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Add --no_simple_bridges option
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@rrwick
rrwick committed Jan 19, 2022
1 parent 8f5ac9d commit 9d7f061
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Showing 3 changed files with 45 additions and 105 deletions.
2 changes: 1 addition & 1 deletion unicycler/bridge_loop_unroll.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ class LoopUnrollingBridge(object):
"""
def __init__(self, graph, start, end, middle, repeat):
"""
This constructor assumes the the start, end, middle and repeat segments form a simple loop
This constructor assumes the start, end, middle and repeat segments form a simple loop
in the graph supported by either a SPAdes contig or a long read alignment. It will use
segment depths to determine the loop count and score the bridge's quality.
"""
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83 changes: 44 additions & 39 deletions unicycler/unicycler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@
tblastn_path_and_version, racon_path_and_version, gfa_path, red
from .spades_func import get_best_spades_graph
from .blast_func import find_start_gene, CannotFindStart
from .unicycler_align import add_aligning_arguments, fix_up_arguments, AlignmentScoringScheme, \
from .unicycler_align import fix_up_arguments, AlignmentScoringScheme, \
semi_global_align_long_reads, load_references, load_long_reads, load_sam_alignments, \
print_alignment_summary_table
from .read_ref import get_read_nickname_dict
Expand Down Expand Up @@ -147,9 +147,10 @@ def main():
bridges += create_miniasm_bridges(graph, string_graph, anchor_segments,
scoring_scheme, args.verbosity, args.min_bridge_qual)

bridges += create_simple_long_read_bridges(graph, args.out, args.keep, args.threads,
read_dict, long_read_filename, scoring_scheme,
anchor_segments)
if not args.no_simple_bridges:
bridges += create_simple_long_read_bridges(graph, args.out, args.keep, args.threads,
read_dict, long_read_filename,
scoring_scheme, anchor_segments)
if not args.no_long_read_alignment:
read_names, min_scaled_score, min_alignment_length = \
align_long_reads_to_assembly_graph(graph, anchor_segments, args, full_command,
Expand Down Expand Up @@ -228,7 +229,6 @@ def get_arguments():
parser = argparse.ArgumentParser(description=full_description, formatter_class=MyHelpFormatter,
add_help=False)

# Help options
help_group = parser.add_argument_group('Help')
help_group.add_argument('-h', '--help', action='help',
help='Show this help message and exit')
Expand All @@ -237,20 +237,16 @@ def get_arguments():
help_group.add_argument('--version', action='version', version='Unicycler v' + __version__,
help="Show Unicycler's version number")

# Short read input options
input_group = parser.add_argument_group('Input')
input_group.add_argument('-1', '--short1', required=False,
help='FASTQ file of first short reads in each pair')
input_group.add_argument('-2', '--short2', required=False,
help='FASTQ file of second short reads in each pair')
input_group.add_argument('-s', '--unpaired', required=False,
help='FASTQ file of unpaired short reads')

# Long read input options
input_group.add_argument('-l', '--long', required=False,
help='FASTQ or FASTA file of long reads')

# Output options
output_group = parser.add_argument_group('Output')
output_group.add_argument('-o', '--out', required=True,
help='Output directory (required)')
Expand Down Expand Up @@ -294,7 +290,6 @@ def get_arguments():
'scaffolding anchors (default: automatic threshold)'
if show_all_args else argparse.SUPPRESS)

# SPAdes assembly options
spades_group = parser.add_argument_group('SPAdes assembly',
'These options control the short-read SPAdes '
'assembly at the beginning of the Unicycler pipeline.'
Expand Down Expand Up @@ -335,7 +330,6 @@ def get_arguments():
'"--phred-offset 33", default: no additional options)'
if show_all_args else argparse.SUPPRESS)

# Miniasm assembly options
miniasm_group = parser.add_argument_group('miniasm+Racon assembly',
'These options control the use of miniasm and Racon '
'to produce long-read bridges.'
Expand All @@ -354,7 +348,43 @@ def get_arguments():
'(default: perform long-read assembly using miniasm/Racon)'
if show_all_args else argparse.SUPPRESS)

# Rotation options
long_group = parser.add_argument_group('Long-read alignment and bridging',
'These options control the use of long-read alignment '
'to produce long-read bridges.'
if show_all_args else argparse.SUPPRESS)
long_group.add_argument('--no_simple_bridges', action='store_true',
help='Skip simple long-read bridging (default: use simple '
'long-read bridging)'
if show_all_args else argparse.SUPPRESS)
long_group.add_argument('--no_long_read_alignment', action='store_true',
help='Skip long-read-alignment-based bridging (default: use long-read '
'alignments to produce bridges)'
if show_all_args else argparse.SUPPRESS)
long_group.add_argument('--contamination', required=False,
help='FASTA file of known contamination in long reads'
if show_all_args else argparse.SUPPRESS)
long_group.add_argument('--scores', type=str, required=False, default='3,-6,-5,-2',
help='Comma-delimited string of alignment scores: match, mismatch, '
'gap open, gap extend'
if show_all_args else argparse.SUPPRESS)
long_group.add_argument('--low_score', type=float, required=False,
help='Score threshold - alignments below this are considered poor '
'(default: set threshold automatically)'
if show_all_args else argparse.SUPPRESS)

cleaning_group = parser.add_argument_group('Graph cleaning',
'These options control the removal of small '
'leftover sequences after bridging is complete.'
if show_all_args else argparse.SUPPRESS)
cleaning_group.add_argument('--min_component_size', type=int, default=1000,
help='Graph components smaller than this size (bp) will be '
'removed from the final graph'
if show_all_args else argparse.SUPPRESS)
cleaning_group.add_argument('--min_dead_end_size', type=int, default=1000,
help='Graph dead ends smaller than this size (bp) will be removed '
'from the final graph'
if show_all_args else argparse.SUPPRESS)

rotation_group = parser.add_argument_group('Assembly rotation',
'These options control the rotation of completed '
'circular sequence near the end of the Unicycler '
Expand Down Expand Up @@ -385,31 +415,6 @@ def get_arguments():
help='Path to the tblastn executable'
if show_all_args else argparse.SUPPRESS)

# Graph cleaning options
cleaning_group = parser.add_argument_group('Graph cleaning',
'These options control the removal of small '
'leftover sequences after bridging is complete.'
if show_all_args else argparse.SUPPRESS)
cleaning_group.add_argument('--min_component_size', type=int, default=1000,
help='Graph components smaller than this size (bp) will be '
'removed from the final graph'
if show_all_args else argparse.SUPPRESS)
cleaning_group.add_argument('--min_dead_end_size', type=int, default=1000,
help='Graph dead ends smaller than this size (bp) will be removed '
'from the final graph'
if show_all_args else argparse.SUPPRESS)

# Add the arguments for the aligner, but suppress the help text.
align_group = parser.add_argument_group('Long-read alignment',
'These options control the alignment of long reads to '
'the assembly graph.'
if show_all_args else argparse.SUPPRESS)
align_group.add_argument('--no_long_read_alignment', action='store_true',
help='Skip long-read-alignment-bases bridging (default: use '
'long-read alignments to produce bridges)'
if show_all_args else argparse.SUPPRESS)
add_aligning_arguments(align_group, show_all_args)

# If no arguments were used, print the entire help (argparse default is to just give an error
# like '--out is required').
if len(sys.argv) == 1:
Expand All @@ -427,8 +432,8 @@ def get_arguments():

if not (args.long and (args.short1 or args.unpaired)): # if not a hybrid assembly
if args.existing_long_read_assembly:
quit_with_error('--existing_long_read_assembly can only be used with hybrid '
'assemblies')
quit_with_error('--existing_long_read_assembly requires both short and long read '
'inputs')

if args.keep < 0 or args.keep > 3:
quit_with_error('--keep must be between 0 and 3 (inclusive)')
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65 changes: 0 additions & 65 deletions unicycler/unicycler_align.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,71 +70,6 @@
VERBOSITY = 0


def get_arguments():
"""
Specifies the command line arguments required by the script.
"""
terminal_width = shutil.get_terminal_size().columns
os.environ['COLUMNS'] = str(terminal_width)

parser = argparse.ArgumentParser(description='Unicycler align - a sensitive semi-global long '
'read aligner',
formatter_class=MyHelpFormatter)

parser.add_argument('--ref', type=str, required=True,
help='FASTA file containing one or more reference sequences')
parser.add_argument('--reads', type=str, required=True,
help='FASTQ or FASTA file of long reads')
parser.add_argument('--sam', type=str, required=True,
help='SAM file of resulting alignments')

add_aligning_arguments(parser, True)

parser.add_argument('--keep_bad', action='store_true',
help='Include alignments in the results even if they are below the low '
'score threshold (default: low-scoring alignments are discarded)')
parser.add_argument('--sensitivity', type=int, default=0,
help='A number from 0 (least sensitive) to 3 (most sensitive)')
parser.add_argument('--threads', type=int, required=False, default=get_default_thread_count(),
help='Number of threads used (default: number of CPUs, up to ' +
str(settings.MAX_AUTO_THREAD_COUNT) + ')')
parser.add_argument('--verbosity', type=int, required=False, default=1,
help='Level of stdout information (0 to 4)')
parser.add_argument('--min_len', type=int, required=False, default=100,
help='Minimum alignment length (bp) - exclude alignments shorter than this '
'length')
parser.add_argument('--allowed_overlap', type=int, required=False, default=100,
help='Allow this much overlap between alignments in a single read')

args = parser.parse_args()

global VERBOSITY
VERBOSITY = args.verbosity
log.logger = log.Log(log_filename=None, stdout_verbosity_level=VERBOSITY)

fix_up_arguments(args)

return args


def add_aligning_arguments(parser, show_help):
"""
Adds some aligning-specific arguments to the parser. These are in a separate function because
other tools (e.g. unicycler.py) can use this function too.
"""
parser.add_argument('--contamination', required=False,
help='FASTA file of known contamination in long reads'
if show_help else argparse.SUPPRESS)
parser.add_argument('--scores', type=str, required=False, default='3,-6,-5,-2',
help='Comma-delimited string of alignment scores: match, mismatch, '
'gap open, gap extend'
if show_help else argparse.SUPPRESS)
parser.add_argument('--low_score', type=float, required=False,
help='Score threshold - alignments below this are considered poor '
'(default: set threshold automatically)'
if show_help else argparse.SUPPRESS)


def fix_up_arguments(args):
# If the user just said 'lambda' for the contamination, then we use the lambda phage FASTA
# included with Unicycler.
Expand Down

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