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Remove sample annotation functionality from geo-import process #1334

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May 3, 2024
Merged

Remove sample annotation functionality from geo-import process #1334

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1 change: 1 addition & 0 deletions docs/CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ Changed
- Rewrite ``expression-aggregator`` process to Python and make it
compatible with the new annotation model
- Use GRCh38.109 genome annotation version in snpEff processes
- Remove sample annotation functionality from ``geo-import`` process

Fixed
-----
Expand Down
147 changes: 1 addition & 146 deletions resolwe_bio/processes/workflows/geo_import.py
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Expand Up @@ -46,141 +46,6 @@ def create_metadata(gse, run_info):
return metadata.set_index(["Sample name"], drop=False)


def construct_annotation(metadata, sample_name):
"""Construct sample annotations from metadata.

Dictionary with GEO metadata that matches the sample annotation
schema is created. Attributes under general that have no
predetermined choices are matched with our naming if they
exist in the metadata. Other fields with choices and the
experimental section are filled separately.
"""

sample_metadata = metadata.loc[sample_name]
sample_metadata = sample_metadata.fillna("")
annotation = {}

species = [
"Caenorhabditis elegans",
"Cricetulus griseus",
"Dictyostelium discoideum",
"Dictyostelium purpureum",
"Drosophila melanogaster",
"Homo sapiens",
"Macaca mulatta",
"Mus musculus",
"Odocoileus virginianus texanus",
"Rattus norvegicus",
"Solanum tuberosum",
]
molecule_choices = [
"total_rna",
"polya_rna",
"cytoplasmic_rna",
"nuclear_rna",
"genomic_dna",
"protein",
"other",
]

assay_types = [
"rna-seq",
"chip-seq",
"atac-seq",
"chipmentation",
"dna-seq",
"nanostring",
"microarray",
"edge-seq",
"other",
]

platform_types = [
"nextseq_500",
"nextseq_550",
"nextseq_550_dx",
"nextseq_1000",
"nextseq_2000",
"hiseq_2500",
"hiseq_2000",
"novaseq_6000",
"novaseq_6000_dx",
"novaseq_x",
"iseq_100",
"miniseq",
"miseq",
"miseq_dx",
"other",
]

if (
"organism_ch1" in metadata.columns
and sample_metadata["organism_ch1"] in species
):
annotation["general.species"] = sample_metadata["organism_ch1"]

if "contact_name" in metadata.columns:
annotation["general.annotator"] = sample_metadata["contact_name"].replace(
",,", " "
)

if "description" in metadata.columns:
annotation["general.description"] = sample_metadata["description"]

if "cell line" in metadata.columns:
annotation["biospecimen_information.experimental_model"] = "cell_line"
annotation["cell_line_information.cell_line_name"] = sample_metadata[
"cell line"
]
elif "tissue" in metadata.columns:
annotation["biospecimen_information.experimental_model"] = "tissue"

if "source_name_ch1" in metadata.columns:
annotation["biospecimen_information.source"] = sample_metadata[
"source_name_ch1"
]

if "cell type" in metadata.columns:
annotation["cell_line_information.cell_type"] = sample_metadata["cell type"]

if "treatment_protocol_ch1" in metadata.columns:
annotation["cell_line_information.treatment_protocol"] = sample_metadata[
"treatment_protocol_ch1"
]

if "library_strategy" in metadata.columns:
formated_assay = sample_metadata["library_strategy"].lower().replace(" ", "-")
if formated_assay in assay_types:
annotation["sample_details.assay_type"] = formated_assay

if "extract_protocol_ch1" in metadata.columns:
annotation["sample_details.extract_protocol"] = sample_metadata[
"extract_protocol_ch1"
]

if "growth_protocol_ch1" in metadata.columns:
annotation["sample_details.growth_protocol"] = sample_metadata[
"growth_protocol_ch1"
]

if "molecule_ch1" in metadata.columns:
formated_molecule = sample_metadata["molecule_ch1"].lower().replace(" ", "_")
if formated_molecule in molecule_choices:
annotation["sample_details.library_type"] = formated_molecule

if "instrument_model" in metadata.columns:
formated_platform = (
sample_metadata["instrument_model"]
.replace("Illumina ", "")
.lower()
.replace(" ", "_")
)
if formated_platform in platform_types:
annotation["sample_details.platform"] = formated_platform

return annotation


class GeoImport(Process):
"""Import all runs from a GEO Series.

Expand Down Expand Up @@ -224,7 +89,7 @@ class GeoImport(Process):
},
}
data_name = "{{ gse_accession }}"
version = "2.7.2"
version = "2.8.0"
process_type = "data:geo"
category = "Import"
scheduling_class = SchedulingClass.BATCH
Expand Down Expand Up @@ -510,13 +375,3 @@ def run(self, inputs, outputs):
metadata = pd.concat(metadata_tables.values(), join="outer", ignore_index=False)
metadata.to_csv(meta_file, sep="\t", index=False)
self.run_process("upload-metadata-unique", {"src": meta_file})

for entity_name in metadata["Sample name"].values:
objects = Data.filter(entity__name=entity_name)
if len(objects) > 1:
self.warning(
f"Multiple samples with entity name {entity_name} are present, annotation will be added only "
"to the last one"
)
obj = objects[-1]
obj.entity.annotations = construct_annotation(metadata, obj.entity_name)
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