "tests/cli_example_report/outputs/subset_table2/disease_cluster_ref_rnd_chunk1",
+    "tests/cli_example_report/outputs/wide_table",
+    "tests/cli_example_report/special_files/hoja1.png",
+    "tests/cli_example_report/special_files/hoja2.png",
+    "tests/cli_example_report/special_files/scRNAseq.htm",
+    "tests/cli_example_report/special_files/scRNAseq.xlsx",
+    "tests/cli_example_report/special_files/scRNAseq_archivos/filelist.xml",
+    "tests/cli_example_report/special_files/scRNAseq_archivos/sheet001.htm",
+    "tests/cli_example_report/special_files/scRNAseq_archivos/sheet002.htm",
+    "tests/cli_example_report/special_files/scRNAseq_archivos/stylesheet.css",
+    "tests/cli_example_report/special_files/scRNAseq_archivos/tabstrip.htm",
+    "tests/cli_example_report/special_files/~$scRNAseq.xlsx",
+    "tests/cli_example_report/styles.css",
+    "tests/cli_example_report/subtemplates/aggregate_column_data",
+    "tests/cli_example_report/subtemplates/column_filter",
+    "tests/cli_example_report/subtemplates/create_metric_table",
+    "tests/cli_example_report/subtemplates/desaggregate_column_data",
+    "tests/cli_example_report/subtemplates/excel_to_tabular",
+    "tests/cli_example_report/subtemplates/filter_by_list",
+    "tests/cli_example_report/subtemplates/get_columns",
+    "tests/cli_example_report/subtemplates/intersect_columns",
+    "tests/cli_example_report/subtemplates/merge_tabular",
+    "tests/cli_example_report/subtemplates/records_count",
+    "tests/cli_example_report/subtemplates/show_n_exec",
+    "tests/cli_example_report/subtemplates/sort_rows_by",
+    "tests/cli_example_report/subtemplates/standard_name_replacer",
+    "tests/cli_example_report/subtemplates/subset_table",
+    "tests/cli_example_report/subtemplates/table_linker",
+    "tests/cli_example_report/subtemplates/tag_table",
+    "tests/cli_example_report/subtemplates/transform_to_latex",
+    "tests/cli_example_report/subtemplates/transpose_table",
+    "tests/cli_example_report/tables/cluster_genes_dis_agg",
+    "tests/cli_example_report/tables/cluster_genes_dis_agg2",
+    "tests/cli_example_report/tables/cluster_genes_dis_desagg",
+    "tests/cli_example_report/tables/cluster_genes_dis_desagg_3cols",
+    "tests/cli_example_report/tables/cluster_genes_dis_desagg_4cols",
+    "tests/cli_example_report/tables/cluster_stats",
+    "tests/cli_example_report/tables/clusts_to_filter",
+    "tests/cli_example_report/tables/disease_cluster",
+    "tests/cli_example_report/tables/disease_cluster_ref_rnd",
+    "tests/cli_example_report/tables/disease_cluster_uniq",
+    "tests/cli_example_report/tables/disease_gene",
+    "tests/cli_example_report/tables/long_disease_cluster",
+    "tests/cli_example_report/tables/long_table",
+    "tests/cli_example_report/tables/metrics_table",
+    "tests/cli_example_report/tables/mondo_to_orpha",
+    "tests/cli_example_report/tables/nets_to_filter",
+    "tests/cli_example_report/tables/organization",
+    "tests/cli_example_report/tables/pats_order",
+    "tests/cli_example_report/tables/simple_table",
+    "tests/cli_example_report/tables/table_to_sort_2cols_header",
+    "tests/cli_example_report/tables/tracker",
+    "tests/cli_example_report/template.txt",
+    "tests/conftest.py",
+    "tests/data_tests/agg_2index_2values.txt",
+    "tests/data_tests/agg_data_3_columns.txt",
+    "tests/data_tests/all_metrics",
+    "tests/data_tests/blacklist",
+    "tests/data_tests/blacklist_partial",
+    "tests/data_tests/cluster_genes.xlsx",
+    "tests/data_tests/cluster_genes_dis_agg",
+    "tests/data_tests/cluster_genes_dis_desagg",
+    "tests/data_tests/cluster_stats",
+    "tests/data_tests/cluster_stats_header",
+    "tests/data_tests/dis_gene_attrs",
+    "tests/data_tests/disease_cluster",
+    "tests/data_tests/disease_cluster_uniq",
+    "tests/data_tests/disease_gene",
+    "tests/data_tests/filterlist",
+    "tests/data_tests/filterlist_partial",
+    "tests/data_tests/hp_long_list.txt",
+    "tests/data_tests/ids2count",
+    "tests/data_tests/ids2count_short",
+    "tests/data_tests/metric_table",
+    "tests/data_tests/mondo_genes",
+    "tests/data_tests/mondo_genes.gz",
+    "tests/data_tests/pats_order",
+    "tests/data_tests/ref_output_scripts/TEST_file",
+    "tests/data_tests/ref_output_scripts/TEST_file_transposed",
+    "tests/data_tests/ref_output_scripts/agg_2index_2values.txt",
+    "tests/data_tests/ref_output_scripts/agg_2index_2values_several_aggregators.txt",
+    "tests/data_tests/ref_output_scripts/agg_data_3_columns_result.txt",
+    "tests/data_tests/ref_output_scripts/cluster_genes_dis_AGG",
+    "tests/data_tests/ref_output_scripts/cluster_genes_dis_AGG_stdin",
+    "tests/data_tests/ref_output_scripts/cluster_genes_dis_DESAGG",
+    "tests/data_tests/ref_output_scripts/cluster_genes_dis_DESAGG_stdin",
+    "tests/data_tests/ref_output_scripts/cluster_genes_from_excel.txt",
+    "tests/data_tests/ref_output_scripts/column_matching_hard",
+    "tests/data_tests/ref_output_scripts/column_matching_hard_various_keys",
+    "tests/data_tests/ref_output_scripts/column_matching_hard_various_keys_and_every_columns",
+    "tests/data_tests/ref_output_scripts/column_matching_hard_various_keys_and_every_columns_header",
+    "tests/data_tests/ref_output_scripts/column_matching_hard_various_keys_and_some_columns",
+    "tests/data_tests/ref_output_scripts/column_matching_soft",
+    "tests/data_tests/ref_output_scripts/column_matching_soft_1_column",
+    "tests/data_tests/ref_output_scripts/column_matching_soft_1_column_reverse",
+    "tests/data_tests/ref_output_scripts/column_matching_soft_1_column_uniq",
+    "tests/data_tests/ref_output_scripts/column_matching_soft_and_every_columns",
+    "tests/data_tests/ref_output_scripts/column_matching_soft_and_some_columns",
+    "tests/data_tests/ref_output_scripts/ids2count",
+    "tests/data_tests/ref_output_scripts/intersect_columns_count",
+    "tests/data_tests/ref_output_scripts/intersect_columns_default",
+    "tests/data_tests/ref_output_scripts/intersect_columns_default_stdin_a",
+    "tests/data_tests/ref_output_scripts/intersect_columns_default_stdin_b",
+    "tests/data_tests/ref_output_scripts/intersect_columns_full",
+    "tests/data_tests/ref_output_scripts/linked_table",
+    "tests/data_tests/ref_output_scripts/linked_table3",
+    "tests/data_tests/ref_output_scripts/linked_table_2",
+    "tests/data_tests/ref_output_scripts/linked_table_matches",
+    "tests/data_tests/ref_output_scripts/merge_disease_cluster_gene",
+    "tests/data_tests/ref_output_scripts/metric_table",
+    "tests/data_tests/ref_output_scripts/mondo_genes_transposed",
+    "tests/data_tests/ref_output_scripts/mondo_genes_transposed.gz",
+    "tests/data_tests/ref_output_scripts/replaced_name",
+    "tests/data_tests/ref_output_scripts/replaced_name_untranslated",
+    "tests/data_tests/ref_output_scripts/subset_table",
+    "tests/data_tests/ref_output_scripts/subset_table_fold/mondo_genes_chunk0",
+    "tests/data_tests/ref_output_scripts/subset_table_fold/mondo_genes_chunk1",
+    "tests/data_tests/ref_output_scripts/subset_table_fold/mondo_genes_chunk2",
+    "tests/data_tests/ref_output_scripts/table_to_sort_2cols_header",
+    "tests/data_tests/ref_output_scripts/table_to_sort_header_by_cat",
+    "tests/data_tests/ref_output_scripts/table_to_sort_header_by_pat",
+    "tests/data_tests/ref_output_scripts/table_to_sort_header_by_score",
+    "tests/data_tests/ref_output_scripts/table_to_sort_noheader_by_cat",
+    "tests/data_tests/ref_output_scripts/table_to_sort_noheader_by_pat",
+    "tests/data_tests/ref_output_scripts/table_to_sort_noheader_by_score",
+    "tests/data_tests/ref_output_scripts/tag_table",
+    "tests/data_tests/ref_output_scripts/tag_table_header",
+    "tests/data_tests/ref_output_scripts/transposed_cluster_genes_dis_AGG",
+    "tests/data_tests/ref_output_scripts/transposed_cluster_genes_dis_DESAGG",
+    "tests/data_tests/ref_output_scripts/transposed_cluster_genes_from_excel.txt",
+    "tests/data_tests/ref_output_scripts/transposed_column_matching_hard",
+    "tests/data_tests/ref_output_scripts/transposed_intersect_columns_default",
+    "tests/data_tests/ref_output_scripts/transposed_linked_table",
+    "tests/data_tests/ref_output_scripts/transposed_merge_disease_cluster_gene",
+    "tests/data_tests/ref_output_scripts/transposed_metric_table",
+    "tests/data_tests/ref_output_scripts/transposed_replaced_name",
+    "tests/data_tests/ref_output_scripts/transposed_tag_table",
+    "tests/data_tests/simple_table",
+    "tests/data_tests/table_to_sort_2cols_header",
+    "tests/data_tests/table_to_sort_header",
+    "tests/data_tests/table_to_sort_noheader",
+    "tests/data_tests/tracker",
+    "tests/data_tests/transposed/all_metrics",
+    "tests/data_tests/transposed/cluster_genes.xlsx",
+    "tests/data_tests/transposed/cluster_genes_dis_agg",
+    "tests/data_tests/transposed/cluster_genes_dis_desagg",
+    "tests/data_tests/transposed/cluster_stats",
+    "tests/data_tests/transposed/disease_cluster",
+    "tests/data_tests/transposed/disease_cluster_uniq",
+    "tests/data_tests/transposed/disease_gene",
+    "tests/data_tests/transposed/tranpose_data.py",
+    "tests/test_cli_manager.py",
+    "tests/test_cmdtabs_lib.py",
+    "tests/test_compressed_pipes.sh",
+    "tests/test_expanded_methods.py",
+    "tests/test_input_parsing.py",
+    "tests/test_io.py",
+    "tox.ini"
+  ]
+}

py_cmdtabs-1.2.2/src/py_cmdtabs.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "1.2.2",
+  "distance": 0,
+  "node": "g55eecaff40c04731bc2ee9c5039e304cb5d1c732",
+  "dirty": false,
+  "branch": "master",
+  "node_date": "2026-10-07"
+}