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constants.py
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import os
SQL_BATCH_UPLOAD_ROWS = 1000
SQL_BATCH_DOWNLOAD_ROWS = 10000
DATA_DIR = "data"
OXYTRI_MAC_2020_GENE_GFF = os.path.join(DATA_DIR, "O_trifallax_2020-upd3.gff3")
OXYTRI_MAC_2020_GENE_TSV = os.path.join(DATA_DIR, "O_trifallax_2020-upd3_gene.tsv")
OXYTRI_MAC_2012_GENE_GFF = os.path.join(DATA_DIR, "Oxytricha_trifallax_022112.gff3")
OXYTRI_MAC_2012_GENE_TSV = os.path.join(DATA_DIR, "Oxytricha_trifallax_022112_gene.tsv")
OXYTRI_MIC_2014_GENE_GFF = os.path.join(DATA_DIR, "oxy_tri_jrb310_mic_2014.gff")
OXYTRI_MIC_2014_GENE_TSV = os.path.join(DATA_DIR, "oxy_tri_jrb310_mic_2014_gene.tsv")
OXYTRI_MIC_2014_GENE_HIGHTXN_GFF = os.path.join(DATA_DIR, "tglo_final_hightxn.gff")
OXYTRI_MIC_2014_GENE_HIGHTXN_TSV = os.path.join(DATA_DIR, "tglo_final_hightxn.tsv")
OXYTRI_MIC_2014_GENE_LOWTXN_GFF = os.path.join(DATA_DIR, "tglo_final_lowtxn.gff")
OXYTRI_MIC_2014_GENE_LOWTXN_TSV = os.path.join(DATA_DIR, "tglo_final_lowtxn.tsv")
TETSP_MAC_2015_GENE_GFF = os.path.join(DATA_DIR, "MDS_IES_DB_renamed_tetpusstrmac_2019.gff3")
TETSP_MAC_2015_GENE_TSV = os.path.join(DATA_DIR, "MDS_IES_DB_renamed_tetpusstrmac_2019.tsv")
EUPWOO_MAC_2022_GENE_GFF = os.path.join(DATA_DIR, "NCBI_renamed_oriented_Ewoo_EVM.all.v4.4.gff3")
EUPWOO_MAC_2022_GENE_TSV = os.path.join(DATA_DIR, "NCBI_renamed_oriented_Ewoo_EVM.all.v4.4.tsv")
OXYTRI_MAC_2012_ALIAS = os.path.join(DATA_DIR, "oxy_tri_jrb310_mac_2012_alias.tsv")
OXYTRI_MAC_2020_ALIAS = os.path.join(DATA_DIR, "oxy_tri_jrb310_mac_2020_alias.tsv")
OXYTRI_MIC_2014_ALIAS = os.path.join(DATA_DIR, "oxy_tri_jrb310_mic_2014_alias.tsv")
TETSP_MAC_2015_ALIAS = os.path.join(DATA_DIR, "tet_sp_sej2015_mac_2015_alias.tsv")
TETSP_MIC_2022_ALIAS = os.path.join(DATA_DIR, "tet_sp_sej2015_mic_2022_alias.tsv")
EUPWOO_MAC_2022_ALIAS = os.path.join(DATA_DIR, "eup_woo_iz01_mac_2022_alias.tsv")
EUPWOO_MIC_2022_ALIAS = os.path.join(DATA_DIR, "eup_woo_iz01_mic_2022_alias.tsv")
OXYTRI_MAC_2020_VARIANT = os.path.join(DATA_DIR, "oxy_tri_jrb310_mac_2020_variant.tsv")
OXYTRI_MAC_2012_PROTEIN = os.path.join(DATA_DIR, "Oxytricha_trifallax_022112_aa.tsv")
OXYTRI_MAC_2020_PROTEIN = os.path.join(DATA_DIR, "oxytrijrb310pacbio_aa.tsv")
TABLE_DUMP_LIST = [
"alias",
"contig",
"count",
"coverage",
"gene",
"ies_strict",
"ies_weak",
"match",
"parameter",
"pointer",
"properties",
"protein",
"stats",
"variant",
]
PRESETS = {
"none": {
"mac_name_regex": ".*",
"mic_name_regex": ".*",
},
"oxytri_mac2012_mic2014": {
"mac_name_regex": "Contig.*",
"mic_name_regex": "OXYTRI.*",
"gene_files": [
OXYTRI_MAC_2012_GENE_TSV,
OXYTRI_MIC_2014_GENE_TSV,
OXYTRI_MIC_2014_GENE_HIGHTXN_TSV,
OXYTRI_MIC_2014_GENE_LOWTXN_TSV,
],
"alias_files": [
{"file": OXYTRI_MAC_2012_ALIAS, "table": "contig", "nucleus": "mac"},
{"file": OXYTRI_MIC_2014_ALIAS, "table": "contig", "nucleus": "mic"},
],
"protein_files": [
OXYTRI_MAC_2012_PROTEIN
],
"name": "Oxytricha trifallax JRB310 (MAC 2013/MIC 2014)",
"description": "Oxytricha trifallax JRB310 - SDRAP MDS/IES Annotation - MAC 2013 - MIC 2014",
"organism": "oxy_tri_jrb310",
"assembly": "mac_2012,mic_2014",
"url": "oxy_tri_jrb310_mac_2013_mic_2014",
"genus": "Oxytricha",
"species": "Oxytricha trifallax",
"strain": "JRB310",
"taxonomy_id": "1172189",
},
"oxytri_mac2020_mic2014": {
"mac_name_regex": "Contig.*",
"mic_name_regex": "OXYTRI.*",
"gene_files": [
OXYTRI_MAC_2020_GENE_TSV,
OXYTRI_MIC_2014_GENE_TSV,
OXYTRI_MIC_2014_GENE_HIGHTXN_TSV,
OXYTRI_MIC_2014_GENE_LOWTXN_TSV,
],
"alias_files": [
{"file": OXYTRI_MAC_2020_ALIAS, "table": "contig", "nucleus": "mac"},
{"file": OXYTRI_MIC_2014_ALIAS, "table": "contig", "nucleus": "mic"},
],
"variant_files": [
OXYTRI_MAC_2020_VARIANT
],
"protein_files": [
OXYTRI_MAC_2020_PROTEIN
],
"name": "Oxytricha trifallax JRB310 (MAC 2019/MIC 2014)",
"description": "Oxytricha trifallax JRB310 - SDRAP MDS/IES Annotation - MAC 2019 - MIC 2014",
"organism": "oxy_tri_jrb310",
"assembly": "mac_2020,mic_2014",
"url": "oxy_tri_jrb310_mac_2019_mic_2014",
"genus": "Oxytricha",
"species": "Oxytricha trifallax",
"strain": "JRB310",
"taxonomy_id": "1172189",
},
"tetsp_mac2015_mic2022": {
"mac_name_regex": "^LASU.*$",
"mic_name_regex": "^TMEMEN_MIC_.*$",
"gene_files": [TETSP_MAC_2015_GENE_TSV],
"alias_files": [
{"file": TETSP_MAC_2015_ALIAS, "table": "contig", "nucleus": "mac"},
{"file": TETSP_MIC_2022_ALIAS, "table": "contig", "nucleus": "mic"},
],
"variant_files": [],
"protein_files": [],
"name": "Tetmemena sp. SeJ-2015 (MAC 2015/MIC 2022)",
"description": "Tetmemena sp. SeJ-2015 - SDRAP MDS/IES Annotation - MAC 2015 - MIC 2022",
"organism": "tet_sp_sej2015",
"assembly": "mac_2015,mic_2022",
"url": "tet_sp_sej2015_mac_2015_mic_2022",
"genus": "Tetmemena",
"species": "Tetmemena sp.",
"strain": "SeJ-2015",
"taxonomy_id": "200606",
},
"eupwoo_mac2022_mic2022": {
"mac_name_regex": "^EUPWOO_MAC_.*$",
"mic_name_regex": "^EUPWOO_MIC_.*$",
"gene_files": [EUPWOO_MAC_2022_GENE_TSV],
"alias_files": [
{"file": EUPWOO_MAC_2022_ALIAS, "table": "contig", "nucleus": "mac"},
{"file": EUPWOO_MIC_2022_ALIAS, "table": "contig", "nucleus": "mic"},
],
"variant_files": [],
"protein_files": [],
"name": "Euplotes woodruffi Iz01 (MAC 2022/MIC 2022)",
"description": "Euplotes woodruffi Iz01 - SDRAP MDS/IES Annotation - MAC 2022 - MIC 2022",
"organism": "eup_woo_iz01",
"assembly": "mac_2022,mic_2022",
"url": "eup_woo_iz01_mac_2022_mic_2022",
"genus": "Euplotes",
"species": "Euplotes woodruffi",
"strain": "Iz01",
"taxonomy_id": "5942",
},
}
STAGES = [
"all",
"create",
"contig",
"match",
"pointer",
"properties",
"parameter",
"coverage",
"gene",
"ies_strict",
"ies_weak",
"count",
"alias",
"variant",
"stats",
"protein",
"directory",
"dump",
"drop_temp",
]