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added --custom_adapters option to include adapters from a csv file #46

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added --custom_adapters option to include adapters from a csv file #46

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55 changes: 49 additions & 6 deletions porechop/porechop.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,10 +36,10 @@ def main():

matching_sets = find_matching_adapter_sets(check_reads, args.verbosity, args.end_size,
args.scoring_scheme_vals, args.print_dest,
args.adapter_threshold, args.threads)
args.adapter_threshold, args.threads, custom_adapters=args.custom_adapters)
matching_sets = exclude_end_adapters_for_rapid(matching_sets)
matching_sets = fix_up_1d2_sets(matching_sets)
display_adapter_set_results(matching_sets, args.verbosity, args.print_dest)
display_adapter_set_results(matching_sets, args.verbosity, args.print_dest, custom_adapters=args.custom_adapters)
matching_sets = add_full_barcode_adapter_sets(matching_sets)

if args.barcode_dir:
Expand Down Expand Up @@ -143,7 +143,9 @@ def get_arguments():
adapter_search_group.add_argument('--scoring_scheme', type=str, default='3,-6,-5,-2',
help='Comma-delimited string of alignment scores: match, '
'mismatch, gap open, gap extend')

adapter_search_group.add_argument('--custom_adapters', type=str, default=None,
help='Filepath to complementary custom adapters in csv format: '
'name,name start|end,sequence,barcode (boolean)')
end_trim_group = parser.add_argument_group('End adapter settings',
'Control the trimming of adapters from read ends')
end_trim_group.add_argument('--end_size', type=int, default=150,
Expand Down Expand Up @@ -281,8 +283,39 @@ def get_albacore_barcode_from_path(albacore_path):
return None


def load_custom_adapters(custom_adapters):
'''
Load a set of custom adapters. The format should be:

name,name start|end,sequence,barcode (boolean)

e.g.

pcr,pcr_forward,AGTC
pcr,pcr_reverse,TTGC
Barcode 01,bc01_forward,GGTA
Barcode 01,bc01_reverse,TTCT

Note that currently only pairs of adapters (start, end) are supported.
'''
from .adapters import Adapter
import csv

with open(custom_adapters, 'r') as fp:
f = csv.reader(fp, delimiter=',')

while True:
name, start, sequence_start = next(f)
_, end, sequence_end = next(f)

yield Adapter(
name=name,
start_sequence=(start, sequence_start),
end_sequence=(end, sequence_end))


def find_matching_adapter_sets(check_reads, verbosity, end_size, scoring_scheme_vals, print_dest,
adapter_threshold, threads):
adapter_threshold, threads, custom_adapters):
"""
Aligns all of the adapter sets to the start/end of reads to see which (if any) matches best.
"""
Expand All @@ -291,7 +324,15 @@ def find_matching_adapter_sets(check_reads, verbosity, end_size, scoring_scheme_
print(bold_underline('Looking for known adapter sets'), flush=True, file=print_dest)
output_progress_line(0, read_count, print_dest)

search_adapters = [a for a in ADAPTERS if '(full sequence)' not in a.name]

if not custom_adapters:
search_adapters = [a for a in ADAPTERS if '(full sequence)' not in a.name]
else:
# Append custom_adapters to the default search_adapters.
CUSTOM_ADAPTERS = load_custom_adapters(custom_adapters)
[ADAPTERS.append(a) for a in CUSTOM_ADAPTERS]
search_adapters = [a for a in ADAPTERS if '(full sequence)' not in a.name]

search_adapter_count = len(search_adapters)

# If single-threaded, do the work in a simple loop.
Expand Down Expand Up @@ -380,13 +421,15 @@ def fix_up_1d2_sets(matching_sets):
return matching_sets


def display_adapter_set_results(matching_sets, verbosity, print_dest):
def display_adapter_set_results(matching_sets, verbosity, print_dest, custom_adapters):
if verbosity < 1:
return
table = [['Set', 'Best read start %ID', 'Best read end %ID']]
row_colours = {}
matching_set_names = [x.name for x in matching_sets]

search_adapters = [a for a in ADAPTERS if '(full sequence)' not in a.name]

for adapter_set in search_adapters:
start_score = '%.1f' % adapter_set.best_start_score
end_score = '%.1f' % adapter_set.best_end_score
Expand Down