def processGeneCalls(first_file, second_file, input_directory, output_file,
output_directory, lines_skip):
from xlsxwriter.workbook import Workbook
import methodslist as ml
import os
# Set directory
old_dir = os.getcwd()
os.chdir(output_directory)
print('\nStarting at %r' % input_directory)
# Import text to tables
table1 = ml.importTable(first_file, input_directory, lines_skip)
table2 = ml.importTable(second_file, input_directory, lines_skip)
# Find mutated rows with that are matched and unmatched
total_comparison = ml.compareTables(table1, table2)
matched1 = total_comparison[0]
matched2 = total_comparison[1]
unmatched1 = total_comparison[2]
unmatched2 = total_comparison[3]
'''
#Select only certain categories
keeps1 = ml.saveByCategory(keeps1)
keeps2 = ml.saveByCategory(keeps2)
matched_reject2_unmatched1 = ml.saveByCategory(matched_reject2_unmatched1)
matched_reject1_unmatched2 = ml.saveByCategory(matched_reject1_unmatched2)
'''
# Calculate condordance
condordance_table = ml.calcCondordance(unmatched1, unmatched2, matched1)
# Write tables to text files
book = Workbook(output_file)
ml.outputTable(book, condordance_table, 'Concordance Summary',
output_directory)
ml.outputTable(book, table1, 'NC TC Input', output_directory)
ml.outputTable(book, table2, 'NF TF Input', output_directory)
ml.outputTable(book, matched1, 'NC TC Matches', output_directory)
ml.outputTable(book, matched2, 'NF TF Matches', output_directory)
book.close()
os.chdir(old_dir)
print('Finished')
def processMutations(first_file, second_file , input_directory, output_file, output_directory, lines_skip):
from xlsxwriter.workbook import Workbook
import methodslist as ml
import os
# Set directory
old_dir = os.getcwd()
os.chdir(output_directory)
print('\nStarting at %r' % input_directory)
# Import text to tables
table1 = ml.importTable(first_file, input_directory, lines_skip)
table2 = ml.importTable(second_file, input_directory, lines_skip)
# Save rows with detected mutations
keeps1 = ml.saveByValue(table1, 'judgement', 'KEEP')
keeps2 = ml.saveByValue(table2, 'judgement', 'KEEP')
# Find mutated rows with that are matched and unmatched
total_comparison = ml.compareTables(keeps1, keeps2)
'''
Comparision array:
0 is same_first_table
1 is same_second_table
2 is diff_first_table
3 is diff_second_table
'''
matched_keeps1 = total_comparison[0]
matched_keeps2 = total_comparison[1]
unmatched_keeps1 = total_comparison[2]
unmatched_keeps2 = total_comparison[3]
# Save rows with no detected mutations
rejects1 = ml.saveByValue(table1, 'judgement', 'REJECT')
rejects2 = ml.saveByValue(table2, 'judgement', 'REJECT')
# Compare unmatched KEEP rows of one table to REJECT rows of other table
total_compare_reject2_unmatched1 = ml.compareTables(unmatched_keeps1, rejects2)
matched_reject2_unmatched1 = total_compare_reject2_unmatched1[1] # 1 is the second column
total_compare_reject1_unmatched2 = ml.compareTables(unmatched_keeps2, rejects1)
matched_reject1_unmatched2 = total_compare_reject1_unmatched2[1]
# Select only certain categories
keeps1 = ml.saveByCategory(keeps1)
keeps2 = ml.saveByCategory(keeps2)
matched_reject2_unmatched1 = ml.saveByCategory(matched_reject2_unmatched1)
matched_reject1_unmatched2 = ml.saveByCategory(matched_reject1_unmatched2)
# Calculate concordance between NC TC and NF TF
concordance_table = ml.calcCondordance(unmatched_keeps1, unmatched_keeps2, matched_keeps1)
# Write tables to text files
book = Workbook(output_file)
ml.outputTable(book, concordance_table, 'Concordance Summary', output_directory)
ml.outputTable(book, keeps1, 'NC TC KEEP', output_directory)
ml.outputTable(book, keeps2, 'NF TF KEEP', output_directory)
ml.outputTable(book, matched_reject2_unmatched1, 'NF TF Matched REJECTS', output_directory)
ml.outputTable(book, matched_reject1_unmatched2, 'NC TC Matched REJECTS', output_directory)
book.close()
os.chdir(old_dir)
print('Finished')
