def test_hamming_expansion_collisions(self):
b = barcodeFileParser.BarcodeParser()
b.addBarcode(barcodeFileAlias='test', barcode='AAA', index='TEST1')
b.addBarcode(barcodeFileAlias='test', barcode='AAT', index='TEST2')
b.addBarcode(barcodeFileAlias='test', barcode='TTT', index='TEST3')
b.expand(2, 'test')
index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance(
'AAG', 'test')
self.assertIsNone(index)
index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance(
'AAG', 'test')
self.assertIsNone(index)
index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance(
'TCA', 'test')
self.assertIsNone(index)
index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance(
'AAA', 'test')
self.assertEqual(index, 'TEST1')
self.assertEqual(barcode, 'AAA')
self.assertEqual(hd, 0)
index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance(
'TAA', 'test')
self.assertEqual(index, 'TEST1')
self.assertEqual(barcode, 'AAA')
self.assertEqual(hd, 1)
def test_insert(self):
b = barcodeFileParser.BarcodeParser()
b.addBarcode(barcodeFileAlias='test', barcode='AAA', index='TEST1')
index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance(
'AAA', 'test')
self.assertEqual(index, 'TEST1')
self.assertEqual(barcode, 'AAA')
self.assertEqual(hd, 0)
def test_hamming_expansion(self):
b = barcodeFileParser.BarcodeParser()
b.addBarcode(barcodeFileAlias='test', barcode='AAA', index='TEST1')
b.addBarcode(barcodeFileAlias='test', barcode='AAT', index='TEST2')
b.addBarcode(barcodeFileAlias='test', barcode='TTT', index='TEST3')
b.expand(2, 'test')
index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance(
'CTC', 'test')
self.assertEqual(index, 'TEST3')
self.assertEqual(barcode, 'TTT')
self.assertEqual(hd, 2)
def test_hamming_expansion(self):
b = barcodeFileParser.BarcodeParser()
b.addBarcode(barcodeFileAlias='test', barcode='AAA', index='TEST1')
b.expand(1, 'test')
# Postive examples:
for positive in ['AAT', 'CAA', 'AGA', 'TAA']:
index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance(
positive, 'test')
self.assertEqual(index, 'TEST1')
self.assertEqual(barcode, 'AAA')
self.assertEqual(hd, 1)
#Negative examples
for negative in ['TAT', 'CCA', 'GGA', 'TCA']:
index, barcode, hd = b.getIndexCorrectedBarcodeAndHammingDistance(
negative, 'test')
self.assertNotEqual(barcode, 'AAA')
if not args.fastqfiles[0].endswith(
'.gz') and not args.fastqfiles[0].endswith(
'.fastq') and not args.fastqfiles[0].endswith('.fq'):
# File list:
print('Input is interpreted as a list of files..')
with open(args.fastqfiles[0]) as f:
fqFiles = []
for line in f:
fqFiles.append(line.strip())
args.fastqfiles = fqFiles
# Sort the fastq files..
args.fastqfiles = sorted(args.fastqfiles)
# Load barcodes
barcodeParser = barcodeFileParser.BarcodeParser(
hammingDistanceExpansion=args.hd, barcodeDirectory=args.barcodeDir)
# Setup the index parser
indexFileAlias = args.ifa # let the multiplex methods decide which index file to use
if args.si: # the user defines the sequencing indices
useSequencingIndices = args.si.split(',')
print(
f"{Style.BRIGHT} Only these sequencing indices will be kept: {Style.RESET_ALL}"
)
for sequencingIndex in useSequencingIndices:
print(f"{Fore.GREEN}{sequencingIndex}{Style.RESET_ALL}")
indexParser = barcodeFileParser.BarcodeParser()
indexFileAlias = 'user'
for index, sequencingIndex in enumerate(useSequencingIndices):
import pkg_resources
import singlecellmultiomics.barcodeFileParser.barcodeFileParser as barcodeFileParser
from singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader import DemultiplexingStrategyLoader
import singlecellmultiomics.libraryDetection.sequencingLibraryListing as sequencingLibraryListing
import glob
import fnmatch
import os
from types import SimpleNamespace
if __name__ == '__main__':
barcode_dir = pkg_resources.resource_filename(
'singlecellmultiomics', 'modularDemultiplexer/barcodes/')
index_dir = pkg_resources.resource_filename(
'singlecellmultiomics', 'modularDemultiplexer/indices/')
barcode_parser = barcodeFileParser.BarcodeParser(
hammingDistanceExpansion=0, barcodeDirectory=barcode_dir)
index_parser = barcodeFileParser.BarcodeParser(hammingDistanceExpansion=1,
barcodeDirectory=index_dir)
dmx = DemultiplexingStrategyLoader(barcodeParser=barcode_parser,
indexParser=index_parser,
indexFileAlias=None)
argparser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description="""Check multiplexability of many fastq files""")
argparser.add_argument('-locations', default='.')
arguments = argparser.parse_args()
sequencing_dirs = arguments.locations.split(',')