def create_report(n_reads, reads_per_cell, no_match, version, start_time,
ordered_tags_map, umis_corrected, bcs_corrected, bad_cells,
args):
"""
Creates a report with details about the run in a yaml format.
Args:
n_reads (int): Number of reads that have been processed.
reads_matrix (scipy.sparse.dok_matrix): A sparse matrix continining read counts.
no_match (Counter): Counter of unmapped tags.
version (string): CITE-seq-Count package version.
start_time (time): Start time of the run.
args (arg_parse): Arguments provided by the user.
"""
total_unmapped = sum(no_match.values())
total_mapped = sum(reads_per_cell.values()) - total_unmapped
mapped_perc = round((total_mapped / n_reads) * 100)
unmapped_perc = round((total_unmapped / n_reads) * 100)
with open(os.path.join(args.outfolder, 'run_report.yaml'),
'w') as report_file:
report_file.write("""Date: {}
Running time: {}
CITE-seq-Count Version: {}
Reads processed: {}
Percentage mapped: {}
Percentage unmapped: {}
Uncorrected cells: {}
Correction:
\tCell barcodes collapsing threshold: {}
\tCell barcodes corrected: {}
\tUMI collapsing threshold: {}
\tUMIs corrected: {}
Run parameters:
\tRead1_filename: {}
\tRead2_filename: {}
\tCell barcode:
\t\tFirst position: {}
\t\tLast position: {}
\tUMI barcode:
\t\tFirst position: {}
\t\tLast position: {}
\tExpected cells: {}
\tTags max errors: {}
\tStart trim: {}
""".format(datetime.datetime.today().strftime('%Y-%m-%d'),
secondsToText.secondsToText(time.time() - start_time), version,
n_reads, mapped_perc, unmapped_perc, len(bad_cells),
args.bc_threshold, bcs_corrected, args.umi_threshold,
umis_corrected, args.read1_path, args.read2_path, args.cb_first,
args.cb_last, args.umi_first, args.umi_last, args.expected_cells,
args.max_error, args.start_trim))
def map_reads(read1_path, read2_path, tags, barcode_slice, umi_slice, indexes,
whitelist, debug, start_trim, maximum_distance):
"""Read through R1/R2 files and generate a islice starting at a specific index.
It reads both Read1 and Read2 files, creating a dict based on cell barcode.
Args:
read1_path (string): Path to R1.fastq.gz
read2_path (string): Path to R2.fastq.gz
chunk_size (int): The number of lines to process
tags (dict): A dictionary with the TAGs + TAG Names.
barcode_slice (slice): A slice for extracting the Barcode portion from the
sequence.
umi_slice (slice): A slice for extracting the UMI portion from the
sequence.
indexes (list): Pair of first and last index for islice
whitelist (set): The set of white-listed barcodes.
debug (bool): Print debug messages. Default is False.
start_trim (int): Number of bases to trim at the start.
maximum_distance (int): Maximum distance given by the user.
Returns:
results (dict): A dict of dict of Counters with the mapping results.
no_match (Counter): A counter with unmapped sequences.
"""
# Initiate values
results = {}
no_match = Counter()
n = 1
t = time.time()
with gzip.open(read1_path, 'rt') as textfile1, \
gzip.open(read2_path, 'rt') as textfile2:
# Read all 2nd lines from 4 line chunks. If first_n not None read only 4 times the given amount.
secondlines = islice(zip(textfile1, textfile2), indexes[0] * 4 + 1,
indexes[1] * 4 + 1, 4)
for read1, read2 in secondlines:
read1 = read1.strip()
read2 = read2.strip()
# Progress info
if n % 1000000 == 0:
print("Processed 1,000,000 reads in {}. Total "
"reads: {:,} in child {}".format(
secondsToText.secondsToText(time.time() - t), n,
os.getpid()))
sys.stdout.flush()
t = time.time()
# Get cell and umi barcodes.
cell_barcode = read1[barcode_slice]
# This change in bytes is required by umi_tools for umi correction
UMI = bytes(read1[umi_slice], 'ascii')
# Trim potential starting sequences
TAG_seq = read2[start_trim:]
if cell_barcode not in results:
results[cell_barcode] = defaultdict(Counter)
best_match = find_best_match(TAG_seq, tags, maximum_distance)
results[cell_barcode][best_match][UMI] += 1
if (best_match == 'unmapped'):
no_match[TAG_seq] += 1
if debug:
print(
"\nline:{0}\n"
"cell_barcode:{1}\tUMI:{2}\tTAG_seq:{3}\n"
"line length:{4}\tcell barcode length:{5}\tUMI length:{6}\tTAG sequence length:{7}\n"
"Best match is: {8}".format(read1 + read2,
cell_barcode, UMI, TAG_seq,
len(read1 + read2),
len(cell_barcode), len(UMI),
len(TAG_seq), best_match))
sys.stdout.flush()
n += 1
print("Mapping done for process {}. Processed {:,} reads".format(
os.getpid(), n - 1))
sys.stdout.flush()
return (results, no_match)