diff --git a/CHANGELOG.md b/CHANGELOG.md
index bd6bb75f..01143dde 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,12 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
## [Unreleased]
+## [1.4.6-rc3] - 2025-03-10
+
+- Added --skip-failed flag to callVariant, parseArriba, parserSTARFusion, parseFusionCatcher.
+
+- Added tally table to parseREDITools, parseCIRCExplorer, and parseRMATS
+
## [1.4.6-rc2] - 2025-03-03
### Fixed
diff --git a/moPepGen/__init__.py b/moPepGen/__init__.py
index d0a27169..7cb69223 100644
--- a/moPepGen/__init__.py
+++ b/moPepGen/__init__.py
@@ -8,7 +8,7 @@
from . import constant
-__version__ = '1.4.6-rc2'
+__version__ = '1.4.6-rc3'
## Error messages
ERROR_INDEX_IN_INTRON = 'The genomic index seems to be in an intron'
diff --git a/moPepGen/cli/call_variant_peptide.py b/moPepGen/cli/call_variant_peptide.py
index b95fe9cb..af640338 100644
--- a/moPepGen/cli/call_variant_peptide.py
+++ b/moPepGen/cli/call_variant_peptide.py
@@ -32,6 +32,7 @@
INPUT_FILE_FORMATS = ['.gvf']
OUTPUT_FILE_FORMATS = ['.fasta', '.fa']
+
# pylint: disable=W0212
def add_subparser_call_variant(subparsers:argparse._SubParsersAction):
""" CLI for moPepGen callPeptides """
@@ -143,6 +144,7 @@ def add_subparser_call_variant(subparsers:argparse._SubParsersAction):
default=1,
metavar='<number>'
)
+ common.add_args_skip_failed(p)
common.add_args_reference(p)
common.add_args_cleavage(p)
common.add_args_debug_level(p)
@@ -158,6 +160,12 @@ def __init__(self, logger:Logger):
""" constructor """
self.n_transcripts_total = 0
self.n_transcripts_processed = 0
+ self.n_transcripts_invalid = 0
+ self.n_transcripts_failed = {
+ 'variant': 0,
+ 'fusion': 0,
+ 'circRNA': 0
+ }
self.n_total_peptides = 0
self.n_valid_peptides = 0
self.logger = logger
@@ -167,6 +175,11 @@ def log(self):
self.logger.info("callVariant summary:")
self.logger.info("Total transcripts with variants: %i", self.n_transcripts_total)
self.logger.info("Total transcripts processed: %i", self.n_transcripts_processed)
+ self.logger.info("Number of invalid transcripts: %i", self.n_transcripts_invalid)
+ self.logger.info("Number of transcripts failed when calling for:")
+ self.logger.info(" Variant peptides: %i", self.n_transcripts_failed['variant'])
+ self.logger.info(" Fusion peptides: %i", self.n_transcripts_failed['fusion'])
+ self.logger.info(" circRNA peptides: %i", self.n_transcripts_failed['circRNA'])
self.logger.info(
"Total variant peptides generated (including redundant): %i",
self.n_total_peptides
@@ -300,16 +313,112 @@ def write_pgraphs(self, tx_id:str, pgraphs:TypePGraphs):
with open(self.graph_output_dir/f"{tx_id}_circRNA_{var_id}_PVG.json", 'wt') as handle:
json.dump(data, handle)
-TypeDGraphs = Tuple[
- svgraph.ThreeFrameTVG,
- Dict[str, svgraph.ThreeFrameTVG],
- Dict[str, svgraph.ThreeFrameCVG]
-]
-TypePGraphs = Tuple[
- svgraph.PeptideVariantGraph,
- Dict[str, svgraph.PeptideVariantGraph],
- Dict[str, svgraph.PeptideVariantGraph]
-]
+ def gather_data_for_call_variant(self, tx_id:str, pool:seqvar.VariantRecordPoolOnDisk):
+ """ Gather data for callVariant """
+ ref = self.reference_data
+ tx_ids = [tx_id]
+ tx_model = ref.anno.transcripts[tx_id]
+ try:
+ variant_series = pool[tx_id]
+ except ValueError:
+ if self.args.skip_failed:
+ self.tally.n_transcripts_invalid += 1
+ return None
+ raise
+ if variant_series.is_empty():
+ return None
+ if self.noncanonical_transcripts and \
+ not variant_series.has_any_noncanonical_transcripts():
+ return None
+ tx_ids += variant_series.get_additional_transcripts()
+
+ gene_seqs = {}
+ if variant_series.is_gene_sequence_needed():
+ gene_id = tx_model.transcript.gene_id
+ _chrom = tx_model.transcript.chrom
+ gene_model = ref.anno.genes[gene_id]
+ gene_seq = gene_model.get_gene_sequence(ref.genome[_chrom])
+ gene_seqs[gene_id] = gene_seq
+
+ tx_seqs = {}
+ for _tx_id in tx_ids:
+ _tx_model = ref.anno.transcripts[_tx_id]
+ _chrom = _tx_model.transcript.chrom
+ tx_seqs[_tx_id] = _tx_model.get_transcript_sequence(ref.genome[_chrom])
+ _gene_id = _tx_model.transcript.gene_id
+ if _gene_id not in gene_seqs:
+ _gene_model = ref.anno.genes[_gene_id]
+ _gene_seq = _gene_model.get_gene_sequence(ref.genome[_chrom])
+ gene_seqs[_gene_id] = _gene_seq
+ gene_ids = list({ref.anno.transcripts[x].transcript.gene_id for x in tx_ids})
+
+ gene_models = {}
+ for gene_id in gene_ids:
+ dummy_gene_model = copy.deepcopy(ref.anno.genes[gene_id])
+ dummy_gene_model.transcripts = [x for x in dummy_gene_model.transcripts
+ if x in tx_ids]
+ gene_models[gene_id] = dummy_gene_model
+
+ dummy_anno = gtf.GenomicAnnotation(
+ genes=gene_models,
+ transcripts={tx_id: ref.anno.transcripts[tx_id] for tx_id in tx_ids},
+ source=ref.anno.source
+ )
+ reference_data = params.ReferenceData(
+ genome=None,
+ anno=dummy_anno,
+ canonical_peptides=set() # Not providing canonical peptide at this point.
+ )
+ dummy_pool = seqvar.VariantRecordPool()
+ dummy_pool.anno = dummy_anno
+ dummy_pool.data[tx_id] = variant_series
+ for add_tx in tx_ids:
+ if add_tx != tx_id:
+ try:
+ dummy_pool[add_tx] = pool[add_tx]
+ except KeyError:
+ continue
+
+ return {
+ 'tx_id': tx_id,
+ 'variant_series': variant_series,
+ 'tx_seqs': tx_seqs,
+ 'gene_seqs': gene_seqs,
+ 'reference_data': reference_data,
+ 'pool': dummy_pool,
+ 'cleavage_params': self.cleavage_params,
+ 'noncanonical_transcripts': self.noncanonical_transcripts,
+ 'max_adjacent_as_mnv': self.max_adjacent_as_mnv,
+ 'truncate_sec': self.truncate_sec,
+ 'w2f_reassignment': self.w2f_reassignment,
+ 'save_graph': self.graph_output_dir is not None,
+ 'timeout': self.args.timeout_seconds,
+ 'max_variants_per_node': tuple(self.args.max_variants_per_node),
+ 'additional_variants_per_misc': tuple(self.args.additional_variants_per_misc),
+ 'backsplicing_only': self.args.backsplicing_only,
+ 'coding_novel_orf': self.args.coding_novel_orf,
+ 'skip_failed': self.args.skip_failed
+ }
+
+
+if TYPE_CHECKING:
+ TypeDGraphs = Tuple[
+ svgraph.ThreeFrameTVG,
+ Dict[str, svgraph.ThreeFrameTVG],
+ Dict[str, svgraph.ThreeFrameCVG]
+ ]
+ TypePGraphs = Tuple[
+ svgraph.PeptideVariantGraph,
+ Dict[str, svgraph.PeptideVariantGraph],
+ Dict[str, svgraph.PeptideVariantGraph]
+ ]
+ CallVariantOutput = Tuple[
+ Dict[Seq, List[AnnotatedPeptideLabel]],
+ str,
+ TypeDGraphs,
+ TypePGraphs,
+ Tuple[bool,bool,bool]
+ ]
# pylint: disable=unused-argument
@common.timeout()
def call_variant_peptides_wrapper(tx_id:str,
@@ -326,9 +435,11 @@ def call_variant_peptides_wrapper(tx_id:str,
backsplicing_only:bool,
save_graph:bool,
coding_novel_orf:bool,
+ skip_failed:bool,
**kwargs
- ) -> Tuple[Dict[Seq, List[AnnotatedPeptideLabel]], str, TypeDGraphs, TypePGraphs]:
+ ) -> CallVariantOutput:
""" wrapper function to call variant peptides """
+ # pylint: disable=W0702
logger = get_logger()
peptide_anno:Dict[Seq, Dict[str, AnnotatedPeptideLabel]] = {}
@@ -347,6 +458,7 @@ def add_peptide_anno(x:Dict[Seq, List[AnnotatedPeptideLabel]]):
)
dgraphs:TypeDGraphs = (None, {}, {})
pgraphs:TypePGraphs = (None, {}, {})
+ success_flags = (True, True, True)
if variant_series.transcriptional:
try:
if not noncanonical_transcripts or \
@@ -368,8 +480,12 @@ def add_peptide_anno(x:Dict[Seq, List[AnnotatedPeptideLabel]]):
pgraphs = (pgraph, pgraphs[1], pgraphs[2])
add_peptide_anno(peptide_map)
except:
- logger.error('Exception raised from %s', tx_id)
- raise
+ if skip_failed:
+ logger.warning('Variant peptides calling failed from %s', tx_id)
+ success_flags = (False, success_flags[1], success_flags[2])
+ else:
+ logger.error('Exception raised from %s', tx_id)
+ raise
exclude_variant_types = ['Fusion', 'Insertion', 'Deletion', 'Substitution', 'circRNA']
for variant in variant_series.fusion:
@@ -398,11 +514,18 @@ def add_peptide_anno(x:Dict[Seq, List[AnnotatedPeptideLabel]]):
pgraphs[1][variant.id] = pgraph
add_peptide_anno(peptide_map)
except:
- logger.error(
- "Exception raised from fusion %s, donor: %s, accepter: %s",
- variant.id, tx_id, variant.attrs['ACCEPTER_TRANSCRIPT_ID']
- )
- raise
+ if skip_failed:
+ logger.warning(
+ 'Variant peptides calling failed from %s with fusion: %s',
+ tx_id, variant.id
+ )
+ success_flags = (success_flags[0], False, success_flags[2])
+ else:
+ logger.error(
+ "Exception raised from fusion %s, donor: %s, accepter: %s",
+ variant.id, tx_id, variant.attrs['ACCEPTER_TRANSCRIPT_ID']
+ )
+ raise
if main_peptides:
denylist.update([str(x) for x in main_peptides])
@@ -417,15 +540,22 @@ def add_peptide_anno(x:Dict[Seq, List[AnnotatedPeptideLabel]]):
)
except:
- logger.error("Exception raised from %s", circ_model.id)
- raise
+ if skip_failed:
+ logger.warning(
+ 'Variant peptides calling failed from %s with circRNA: %s',
+ tx_id, circ_model.id
+ )
+ success_flags = (success_flags[0], success_flags[1], False)
+ else:
+ logger.error("Exception raised from %s", circ_model.id)
+ raise
dgraphs[2][circ_model.id] = cgraph
pgraphs[2][circ_model.id] = pgraph
add_peptide_anno(peptide_map)
peptide_anno = {k:list(v.values()) for k,v in peptide_anno.items()}
- return peptide_anno, tx_id, dgraphs, pgraphs
+ return peptide_anno, tx_id, dgraphs, pgraphs, success_flags
def caller_reducer(dispatch):
""" wrapper for ParallelPool. Also reduces the complexity if the run is timed out. """
@@ -462,7 +592,6 @@ def call_variant_peptide(args:argparse.Namespace) -> None:
common.print_start_message(args)
caller.load_reference()
caller.create_in_disk_variant_pool()
- noncanonical_transcripts = caller.noncanonical_transcripts
ref = caller.reference_data
logger = get_logger()
caller.logger = logger
@@ -482,9 +611,6 @@ def call_variant_peptide(args:argparse.Namespace) -> None:
logger.info('Variants sorted')
caller.tally.n_transcripts_total = len(tx_sorted)
- # Not providing canonical peptide pool to each task for now.
- canonical_peptides = set()
-
if caller.threads > 1:
process_pool = ParallelPool(ncpus=caller.threads)
@@ -493,82 +619,9 @@ def call_variant_peptide(args:argparse.Namespace) -> None:
dispatches = []
i = 0
for tx_id in tx_sorted:
- tx_ids = [tx_id]
- tx_model = ref.anno.transcripts[tx_id]
- variant_series = pool[tx_id]
- if variant_series.is_empty():
+ dispatch = caller.gather_data_for_call_variant(tx_id, pool)
+ if not dispatch:
continue
- if noncanonical_transcripts and \
- not variant_series.has_any_noncanonical_transcripts():
- continue
- tx_ids += variant_series.get_additional_transcripts()
-
- gene_seqs = {}
- if variant_series.is_gene_sequence_needed():
- gene_id = tx_model.transcript.gene_id
- _chrom = tx_model.transcript.chrom
- gene_model = ref.anno.genes[gene_id]
- gene_seq = gene_model.get_gene_sequence(ref.genome[_chrom])
- gene_seqs[gene_id] = gene_seq
-
- tx_seqs = {}
- for _tx_id in tx_ids:
- _tx_model = ref.anno.transcripts[_tx_id]
- _chrom = _tx_model.transcript.chrom
- tx_seqs[_tx_id] = _tx_model.get_transcript_sequence(ref.genome[_chrom])
- _gene_id = _tx_model.transcript.gene_id
- if _gene_id not in gene_seqs:
- _gene_model = ref.anno.genes[_gene_id]
- _gene_seq = _gene_model.get_gene_sequence(ref.genome[_chrom])
- gene_seqs[_gene_id] = _gene_seq
- gene_ids = list({ref.anno.transcripts[x].transcript.gene_id for x in tx_ids})
-
- gene_models = {}
- for gene_id in gene_ids:
- dummy_gene_model = copy.deepcopy(ref.anno.genes[gene_id])
- dummy_gene_model.transcripts = [x for x in dummy_gene_model.transcripts
- if x in tx_ids]
- gene_models[gene_id] = dummy_gene_model
-
- dummy_anno = gtf.GenomicAnnotation(
- genes=gene_models,
- transcripts={tx_id:ref.anno.transcripts[tx_id] for tx_id in tx_ids},
- source=ref.anno.source
- )
- reference_data = params.ReferenceData(
- genome=None,
- anno=dummy_anno,
- canonical_peptides=canonical_peptides
- )
- dummy_pool = seqvar.VariantRecordPool()
- dummy_pool.anno = dummy_anno
- dummy_pool.data[tx_id] = variant_series
- for add_tx in tx_ids:
- if add_tx != tx_id:
- try:
- dummy_pool[add_tx] = caller.variant_record_pool[add_tx]
- except KeyError:
- continue
-
- dispatch = {
- 'tx_id': tx_id,
- 'variant_series': variant_series,
- 'tx_seqs': tx_seqs,
- 'gene_seqs': gene_seqs,
- 'reference_data': reference_data,
- 'pool': dummy_pool,
- 'cleavage_params': caller.cleavage_params,
- 'noncanonical_transcripts': noncanonical_transcripts,
- 'max_adjacent_as_mnv': caller.max_adjacent_as_mnv,
- 'truncate_sec': caller.truncate_sec,
- 'w2f_reassignment': caller.w2f_reassignment,
- 'save_graph': caller.graph_output_dir is not None,
- 'timeout': args.timeout_seconds,
- 'max_variants_per_node': tuple(args.max_variants_per_node),
- 'additional_variants_per_misc': tuple(args.additional_variants_per_misc),
- 'backsplicing_only': args.backsplicing_only,
- 'coding_novel_orf': args.coding_novel_orf
- }
dispatches.append(dispatch)
caller.tally.n_transcripts_processed += 1
@@ -586,7 +639,7 @@ def call_variant_peptide(args:argparse.Namespace) -> None:
results = [ caller_reducer(dispatches[0]) ]
# pylint: disable=W0621
- for peptide_anno, tx_id, dgraphs, pgraphs in results:
+ for peptide_anno, tx_id, dgraphs, pgraphs, success_flags in results:
caller.tally.n_total_peptides += len(peptide_anno)
for peptide in peptide_anno:
is_valid = peptide_table.is_valid(
@@ -600,6 +653,12 @@ def call_variant_peptide(args:argparse.Namespace) -> None:
if caller.graph_output_dir is not None:
caller.write_dgraphs(tx_id, dgraphs)
caller.write_pgraphs(tx_id, pgraphs)
+ if not success_flags[0]:
+ caller.tally.n_transcripts_failed['variant'] += 1
+ if not success_flags[1]:
+ caller.tally.n_transcripts_failed['fusion'] += 1
+ if not success_flags[2]:
+ caller.tally.n_transcripts_failed['circRNA'] += 1
dispatches = []
i += 1
diff --git a/moPepGen/cli/parse_arriba.py b/moPepGen/cli/parse_arriba.py
index 39abf58f..4ffc1ded 100644
--- a/moPepGen/cli/parse_arriba.py
+++ b/moPepGen/cli/parse_arriba.py
@@ -2,13 +2,18 @@
[Arriba](https://github.com/suhrig/arriba) and saves as a GVF file. The GVF
file can be later used to call variant peptides using
[callVariant](call-variant.md)."""
-from typing import List
+from __future__ import annotations
+from typing import TYPE_CHECKING
from pathlib import Path
import argparse
from moPepGen import get_logger, seqvar, parser, err
from moPepGen.cli import common
+if TYPE_CHECKING:
+ from typing import List
+ from logging import Logger
+
INPUT_FILE_FORMATS = ['.tsv', '.txt']
OUTPUT_FILE_FORMATS = ['.gvf']
@@ -50,6 +55,7 @@ def add_subparser_parse_arriba(subparsers:argparse._SubParsersAction):
metavar='<choice>',
default='medium'
)
+ common.add_args_skip_failed(p)
common.add_args_source(p)
common.add_args_reference(p, proteome=False)
common.add_args_debug_level(p)
@@ -57,9 +63,42 @@ def add_subparser_parse_arriba(subparsers:argparse._SubParsersAction):
common.print_help_if_missing_args(p)
return p
+class TallyTable():
+ """ Tally table """
+ def __init__(self, logger:Logger):
+ """ Constructor """
+ self.total:int = 0
+ self.succeed:int = 0
+ self.skipped:TallyTableSkipped = TallyTableSkipped()
+ self.logger = logger
+
+ def log(self):
+ """ Show tally results """
+ self.logger.info("Summary:")
+ self.logger.info("Totally records read: %i", self.total)
+ self.logger.info("Records successfully processed: %i", self.succeed)
+ self.logger.info("Records skipped: %i", self.skipped.total)
+ if self.skipped.total > 0:
+ self.logger.info("Out of those skipped,")
+ self.logger.info(" Invalid gene ID: %i", self.skipped.invalid_gene_id)
+ self.logger.info(" Invalid position: %i", self.skipped.invalid_position)
+ self.logger.info(" Insufficient evidence: %i", self.skipped.insufficient_evidence)
+ self.logger.info(" Antisense strand: %i", self.skipped.antisense_strand)
+
+class TallyTableSkipped():
+ """ Tally table for failed ones """
+ def __init__(self):
+ """ constructor """
+ self.invalid_gene_id:int = 0
+ self.invalid_position:int = 0
+ self.insufficient_evidence:int = 0
+ self.antisense_strand:int = 0
+ self.total:int = 0
+
def parse_arriba(args:argparse.Namespace) -> None:
""" Parse Arriba output and save it in GVF format. """
logger = get_logger()
+ tally = TallyTable(logger)
# unpack args
fusion = args.input_path
output_path:Path = args.output_path
@@ -82,17 +121,33 @@ def parse_arriba(args:argparse.Namespace) -> None:
with open(fusion, 'rt') as handle:
for record in parser.ArribaParser.parse(handle):
+ tally.total += 1
if not record.gene_id1 in anno.genes or not record.gene_id2 in anno.genes:
+ tally.skipped.invalid_gene_id += 1
+ tally.skipped.total += 1
continue
if not record.is_valid(min_split_read1, min_split_read2, min_confidence):
+ tally.skipped.insufficient_evidence += 1
+ tally.skipped.total += 1
continue
if record.transcript_on_antisense_strand(anno):
+ tally.skipped.antisense_strand += 1
+ tally.skipped.total += 1
continue
try:
var_records = record.convert_to_variant_records(anno, genome)
+ variants.extend(var_records)
+ tally.succeed += 1
except err.GeneNotFoundError:
+ tally.skipped.invalid_gene_id += 1
+ tally.skipped.total += 1
continue
- variants.extend(var_records)
+ except:
+ if args.skip_failed:
+ tally.skipped.invalid_position += 1
+ tally.skipped.total += 1
+ continue
+ raise
logger.info('Arriba output %s loaded.', fusion)
@@ -110,3 +165,5 @@ def parse_arriba(args:argparse.Namespace) -> None:
seqvar.io.write(variants, output_path, metadata)
logger.info("Variants written to disk.")
+
+ tally.log()
diff --git a/moPepGen/cli/parse_circexplorer.py b/moPepGen/cli/parse_circexplorer.py
index ad7adf3e..0060f551 100644
--- a/moPepGen/cli/parse_circexplorer.py
+++ b/moPepGen/cli/parse_circexplorer.py
@@ -4,14 +4,18 @@
[callVariant](call-variant.md). Noted that only known circRNA is supported (
\*_circular_known.txt) """
from __future__ import annotations
+from typing import TYPE_CHECKING
import argparse
-from typing import List, Dict
from pathlib import Path
from moPepGen import get_logger, circ, err
from moPepGen.parser import CIRCexplorerParser
from moPepGen.cli import common
+if TYPE_CHECKING:
+ from typing import List, Dict
+ from logging import Logger
+
INPUT_FILE_FORMATS = ['.tsv', '.txt']
OUTPUT_FILE_FORMATS = ['.gvf']
@@ -74,6 +78,7 @@ def add_subparser_parse_circexplorer(subparsers:argparse._SubParsersAction):
default='-100,5',
metavar='<number>'
)
+ common.add_args_skip_failed(p)
common.add_args_source(p)
common.add_args_reference(p, genome=False, proteome=False)
common.add_args_debug_level(p)
@@ -81,9 +86,40 @@ def add_subparser_parse_circexplorer(subparsers:argparse._SubParsersAction):
common.print_help_if_missing_args(p)
return p
+class TallyTable():
+ """ Tally table """
+ def __init__(self, logger:Logger):
+ """ Constructor """
+ self.total:int = 0
+ self.succeed:int = 0
+ self.skipped:TallyTableSkipped = TallyTableSkipped()
+ self.logger = logger
+
+ def log(self):
+ """ Show tally results """
+ self.logger.info("Summary:")
+ self.logger.info("Totally records read: %i", self.total)
+ self.logger.info("Records successfully processed: %i", self.succeed)
+ self.logger.info("Records skipped: %i", self.skipped.total)
+ if self.skipped.total > 0:
+ self.logger.info("Out of those skipped,")
+ self.logger.info(" Invalid circRNA record: %i", self.skipped.invalid_record)
+ self.logger.info(" Insufficient evidence: %i", self.skipped.insufficient_evidence)
+
+class TallyTableSkipped():
+ """ Tally table for failed ones """
+ def __init__(self):
+ """ constructor """
+ self.invalid_gene_id:int = 0
+ self.invalid_position:int = 0
+ self.insufficient_evidence:int = 0
+ self.invalid_record:int = 0
+ self.total:int = 0
+
def parse_circexplorer(args:argparse.Namespace):
""" Parse circexplorer known circRNA results. """
logger = get_logger()
+ tally = TallyTable(logger)
input_path:Path = args.input_path
output_path:Path = args.output_path
@@ -104,11 +140,16 @@ def parse_circexplorer(args:argparse.Namespace):
circ_records:Dict[str, List[circ.CircRNAModel]] = {}
for record in CIRCexplorerParser.parse(input_path, args.circexplorer3):
+ tally.total += 1
if not args.circexplorer3:
if not record.is_valid(args.min_read_number):
+ tally.skipped.total += 1
+ tally.skipped.insufficient_evidence += 1
continue
elif not record.is_valid(args.min_read_number, args.min_fbr_circ, \
args.min_circ_score):
+ tally.skipped.total += 1
+ tally.skipped.insufficient_evidence += 1
continue
try:
circ_record = record.convert_to_circ_rna(anno, intron_start_range,
@@ -119,6 +160,8 @@ def parse_circexplorer(args:argparse.Namespace):
" Skipping it from parsing.",
record.name, record.isoform_name
)
+ tally.skipped.invalid_record += 1
+ tally.skipped.total += 1
continue
except err.IntronNotFoundError:
logger.warning(
@@ -126,6 +169,8 @@ def parse_circexplorer(args:argparse.Namespace):
" intron. Skipping it from parsing.",
record.name, record.isoform_name
)
+ tally.skipped.invalid_record += 1
+ tally.skipped.total += 1
continue
except:
logger.error('Exception raised from record: %s', record.name)
@@ -135,21 +180,20 @@ def parse_circexplorer(args:argparse.Namespace):
circ_records[gene_id] = []
circ_records[gene_id].append(circ_record)
- if not circ_records:
- logger.warning('No variant record is saved.')
- return
+ if circ_records:
+ genes_rank = anno.get_genes_rank()
+ ordered_keys = sorted(circ_records.keys(), key=lambda x:genes_rank[x])
- genes_rank = anno.get_genes_rank()
- ordered_keys = sorted(circ_records.keys(), key=lambda x:genes_rank[x])
+ records = []
+ for key in ordered_keys:
+ val = circ_records[key]
+ records.extend(val)
- records = []
- for key in ordered_keys:
- val = circ_records[key]
- records.extend(val)
+ metadata = common.generate_metadata(args)
- metadata = common.generate_metadata(args)
+ with open(output_path, 'w') as handle:
+ circ.io.write(records, metadata, handle)
- with open(output_path, 'w') as handle:
- circ.io.write(records, metadata, handle)
+ logger.info("CircRNA records written to disk.")
- logger.info("CircRNA records written to disk.")
+ tally.log()
diff --git a/moPepGen/cli/parse_fusion_catcher.py b/moPepGen/cli/parse_fusion_catcher.py
index c9f3ec42..1b71ecc4 100644
--- a/moPepGen/cli/parse_fusion_catcher.py
+++ b/moPepGen/cli/parse_fusion_catcher.py
@@ -2,13 +2,18 @@
[FusionCatcher](https://github.com/ndaniel/fusioncatcher) and save as a
GVF file. The GVF file can be later used to call variant peptides using
[callVariant](call-variant.md)."""
-from typing import List
+from __future__ import annotations
+from typing import TYPE_CHECKING
from pathlib import Path
import argparse
from moPepGen import get_logger, seqvar, parser, err
from moPepGen.cli import common
+if TYPE_CHECKING:
+ from typing import List
+ from logging import Logger
+
INPUT_FILE_FORMATS = ['.tsv', '.txt']
OUTPUT_FILE_FORMATS = ['.gvf']
@@ -42,6 +47,7 @@ def add_subparser_parse_fusion_catcher(subparsers:argparse._SubParsersAction):
default=5,
metavar='<number>'
)
+ common.add_args_skip_failed(p)
common.add_args_source(p)
common.add_args_reference(p, proteome=False)
common.add_args_debug_level(p)
@@ -49,9 +55,40 @@ def add_subparser_parse_fusion_catcher(subparsers:argparse._SubParsersAction):
common.print_help_if_missing_args(p)
return p
+class TallyTable():
+ """ Tally table """
+ def __init__(self, logger:Logger):
+ """ Constructor """
+ self.total:int = 0
+ self.succeed:int = 0
+ self.skipped:TallyTableSkipped = TallyTableSkipped()
+ self.logger = logger
+
+ def log(self):
+ """ Show tally results """
+ self.logger.info("Summary:")
+ self.logger.info("Totally records read: %i", self.total)
+ self.logger.info("Records successfully processed: %i", self.succeed)
+ self.logger.info("Records skipped: %i", self.skipped.total)
+ if self.skipped.total > 0:
+ self.logger.info("Out of those skipped,")
+ self.logger.info(" Invalid gene ID: %i", self.skipped.invalid_gene_id)
+ self.logger.info(" Invalid position: %i", self.skipped.invalid_position)
+ self.logger.info(" Insufficient evidence: %i", self.skipped.insufficient_evidence)
+
+class TallyTableSkipped():
+ """ Tally table for failed ones """
+ def __init__(self):
+ """ constructor """
+ self.invalid_gene_id:int = 0
+ self.invalid_position:int = 0
+ self.insufficient_evidence:int = 0
+ self.total:int = 0
+
def parse_fusion_catcher(args:argparse.Namespace) -> None:
""" Parse FusionCatcher output and save it in GVF format. """
logger = get_logger()
+ tally = TallyTable(logger)
# unpack args
fusion = args.input_path
output_path:Path = args.output_path
@@ -69,15 +106,26 @@ def parse_fusion_catcher(args:argparse.Namespace) -> None:
variants:List[seqvar.VariantRecord] = []
for record in parser.FusionCatcherParser.parse(fusion):
- if record.counts_of_common_mapping_reads > args.max_common_mapping:
- continue
- if record.spanning_unique_reads < args.min_spanning_unique:
+ tally.total += 1
+ if record.counts_of_common_mapping_reads > args.max_common_mapping \
+ or record.spanning_unique_reads < args.min_spanning_unique:
+ tally.skipped.insufficient_evidence += 1
+ tally.skipped.total += 1
continue
try:
var_records = record.convert_to_variant_records(anno, genome)
+ variants.extend(var_records)
+ tally.succeed += 1
except err.GeneNotFoundError:
+ tally.skipped.invalid_gene_id += 1
+ tally.skipped.total += 1
continue
- variants.extend(var_records)
+ except:
+ if args.skip_failed:
+ tally.skipped.total += 1
+ tally.skipped.invalid_position += 1
+ continue
+ raise
logger.info('FusionCatcher output %s loaded.', fusion)
@@ -95,3 +143,5 @@ def parse_fusion_catcher(args:argparse.Namespace) -> None:
seqvar.io.write(variants, output_path, metadata)
logger.info("Variants written to disk.")
+
+ tally.log()
diff --git a/moPepGen/cli/parse_reditools.py b/moPepGen/cli/parse_reditools.py
index b1542d8c..63ff9867 100644
--- a/moPepGen/cli/parse_reditools.py
+++ b/moPepGen/cli/parse_reditools.py
@@ -4,13 +4,17 @@
[callVariant](call-variant.md)
"""
from __future__ import annotations
+from typing import TYPE_CHECKING
import argparse
from pathlib import Path
-from typing import Dict, List
from moPepGen import get_logger, seqvar, parser
from moPepGen.cli import common
+if TYPE_CHECKING:
+ from typing import Dict, List
+ from logging import Logger
+
INPUT_FILE_FORMATS = ['.tsv', '.txt']
OUTPUT_FILE_FORMATS = ['.gvf']
@@ -76,9 +80,26 @@ def add_subparser_parse_reditools(subparsers:argparse._SubParsersAction):
common.print_help_if_missing_args(p)
return p
+class TallyTable():
+ """ Tally table """
+ def __init__(self, logger:Logger):
+ """ Constructor """
+ self.total:int = 0
+ self.succeed:int = 0
+ self.skipped:int = 0
+ self.logger = logger
+
+ def log(self):
+ """ Show tally results """
+ self.logger.info("Summary:")
+ self.logger.info("Totally records read: %i", self.total)
+ self.logger.info("Records successfully processed: %i", self.succeed)
+ self.logger.info("Records skipped: %i", self.skipped)
+
def parse_reditools(args:argparse.Namespace) -> None:
""" Parse REDItools output and save it in the GVF format. """
logger = get_logger()
+ tally = TallyTable(logger)
# unpack args
table_file:Path = args.input_path
output_path:Path = args.output_path
@@ -102,6 +123,7 @@ def parse_reditools(args:argparse.Namespace) -> None:
variants:Dict[str, List[seqvar.VariantRecord]] = {}
for record in parser.REDItoolsParser.parse(table_file, transcript_id_column):
+ tally.total += 1
_vars = record.convert_to_variant_records(
anno=anno,
min_coverage_alt=min_coverage_alt,
@@ -109,6 +131,10 @@ def parse_reditools(args:argparse.Namespace) -> None:
min_coverage_rna=min_coverage_rna,
min_coverage_dna=min_coverage_dna
)
+ if not _vars:
+ tally.skipped += 1
+ else:
+ tally.succeed += 1
for variant in _vars:
gene_id = variant.location.seqname
if gene_id not in variants:
@@ -139,3 +165,5 @@ def parse_reditools(args:argparse.Namespace) -> None:
seqvar.io.write(all_records, output_path, metadata)
logger.info('Variants written to disk.')
+
+ tally.log()
diff --git a/moPepGen/cli/parse_rmats.py b/moPepGen/cli/parse_rmats.py
index 2b6c82f6..f0f9a246 100644
--- a/moPepGen/cli/parse_rmats.py
+++ b/moPepGen/cli/parse_rmats.py
@@ -7,14 +7,18 @@
[callVariant](call-variant.md)
"""
from __future__ import annotations
+from typing import TYPE_CHECKING
import argparse
-from typing import Dict, Set
from pathlib import Path
from moPepGen import get_logger, seqvar
from moPepGen.parser import RMATSParser
from moPepGen.cli import common
+if TYPE_CHECKING:
+ from typing import Dict, Set
+ from logging import Logger
+
INPUT_FILE_FORMATS = ['.tsv', '.txt']
OUTPUT_FILE_FORMATS = ['.gvf']
@@ -102,9 +106,27 @@ def add_subparser_parse_rmats(subparsers:argparse._SubParsersAction):
common.print_help_if_missing_args(p)
return p
+class TallyTable():
+ """ Tally table """
+ def __init__(self, logger:Logger):
+ """ Constructor """
+ self.total:int = 0
+ self.succeed:int = 0
+ self.skipped:int = 0
+ self.logger = logger
+
+ def log(self):
+ """ Show tally results """
+ self.logger.info("Summary:")
+ self.logger.info("Totally records read: %i", self.total)
+ self.logger.info("Records successfully processed: %i", self.succeed)
+ self.logger.info("Records skipped: %i", self.skipped)
+
+
def parse_rmats(args:argparse.Namespace) -> None:
""" Parse rMATS results into TSV """
logger = get_logger()
+ tally = TallyTable(logger)
skipped_exon = args.skipped_exon
alternative_5 = args.alternative_5_splicing
@@ -136,6 +158,7 @@ def parse_rmats(args:argparse.Namespace) -> None:
if path:
logger.info("Start parsing %s file %s", event_type, path)
for record in RMATSParser.parse(path, event_type):
+ tally.total += 1
try:
var_records = record.convert_to_variant_records(
anno=anno, genome=genome,
@@ -144,6 +167,10 @@ def parse_rmats(args:argparse.Namespace) -> None:
except:
logger.error(record.gene_id)
raise
+ if var_records:
+ tally.succeed += 1
+ else:
+ tally.skipped += 1
for var_record in var_records:
tx_id = var_record.transcript_id
if tx_id not in variants:
@@ -168,3 +195,5 @@ def parse_rmats(args:argparse.Namespace) -> None:
seqvar.io.write(variants_sorted, output_path, metadata)
logger.info('Variants written to disk.')
+
+ tally.log()
diff --git a/moPepGen/cli/parse_star_fusion.py b/moPepGen/cli/parse_star_fusion.py
index aa44909f..db3bd065 100644
--- a/moPepGen/cli/parse_star_fusion.py
+++ b/moPepGen/cli/parse_star_fusion.py
@@ -3,12 +3,16 @@
GVF file. The GVF file can be later used to call variant peptides using
[callVariant](call-variant.md)."""
from __future__ import annotations
+from typing import TYPE_CHECKING
import argparse
-from typing import List
from moPepGen import get_logger, seqvar, parser, err
from moPepGen.cli import common
+if TYPE_CHECKING:
+ from typing import List
+ from logging import Logger
+
INPUT_FILE_FORMATS = ['.tsv', '.txt']
OUTPUT_FILE_FORMATS = ['.gvf']
@@ -37,6 +41,7 @@ def add_subparser_parse_star_fusion(subparsers:argparse._SubParsersAction):
default=5.0,
metavar='<number>'
)
+ common.add_args_skip_failed(p)
common.add_args_source(p)
common.add_args_reference(p, proteome=False)
common.add_args_debug_level(p)
@@ -44,9 +49,40 @@ def add_subparser_parse_star_fusion(subparsers:argparse._SubParsersAction):
common.print_help_if_missing_args(p)
return p
+class TallyTable():
+ """ Tally table """
+ def __init__(self, logger:Logger):
+ """ Constructor """
+ self.total:int = 0
+ self.succeed:int = 0
+ self.skipped:TallyTableSkipped = TallyTableSkipped()
+ self.logger = logger
+
+ def log(self):
+ """ Show tally results """
+ self.logger.info("Summary:")
+ self.logger.info("Totally records read: %i", self.total)
+ self.logger.info("Records successfully processed: %i", self.succeed)
+ self.logger.info("Records skipped: %i", self.skipped.total)
+ if self.skipped.total > 0:
+ self.logger.info("Out of those skipped,")
+ self.logger.info(" Invalid gene ID: %i", self.skipped.invalid_gene_id)
+ self.logger.info(" Invalid position: %i", self.skipped.invalid_position)
+ self.logger.info(" Insufficient evidence: %i", self.skipped.insufficient_evidence)
+
+class TallyTableSkipped():
+ """ Tally table for failed ones """
+ def __init__(self):
+ """ constructor """
+ self.invalid_gene_id:int = 0
+ self.invalid_position:int = 0
+ self.insufficient_evidence:int = 0
+ self.total:int = 0
+
def parse_star_fusion(args:argparse.Namespace) -> None:
""" Parse the STAR-Fusion's output and save it in GVF format. """
logger = get_logger()
+ tally = TallyTable(logger)
# unpack args
fusion = args.input_path
common.validate_file_format(
@@ -64,13 +100,25 @@ def parse_star_fusion(args:argparse.Namespace) -> None:
variants:List[seqvar.VariantRecord] = []
for record in parser.STARFusionParser.parse(fusion):
+ tally.total += 1
if record.est_j < args.min_est_j:
+ tally.skipped.insufficient_evidence += 1
+ tally.skipped.total += 1
continue
try:
var_records = record.convert_to_variant_records(anno, genome)
+ variants.extend(var_records)
+ tally.succeed += 1
except err.GeneNotFoundError:
+ tally.skipped.invalid_gene_id += 1
+ tally.skipped.total += 1
continue
- variants.extend(var_records)
+ except:
+ if args.skip_failed:
+ tally.skipped.invalid_position += 1
+ tally.skipped.total += 1
+ continue
+ raise
logger.info('STAR-Fusion output %s loaded.', fusion)
@@ -88,3 +136,5 @@ def parse_star_fusion(args:argparse.Namespace) -> None:
seqvar.io.write(variants, output_path, metadata)
logger.info('Variant info written to disk.')
+
+ tally.log()
diff --git a/moPepGen/cli/parse_vep.py b/moPepGen/cli/parse_vep.py
index eb7329d5..60edc0ed 100644
--- a/moPepGen/cli/parse_vep.py
+++ b/moPepGen/cli/parse_vep.py
@@ -59,7 +59,8 @@ def __init__(self, logger:Logger):
def log(self):
""" Show tally results """
- self.logger.info("Records successfully processed: %i", self.total)
+ self.logger.info("Totally records read: %i", self.total)
+ self.logger.info("Records successfully processed: %i", self.succeed)
self.logger.info("Records failed: %i", self.failed.total)
if self.failed.total > 0:
self.logger.info("Out of those failed,")
diff --git a/moPepGen/util/fuzz_test.py b/moPepGen/util/fuzz_test.py
index 7941d7cb..84d00f2c 100644
--- a/moPepGen/util/fuzz_test.py
+++ b/moPepGen/util/fuzz_test.py
@@ -639,6 +639,7 @@ def call_variants(self):
args.debug_level = 1
args.timeout_seconds = 300
args.coding_novel_orf = False
+ args.skip_failed = False
call_variant_peptide(args=args)
def brute_force(self):
diff --git a/moPepGen/util/validate_variant_calling.py b/moPepGen/util/validate_variant_calling.py
index 9c0e66bc..3513cdbe 100644
--- a/moPepGen/util/validate_variant_calling.py
+++ b/moPepGen/util/validate_variant_calling.py
@@ -128,6 +128,7 @@ def call_variant(gvf_files:Path, ref_dir:Path, output_fasta:Path, graph_output_d
args.noncanonical_transcripts = False
args.threads = 1
args.timeout_seconds = 900
+ args.skip_failed = False
call_variant_peptide(args=args)
def call_brute_force(gvf_files:Path, ref_dir:Path, output_path:str, force:bool,
diff --git a/test/integration/test_call_variant_peptides.py b/test/integration/test_call_variant_peptides.py
index c02cb336..f57c83f3 100644
--- a/test/integration/test_call_variant_peptides.py
+++ b/test/integration/test_call_variant_peptides.py
@@ -3,6 +3,7 @@
from typing import List
from pathlib import Path
import sys
+from unittest.mock import Mock
import subprocess as sp
from test.integration import TestCaseIntegration
from test.unit import create_variant
@@ -47,6 +48,7 @@ def create_base_args() -> argparse.Namespace:
args.invalid_protein_as_noncoding = False
args.threads = 1
args.timeout_seconds = 1800
+ args.skip_failed = False
return args
class TestCallVariantPeptides(TestCaseIntegration):
@@ -153,6 +155,33 @@ def test_call_variant_peptide_case1_sect_and_w2f(self):
expected = {'vep_moPepGen.fasta', 'vep_moPepGen_peptide_table.txt'}
self.assertEqual(files, expected)
+ def test_call_variant_peptide_skip_failed(self):
+ """ Test errors were handled by --skip-failed in callVariant """
+ # pylint: disable=import-outside-toplevel
+ import importlib.util
+ spec = importlib.util.spec_from_file_location(
+ "moPepGen.cli.call_variant_peptide",
+ Path(__file__).parent.parent.parent/"moPepGen/cli/call_variant_peptide.py"
+ )
+ call_variant_peptide_module = importlib.util.module_from_spec(spec)
+ sys.modules["moPepGen.cli.call_variant_peptide"] = call_variant_peptide_module
+ spec.loader.exec_module(call_variant_peptide_module)
+
+ call_variant_peptide_module.call_peptide_main = Mock(side_effect=ValueError())
+
+ args = create_base_args()
+ args.input_path = [self.data_dir/'vep'/'vep_gSNP.gvf']
+ args.output_path = self.work_dir/'vep_moPepGen.fasta'
+ args.genome_fasta = self.data_dir/'genome.fasta'
+ args.annotation_gtf = self.data_dir/'annotation.gtf'
+ args.proteome_fasta = self.data_dir/'translate.fasta'
+
+ with self.assertRaises(ValueError):
+ call_variant_peptide_module.call_variant_peptide(args)
+
+ args.skip_failed = True
+ call_variant_peptide_module.call_variant_peptide(args)
+
def test_call_variant_peptide_case2(self):
""" Test variant peptide calling with fusion """
args = create_base_args()
diff --git a/test/integration/test_parse_arriba.py b/test/integration/test_parse_arriba.py
index 5df7e2ec..6876df64 100644
--- a/test/integration/test_parse_arriba.py
+++ b/test/integration/test_parse_arriba.py
@@ -2,14 +2,15 @@
import argparse
import subprocess as sp
import sys
+from unittest import mock
from test.integration import TestCaseIntegration
from moPepGen import cli
class TestParseArriba(TestCaseIntegration):
""" Test cases for moPepGen parseSTARFusion """
- def test_parse_arriba(self):
- """ Test parseArriba """
+ def create_base_args(self) -> argparse.Namespace:
+ """ Create base args """
args = argparse.Namespace()
args.command = 'parseArriba'
args.input_path = self.data_dir/'fusion/arriba.txt'
@@ -24,6 +25,12 @@ def test_parse_arriba(self):
args.min_split_read2 = 1
args.min_confidence = 'medium'
args.quiet = False
+ args.skip_failed = False
+ return args
+
+ def test_parse_arriba(self):
+ """ Test parseArriba """
+ args = self.create_base_args()
cli.parse_arriba(args)
files = {str(file.name) for file in self.work_dir.glob('*')}
expected = {'arriba.gvf'}
@@ -47,3 +54,16 @@ def test_parse_arriba_cli(self):
print(cmd)
print(res.stderr.decode('utf-8'))
raise
+
+ @mock.patch(
+ "moPepGen.parser.ArribaParser.ArribaRecord.convert_to_variant_records",
+ new=mock.MagicMock(side_effect=ValueError())
+ )
+ def test_parse_arriba_skip_failed(self):
+ """ Test parseArriba with skip failed """
+ args = self.create_base_args()
+ with self.assertRaises(ValueError):
+ cli.parse_arriba(args)
+
+ args.skip_failed = True
+ cli.parse_arriba(args)
diff --git a/test/integration/test_parse_fusion_catcher.py b/test/integration/test_parse_fusion_catcher.py
index 61442ca4..d15a030b 100644
--- a/test/integration/test_parse_fusion_catcher.py
+++ b/test/integration/test_parse_fusion_catcher.py
@@ -3,6 +3,7 @@
from pathlib import Path
import subprocess as sp
import sys
+from unittest import mock
from test.unit import load_references
from test.integration import TestCaseIntegration
from moPepGen import cli, parser
@@ -54,11 +55,10 @@ def test_fusioncatcher_parser(self):
right_seq = gene2_seq.seq[_start2:_end2]
self.assertEqual(str(right_seq), fusion_seq[1])
- def test_parse_fusion_catcher(self):
- """ Test parseFusionCatcher """
+ def create_base_args(self) -> argparse.Namespace:
+ """ Create base args """
args = argparse.Namespace()
args.command = 'parseFusionCatcher'
- args.input_path = self.data_dir/'fusion/fusion_catcher.txt'
args.source = 'Fusion'
args.index_dir = None
args.genome_fasta = self.data_dir/'genome.fasta'
@@ -68,9 +68,30 @@ def test_parse_fusion_catcher(self):
args.output_path = self.work_dir/'fusion_catcher.gvf'
args.max_common_mapping = 0
args.min_spanning_unique = 5
+ args.skip_failed = False
args.quiet = True
+ return args
+
+ def test_parse_fusion_catcher(self):
+ """ Test parseFusionCatcher """
+ args = self.create_base_args()
+ args.input_path = self.data_dir/'fusion/fusion_catcher.txt'
cli.parse_fusion_catcher(args)
files = {str(file.name) for file in self.work_dir.glob('*')}
expected = {'fusion_catcher.gvf'}
self.assertEqual(files, expected)
self.assert_gvf_order(args.output_path, args.annotation_gtf)
+
+ @mock.patch(
+ "moPepGen.parser.FusionCatcherParser.FusionCatcherRecord.convert_to_variant_records",
+ new=mock.MagicMock(side_effect=ValueError())
+ )
+ def test_parse_fusion_catcher_skip_failed(self):
+ """ Test parseFusionCatcher with --skip-failed """
+ args = self.create_base_args()
+ args.input_path = self.data_dir/'fusion/fusion_catcher.txt'
+ with self.assertRaises(ValueError):
+ cli.parse_fusion_catcher(args)
+
+ args.skip_failed = True
+ cli.parse_fusion_catcher(args)
diff --git a/test/integration/test_parse_star_fusion.py b/test/integration/test_parse_star_fusion.py
index 0507f5ce..aded4686 100644
--- a/test/integration/test_parse_star_fusion.py
+++ b/test/integration/test_parse_star_fusion.py
@@ -2,6 +2,7 @@
import argparse
import subprocess as sp
import sys
+from unittest import mock
from test.integration import TestCaseIntegration
from moPepGen import cli, seqvar
from moPepGen.cli.common import load_references
@@ -27,12 +28,11 @@ def test_parse_star_fusion_cli(self):
print(res.stderr.decode('utf-8'))
raise
- def test_star_fusion_record_case1(self):
- """ Test parseSTARFusion """
+ def create_base_args(self) -> argparse.Namespace:
+ """ Create base args """
args = argparse.Namespace()
args.command = 'parseSTARFusion'
args.source = 'Fusion'
- args.input_path = self.data_dir/'fusion/star_fusion.txt'
args.index_dir = None
args.genome_fasta = self.data_dir/'genome.fasta'
args.annotation_gtf = self.data_dir/'annotation.gtf'
@@ -40,6 +40,13 @@ def test_star_fusion_record_case1(self):
args.output_path = self.work_dir/'star_fusion.gvf'
args.min_est_j = 3.0
args.quiet = True
+ args.skip_failed =False
+ return args
+
+ def test_star_fusion_record_case1(self):
+ """ Test parseSTARFusion """
+ args = self.create_base_args()
+ args.input_path = self.data_dir/'fusion/star_fusion.txt'
cli.parse_star_fusion(args)
files = {str(file.name) for file in self.work_dir.glob('*')}
expected = {'star_fusion.gvf'}
@@ -64,19 +71,23 @@ def test_star_fusion_record_case1(self):
def test_parse_star_fusion_case1(self):
""" test parseSTARFusion case1 """
- args = argparse.Namespace()
- args.command = 'parseSTARFusion'
+ args = self.create_base_args()
args.input_path = self.data_dir/'fusion/star_fusion.txt'
- args.source = 'Fusion'
- args.index_dir = None
- args.genome_fasta = self.data_dir/'genome.fasta'
- args.annotation_gtf = self.data_dir/'annotation.gtf'
- args.reference_source = None
- args.output_path = self.work_dir/'star_fusion.gvf'
- args.min_est_j = 3.0
- args.quiet = True
cli.parse_star_fusion(args)
files = {str(file.name) for file in self.work_dir.glob('*')}
expected = {'star_fusion.gvf'}
self.assertEqual(files, expected)
self.assert_gvf_order(args.output_path, args.annotation_gtf)
+
+ @mock.patch(
+ "moPepGen.parser.STARFusionParser.STARFusionRecord.convert_to_variant_records",
+ new=mock.MagicMock(side_effect=ValueError())
+ )
+ def test_parse_star_fusion_skip_failed(self):
+ """ test parseSTARFusion case1 """
+ args = self.create_base_args()
+ args.input_path = self.data_dir/'fusion/star_fusion.txt'
+ with self.assertRaises(ValueError):
+ cli.parse_star_fusion(args)
+ args.skip_failed = True
+ cli.parse_star_fusion(args)