Revert "Merge branch '10-count.features' into 'develop'"

This reverts commit 8f536aab

workflow/scripts/check_design.test.py

-#!/usr/bin/env python3
-
-'''Check if design file is correctly formatted and matches files list.'''
-
-import argparse
-import logging
-import pandas as pd
-
-EPILOG = '''
-For more details:
-        %(prog)s --help
-'''
-
-# SETTINGS
-
-logger = logging.getLogger(__name__)
-logger.addHandler(logging.NullHandler())
-logger.propagate = False
-logger.setLevel(logging.INFO)
-
-
-def get_args():
-    '''Define arguments.'''
-
-    parser = argparse.ArgumentParser(
-        description=__doc__, epilog=EPILOG,
-        formatter_class=argparse.RawDescriptionHelpFormatter)
-
-    parser.add_argument('-d', '--design',
-                        help="The design file to run QC (tsv format).",
-                        required=True )
-
-    parser.add_argument('-f', '--fastq',
-                        help="File with list of fastq files (tsv format).",
-                        required=True )
-
-    parser.add_argument('-t', '--feature',
-                        help="Additional features to count?",
-                        required=True )
-
-    args = parser.parse_args()
-    return args
-
-
-def check_design_headers_n(design):
-    '''Check if design file conforms to sequencing type.'''
-
-    # Default headers
-    design_template = [
-        'Sample',
-	    'fastq_R1',
-	    'fastq_R2']
-
-    design_headers = list(design.columns.values)
-
-    # Check if headers
-    logger.info("Running header check.")
-
-    missing_headers = set(design_template) - set(design_headers)
-
-    if len(missing_headers) > 0:
-        logger.error('Missing column headers: %s', list(missing_headers))
-        raise Exception("Missing column headers: %s" % list(missing_headers))
-    
-    return design
-
-def check_design_headers_y(design):
-    '''Check if design file conforms to sequencing type.'''
-
-    # Default headers
-    design_template = [
-        'Sample',
-	    'fastq_R1',
-	    'fastq_R2',
-	    'library_type']
-
-    design_headers = list(design.columns.values)
-
-    # Check if headers
-    logger.info("Running header check.")
-
-    missing_headers = set(design_template) - set(design_headers)
-
-    if len(missing_headers) > 0:
-        logger.error('Missing column headers: %s', list(missing_headers))
-        raise Exception("Missing column headers: %s" % list(missing_headers))
-    
-    return design
-
-def check_files(design, fastq):
-    '''Check if design file has the files found.'''
-
-    logger.info("Running file check.")
-
-    files = list(design['fastq_R1']) + list(design['fastq_R2'])
-
-    files_found = fastq['name']
-
-    missing_files = set(files) - set(files_found)
-
-    if len(missing_files) > 0:
-        logger.error('Missing files from design file: %s', list(missing_files))
-        raise Exception("Missing files from design file: %s" %
-            list(missing_files))
-    else:
-        file_dict = fastq.set_index('name').T.to_dict()
-    
-    design['fastq_R1'] = design['fastq_R1'].apply(lambda x: file_dict[x]['path'])
-    design['fastq_R2'] = design['fastq_R2'].apply(lambda x: file_dict[x]['path'])
-
-    return design
-
-
-def main():
-    args = get_args()
-    design = args.design
-
-    # Create a file handler
-    handler = logging.FileHandler('design.log')
-    logger.addHandler(handler)
-
-    # Read files as dataframes
-    design_df = pd.read_csv(args.design, sep=',')
-    fastq_df = pd.read_csv(args.fastq, sep='\t', names=['name', 'path'])
-
-    # Check design file
-    if args.feature == 'no':
-    	new_design_df = check_design_headers_n(design_df)
-    else:
-    	new_design_df = check_design_headers_y(design_df)
-	#new_design_df[['sample']].to_csv('library.checked.csv', header=True, sep=',', index=False)
-
-    check_files(design_df, fastq_df)
-    new_design_df.drop('library_type', 1).to_csv('design.checked.csv', header=True, sep=',', index=False)
-
-
-
-if __name__ == '__main__':
-    main()