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added several exporter functions to go from PMO to various tables; #64

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Merged
kathrynmurie merged 2 commits into from
Nov 25, 2025
Merged

added several exporter functions to go from PMO to various tables; #64

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b0b9685
added several exporter functions to go from PMO to various tables;
nickjhathaway Nov 25, 2025
673c451
Merge branch 'develop' into feature/add_exporter_functions
nickjhathaway Nov 25, 2025
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81 changes: 67 additions & 14 deletions src/pmotools/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@
from pmotools.scripts.extractors_from_pmo.extract_pmo_with_read_filter import (
extract_pmo_with_read_filter,
)
from pmotools.scripts.extractors_from_pmo.extract_allele_table import (
from pmotools.scripts.pmo_to_tables.extract_allele_table import (
extract_for_allele_table,
)

Expand Down Expand Up @@ -66,13 +66,37 @@
)

# panel info subset
from pmotools.scripts.extract_info_from_pmo.extract_insert_of_panels import (
from pmotools.scripts.pmo_to_tables.extract_insert_of_panels import (
extract_insert_of_panels,
)
from pmotools.scripts.extract_info_from_pmo.extract_refseq_of_inserts_of_panels import (
from pmotools.scripts.pmo_to_tables.extract_refseq_of_inserts_of_panels import (
extract_refseq_of_inserts_of_panels,
)

# pmo to tables

from pmotools.scripts.pmo_to_tables.export_specimen_meta_table import (
export_specimen_meta_table,
)
from pmotools.scripts.pmo_to_tables.export_library_sample_meta_table import (
export_library_sample_meta_table,
)
from pmotools.scripts.pmo_to_tables.export_project_info_meta_table import (
export_project_info_meta_table,
)
from pmotools.scripts.pmo_to_tables.export_sequencing_info_meta_table import (
export_sequencing_info_meta_table,
)
from pmotools.scripts.pmo_to_tables.export_specimen_travel_meta_table import (
export_specimen_travel_meta_table,
)
from pmotools.scripts.pmo_to_tables.export_target_info_meta_table import (
export_target_info_meta_table,
)
from pmotools.scripts.pmo_to_tables.export_panel_info_meta_table import (
export_panel_info_meta_table,
)


@dataclass(frozen=True)
class PmoCommand:
Expand Down Expand Up @@ -115,17 +139,6 @@ class PmoCommand:
"extract_pmo_with_read_filter": PmoCommand(
extract_pmo_with_read_filter, "Extract with a read filter"
),
"extract_allele_table": PmoCommand(
extract_for_allele_table,
"Extract allele tables for tools like dcifer or moire",
),
"extract_insert_of_panels": PmoCommand(
extract_insert_of_panels, "Extract inserts of panels from a PMO"
),
"extract_refseq_of_inserts_of_panels": PmoCommand(
extract_refseq_of_inserts_of_panels,
"Extract ref_seq of panel inserts from a PMO",
),
},
"working_with_multiple_pmos": {
"combine_pmos": PmoCommand(
Expand Down Expand Up @@ -160,6 +173,46 @@ class PmoCommand:
validate_pmo, "Validate a PMO file against a JSON Schema"
)
},
"pmo_to_table": {
"export_specimen_meta_table": PmoCommand(
export_specimen_meta_table, "export the specimen meta table from a PMO file"
),
"export_library_sample_meta_table": PmoCommand(
export_library_sample_meta_table,
"export the library_sample meta table from a PMO file",
),
"export_project_info_meta_table": PmoCommand(
export_project_info_meta_table,
"export the project_info meta table from a PMO file",
),
"export_sequencing_info_meta_table": PmoCommand(
export_sequencing_info_meta_table,
"export the sequencing_info meta table from a PMO file",
),
"export_specimen_travel_meta_table": PmoCommand(
export_specimen_travel_meta_table,
"export the specimen travel_info meta table from a PMO file",
),
"export_target_info_meta_table": PmoCommand(
export_target_info_meta_table,
"export the target info meta table from a PMO file",
),
"export_panel_info_meta_table": PmoCommand(
export_panel_info_meta_table,
"export the panel info meta table from a PMO file",
),
"extract_allele_table": PmoCommand(
extract_for_allele_table,
"Extract allele tables for tools like dcifer or moire",
),
"extract_insert_of_panels": PmoCommand(
extract_insert_of_panels, "Extract inserts of panels from a PMO"
),
"extract_refseq_of_inserts_of_panels": PmoCommand(
extract_refseq_of_inserts_of_panels,
"Extract ref_seq of panel inserts from a PMO",
),
},
}


Expand Down
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