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Added support for genetic codes 2-3, 5-6, 9-10, 12-16, 21-25. The Cre…
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…ateSchema and AlleleCall modules will use the translation table used to create the training file (values passed to --t, --translation-table are ignored if a training file is used).
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@rfm-targa
rfm-targa committed Jun 28, 2024
1 parent 5e2b903 commit f7ca591
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Showing 4 changed files with 97 additions and 39 deletions.
2 changes: 1 addition & 1 deletion CHEWBBACA/SchemaEvaluator/evaluate_schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -577,7 +577,7 @@ def main(schema_directory, output_directory, genes_list, annotations,
annotations : str
Path to a TSV file created by the UniprotFinder module.
translation_table : int
Genetic code used to translate the alleles.
Genetic code used to translate alleles.
size_threshold : float
Allele size variation threshold. Used to determine if the size
of an allele is within the interval of the locus size mode +/-
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63 changes: 47 additions & 16 deletions CHEWBBACA/chewBBACA.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
from ExtractCgMLST import determine_cgmlst
from utils import (join_profiles,
remove_genes,
gene_prediction as gp,
# profiles_sqlitedb as ps,
process_datetime as pdt,
constants as ct,
Expand All @@ -48,6 +49,7 @@
from CHEWBBACA.ExtractCgMLST import determine_cgmlst
from CHEWBBACA.utils import (join_profiles,
remove_genes,
gene_prediction as gp,
# profiles_sqlitedb as ps,
process_datetime as pdt,
constants as ct,
Expand Down Expand Up @@ -102,7 +104,10 @@ def msg(name=None):
parser.add_argument('--ptf', '--training-file', type=str,
required=False, dest='ptf_path',
help='Path to the Prodigal training file used by Pyrodigal '
'to predict genes and added to the schema folder.')
'to predict genes. The translation table used to create '
'this file overrides any value passed to `--t`, '
'`--translation-table`. This file is copied '
'to the schema folder to be used for allele calling.')

parser.add_argument('--bsr', '--blast-score-ratio', type=pv.bsr_type,
required=False, default=ct.DEFAULT_BSR,
Expand All @@ -118,9 +123,11 @@ def msg(name=None):
'sequences (CDSs) shorter than this value are excluded.')

parser.add_argument('--t', '--translation-table', type=pv.translation_table_type,
required=False, default=11, dest='translation_table',
required=False, dest='translation_table',
help='Genetic code used to predict genes and'
' to translate coding sequences (CDSs).')
' to translate coding DNA sequences (CDSs). '
'This value is ignored if a valid training file '
'is passed to `--ptf`, `--training-file`.')

parser.add_argument('--st', '--size-threshold', type=pv.size_threshold_type,
required=False, default=0.2, dest='size_threshold',
Expand Down Expand Up @@ -167,10 +174,21 @@ def msg(name=None):
args = parser.parse_args()
del args.CreateSchema

# Check if PTF exists
if args.ptf_path is not None:
if os.path.isfile(args.ptf_path) is False:
# Check if user passed PTF
if args.ptf_path:
# Check if PTF exists
if not os.path.isfile(args.ptf_path):
sys.exit(ct.INVALID_PTF_PATH)
else:
# Get translation table used to create training file
ptf_table = gp.read_training_file(args.ptf_path).translation_table
args.translation_table = ptf_table
else:
if not args.translation_table:
args.translation_table = ct.GENETIC_CODES_DEFAULT

# Check if translation table is supported
pv.translation_table_type([args.translation_table])

# Create output directory
created = fo.create_directory(args.output_directory)
Expand Down Expand Up @@ -261,7 +279,9 @@ def msg(name=None):
required=False, dest='ptf_path',
help='Path to the Prodigal training file used by Pyrodigal '
'to predict genes. Default is to use the training file '
'included in the schema\'s directory.')
'included in the schema\'s directory. The translation '
'table used to create this file overrides any value '
'passed to `--t`, `--translation-table`.')

parser.add_argument('--gl', '--genes-list', type=str,
required=False, default=False, dest='genes_list',
Expand All @@ -287,9 +307,8 @@ def msg(name=None):
parser.add_argument('--t', '--translation-table', type=pv.translation_table_type,
required=False, dest='translation_table',
help='Genetic code used to predict genes and'
' to translate coding sequences. Must match '
'the genetic code used to create the training '
'file.')
' to translate coding DNA sequences (CDSs). '
'This value will be ignored if a training file is used.')

parser.add_argument('--st', '--size-threshold', type=pv.size_threshold_type,
required=False, dest='size_threshold',
Expand Down Expand Up @@ -886,7 +905,9 @@ def msg(name=None):
required=False, dest='ptf_path',
help='Path to the Prodigal training file that '
'will be included in the directory of the '
'adapted schema.')
'adapted schema. The translation table used to create '
'this file overrides any value passed to `--t`, '
'`--translation-table`.')

parser.add_argument('--bsr', '--blast-score-ratio', type=pv.bsr_type,
required=False, default=ct.DEFAULT_BSR,
Expand All @@ -909,8 +930,10 @@ def msg(name=None):

parser.add_argument('--t', '--translation-table',
type=pv.translation_table_type, required=False,
default=11, dest='translation_table',
help='Genetic code used for allele translation.')
dest='translation_table',
help='Genetic code used for allele translation. This '
'value is ignored if a valid training file '
'is passed to `--ptf`, `--training-file`.')

parser.add_argument('--st', '--size-threshold', type=pv.size_threshold_type,
required=False, default=ct.SIZE_THRESHOLD_DEFAULT,
Expand Down Expand Up @@ -944,10 +967,18 @@ def msg(name=None):
args = parser.parse_args()
del args.PrepExternalSchema

# Check if PTF exists
if args.ptf_path is not None:
if os.path.isfile(args.ptf_path) is False:
# Check if user passed PTF
if args.ptf_path:
# Check if PTF exists
if not os.path.isfile(args.ptf_path):
sys.exit(ct.INVALID_PTF_PATH)
else:
# Get translation table used to create training file
ptf_table = gp.read_training_file(args.ptf_path).translation_table
args.translation_table = ptf_table
else:
if not args.translation_table:
args.translation_table = ct.GENETIC_CODES_DEFAULT

# Define output paths
schema_path = os.path.abspath(args.output_directory)
Expand Down
24 changes: 19 additions & 5 deletions CHEWBBACA/utils/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,11 +77,25 @@
INTRA_CLUSTER_DEFAULT = 0.9

# Genetic codes/translation tables
GENETIC_CODES = {1: 'Standard',
4: 'The mold, protozoan, and coelenterate mitochondrial '
'code and the mycoplasma/spiroplasma code',
11: 'The Bacterial, Archaeal and Plant Plastid code',
25: 'Candidate division SR1 and gracilibacteria code'}
GENETIC_CODES = {1: 'The Standard Code',
2: 'The Vertebrate Mitochondrial Code',
3: 'The Yeast Mitochondrial Code',
4: 'The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code',
5: 'The Invertebrate Mitochondrial Code',
6: 'The Ciliate, Dasycladacean and Hexamita Nuclear Code',
9: 'The Echinoderm and Flatworm Mitochondrial Code',
10: 'The Euplotid Nuclear Code',
11: 'The Bacterial, Archaeal and Plant Plastid Code',
12: 'The Alternative Yeast Nuclear Code',
13: 'The Ascidian Mitochondrial Code',
14: 'The Alternative Flatworm Mitochondrial Code',
15: 'Blepharisma Nuclear Code',
16: 'Chlorophycean Mitochondrial Code',
21: 'Trematode Mitochondrial Code',
22: 'Scenedesmus obliquus Mitochondrial Code',
23: 'Thraustochytrium Mitochondrial Code',
24: 'Rhabdopleuridae Mitochondrial Code',
25: 'Candidate Division SR1 and Gracilibacteria Code'}

GENETIC_CODES_DEFAULT = 11

Expand Down
47 changes: 30 additions & 17 deletions CHEWBBACA/utils/parameters_validation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,12 +24,14 @@

try:
from utils import (constants as ct,
gene_prediction as gp,
file_operations as fo,
chewiens_requests as cr,
fasta_operations as fao,
iterables_manipulation as im)
except ModuleNotFoundError:
from CHEWBBACA.utils import (constants as ct,
gene_prediction as gp,
file_operations as fo,
chewiens_requests as cr,
fasta_operations as fao,
Expand Down Expand Up @@ -242,7 +244,7 @@ def translation_table_type(arg, genetic_codes=ct.GENETIC_CODES):
valid = False

if valid is False:
# format available genetic codes into list
# Format available genetic codes into list
lines = ['\t{0}: {1}'.format(k, v) for k, v in genetic_codes.items()]
gc_table = '\n{0}\n'.format('\n'.join(lines))

Expand Down Expand Up @@ -798,7 +800,6 @@ def validate_ptf(ptf_path, schema_directory, schema_ptfs, force_continue):
True if the training file does not match any of
the training files previously used with the schema.
"""

ptf_path = validate_ptf_path(ptf_path, schema_directory)

# Determine PTF checksum
Expand Down Expand Up @@ -855,26 +856,21 @@ def solve_conflicting_arguments(schema_params, ptf_path, blast_score_ratio,
Dictionary with the arguments validated values that
will be used for allele calling.
"""

# run parameters values
# Parameter values for current run
run_params = {'bsr': blast_score_ratio,
'translation_table': translation_table,
#'translation_table': translation_table,
'minimum_locus_length': minimum_length,
'size_threshold': size_threshold}

# determine user provided arguments values that differ from default
# Determine user provided values that differ from default
unmatch_params = {k: v
for k, v in run_params.items()
if v not in schema_params[k] and v is not None}
# determine arguments values not provided by user
default_params = {k: schema_params[k][0]
for k, v in run_params.items()
if v is None}

# update arguments for current run
for k in run_params:
if k in default_params:
run_params[k] = default_params[k]
# Update run values equal to None
for k, v in run_params.items():
if v is None:
run_params[k] = schema_params[k][0]

if len(unmatch_params) > 0:
print(ct.ARGS_DIFFER)
Expand All @@ -892,11 +888,11 @@ def solve_conflicting_arguments(schema_params, ptf_path, blast_score_ratio,
if params_answer.lower() not in ['y', 'yes']:
sys.exit('Exited.')
else:
# Append new argument values to configs values
# Append new argument values to config values
for p in unmatch_params:
schema_params[p].append(unmatch_params[p])

# default is to get the training file in schema directory
# Default is to get the training file in schema directory
schema_ptfs = schema_params['prodigal_training_file']
ptf_path, ptf_hash, unmatch = validate_ptf(ptf_path, schema_directory,
schema_ptfs, force_continue)
Expand All @@ -906,7 +902,24 @@ def solve_conflicting_arguments(schema_params, ptf_path, blast_score_ratio,
schema_params['prodigal_training_file'].append(ptf_hash)
unmatch_params['prodigal_training_file'] = ptf_hash

# save updated schema config file
# Update translation table
if ptf_path:
# Get translation table used to create training file
ptf_table = gp.read_training_file(ptf_path).translation_table
run_params['translation_table'] = ptf_table
if ptf_table not in schema_params['translation_table']:
schema_params['translation_table'].append(ptf_table)
unmatch_params['translation_table'] = ptf_table
else:
if not translation_table:
run_params['translation_table'] = schema_params['translation_table'][0]
else:
run_params['translation_table'] = translation_table
if translation_table not in schema_params['translation_table']:
schema_params['translation_table'].append(ptf_table)
unmatch_params['translation_table'] = ptf_table

# Update schema config file
if len(unmatch_params) > 0:
fo.pickle_dumper(schema_params, config_file)

Expand Down

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