enterococcus-plasmid-training / prepared_files.json
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{
"configs": {
"enterococcus_clean_v2_host_assemblies": {
"columns": [
"assembly_accession",
"sequence_db_assembly_accession",
"sequence_db_source",
"primary_evidence_assembly_accession",
"evidence_assembly_accessions",
"evidence_sources",
"manifest_match_types",
"n_evidence_assembly_accessions",
"taxid",
"organism_name",
"source_db",
"assembly_level",
"target_group",
"enterococcus_match_evidence",
"n_representative_plasmids",
"n_member_plasmids",
"n_link_rows",
"chunk_id",
"chunk_path",
"n_rows",
"n_plasmid_rows",
"n_non_plasmid_rows",
"n_bp",
"in_sequence_db",
"genus_taxid",
"host_taxa_id",
"non_plasmid_contigs",
"non_plasmid_bp",
"has_non_plasmid_contigs"
],
"config_name": "enterococcus_clean_v2_host_assemblies",
"contains_sequence_column": false,
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"enterococcus_clean_v2_host_contigs": {
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"sequence_id",
"new_contig_id",
"original_contig_id",
"source_contig_id",
"sampler_contig_id",
"seq_length",
"chunk_path"
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"enterococcus_clean_v2_plasmid_to_assembly_links": {
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"source_db",
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"seq_length",
"chr_name",
"sequence_name",
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"genbank_seq_accession",
"accession_class",
"molecule_type",
"plasmid_evidence_fields",
"plasmid_evidence_terms",
"ftp_path",
"assembly_unit",
"role",
"gc_percent",
"ucsc_style_name",
"unlocalized_count",
"assembly_unplaced_count",
"source_batch_id",
"source_requested_accession",
"source_raw_file",
"plasmid_confidence",
"plasmid_heuristic_version",
"has_refseq",
"has_genbank",
"assembly_source_priority",
"_source_link_row",
"paired_assembly_accession",
"assembly_pair_key",
"refseq_assembly_accession",
"genbank_assembly_accession",
"enterococcus_genus_taxid",
"enterococcus_match_evidence",
"sequence_db_assembly_accession",
"manifest_match_type",
"requested_source",
"sequence_db_source"
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"contains_sequence_column": false,
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"enterococcus_clean_v2_plasmids": {
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"cluster_id",
"cluster_size",
"sequence_md5",
"n_member_assemblies",
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"orientation",
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"n_near_complete_chromosome_contigs",
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"config_name": "enterococcus_clean_v2_plasmids",
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"enterococcus_clean_v2_segments": {
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"best_plasmid_qcov",
"best_plasmid_pid",
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"best_plasmid_length",
"host_minimap_aligned",
"n_paf_records",
"best_plasmid_id_ignore_top10",
"best_plasmid_qcov_ignore_top10",
"best_plasmid_pid_ignore_top10",
"best_plasmid_cov_bp_ignore_top10",
"best_plasmid_aln_bp_ignore_top10",
"filtered_by_plasmid_ignore_top10",
"recoverable_if_ignore_top10",
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"newly_filtered_if_ignore_top10",
"host_segment_id",
"host_candidate_id",
"training_eligible_current_clean",
"is_problematic_segment",
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