Added functionality to run the tool as a standalone script
The script takes in the path for the input spreadsheet, the accession number and the list of curator names as command line arguments, and generates the files big_table.csv, project_details.json, and the idf and sdrf files in the directory path backend/script_spreadsheets/<name of the the supplied spreadsheet as folder name>/
The script runs interactively and expects an updated project_details json file which holds selected / chosen values for different fields. I've attached samples of both project_details.json and updated_project_details.json here
Sample run of the script:
python script.py -ac 2 -c AD JFG -d /Users/yhaider/Downloads/DevelopingCardiacSystem_test.xlsx
Converting sheets in excel file to dataframes...
12 sheets converted to dataframes
Enter file path for updated project details file: updated_project_details.json
saving script_spreadsheets/DevelopingCardiacSystem_test/E-HCAD-2.idf.txt
saving script_spreadsheets/DevelopingCardiacSystem_test/E-HCAD-2.sdrf.txt
project_details.json
{
"accession": "2",
"curators": [
"AD",
"JFG"
],
"protocol_columns": {
"collection_protocol": [
"collection_protocol.protocol_core.protocol_id"
],
"library_preparation_protocol": [
"library_preparation_protocol.protocol_core.protocol_id"
],
"sequencing_protocol": [
"sequencing_protocol.protocol_core.protocol_id"
],
"dissociation_protocol": [
"dissociation_protocol.protocol_core.protocol_id_0"
]
},
"protocol_map": {
"collection_protocol": {
"collection_protocol_1": {
"scea_id": "P-HCAD2-1",
"description": "Wild-type, timed pregnant CD1 mice were acquired from Jackson Laboratory (Sacramento, CA, USA). Embryonic day 16.5 (E16.5), wild-type CD1 mice were obtained from pregnant mice. Embryonic mouse hearts were harvested, and 3 zones of microdissection were isolated based on anatomic landmarks and entailed: Zone I\u2014SAN region (superior vena cava/right atrial junction), Zone II\u2014AVN/His region (crux of heart), and Zone III\u2014BB/PF region (luminal side of ventricles). Specifically, Zone II was dissected as a large area at the crux of the heart from the base of the interatrial sep- tum (including the triangle of Koch) to below the plane of the mitral annulus, from the posterior-most aspect of the heart to the anterior-most. Tissues from a total of 6 different embryos were pooled for each zone of dissection. "
}
},
"dissociation_protocol": {
"dissociation_protocol_1": {
"scea_id": "P-HCAD2-2",
"description": "Dissected tissues were dissociated into single cells in a microcentrifuge tube with 100ul of 0.25% trypsin and incubated at 37 degrees celcius for 10 min. Subsequently, 1.4 mL of collagenase A/B (10 mg/ml) and 20% FBS serum in HBSS was added to the micfocentrifuge tubes and tissue samples were returned to 37 degrees celcius in a waterbath for an additional 20 min. Cells were then spun down at 1000 RPM for 5 min, supernatant was removed and cells werw washed in 20% FBS in HBSS. After suspension, cells were resuspended to around 600 cell/ul with 0.04% FBS/HBSS solution for processing on the 10X platform."
}
},
"enrichment_protocol": {},
"library_preparation_protocol": {
"library_protocol_1": {
"scea_id": "P-HCAD2-3",
"description": "Prepared cells were captured with 10X Chromium by following the Chromium single-cell 3' reagent kits v2 user guide. Briefly, single cells were partitioned into nanoliter-scale Gel Bread-In-Emulsions in the Chromium controller. After dissolution of the Gel beads in GEMS, the primers were released, and mRNA were reverse transcribed into a barcoded cDNA library. After further clean-up and amplification, the cDNA was enzymatically fragmented and 3' end fragments were selected for library preparation. After further end repair, A-tailing, adaptor ligation and PCR amplification, sample index, UMI sequences, barcode sequences and sequencing primer P5 and P7 on both ends were added to cDNA."
}
},
"sequencing_protocol": {
"sequencing_protocol_1": {
"scea_id": "P-HCAD2-4",
"description": "Libraries were sequenced using the Illumina HiSeq 4000 instrument.",
"hardware": "Illumina HiSeq 4000"
}
}
},
"project_uuid": "",
"configurable_fields": [
{
"name": "Source Name",
"type": "column",
"source": [
"cell_suspension.biomaterial_core.biomaterial_id",
"cell_suspension.biomaterial_core.biosamples_accession",
"donor_organism.biomaterial_core.biomaterial_id",
"donor_organism.biomaterial_core.biosamples_accession",
"specimen_from_organism.biomaterial_core.biomaterial_id",
"specimen_from_organism.biomaterial_core.biosamples_accession"
]
},
{
"name": "Comment[biomaterial name]",
"type": "column",
"source": [
"cell_suspension.biomaterial_core.biomaterial_id",
"cell_suspension.biomaterial_core.biosamples_accession",
"donor_organism.biomaterial_core.biomaterial_id",
"donor_organism.biomaterial_core.biosamples_accession",
"specimen_from_organism.biomaterial_core.biomaterial_id",
"specimen_from_organism.biomaterial_core.biosamples_accession"
]
},
{
"name": "Material Type_1",
"type": "dropdown",
"source": [
"whole organism",
"organism part",
"cell"
]
},
{
"name": "Extract Name",
"type": "column",
"source": [
"cell_suspension.biomaterial_core.biomaterial_id",
"cell_suspension.biomaterial_core.biosamples_accession",
"donor_organism.biomaterial_core.biomaterial_id",
"donor_organism.biomaterial_core.biosamples_accession",
"specimen_from_organism.biomaterial_core.biomaterial_id",
"specimen_from_organism.biomaterial_core.biosamples_accession"
]
},
{
"name": "Material Type_2",
"source": "RNA"
},
{
"name": "Comment[primer]",
"source": "oligo-DT"
},
{
"name": "Comment[umi barcode read]",
"source": "read1"
},
{
"name": "Comment[umi barcode offset]",
"source": "16.0"
},
{
"name": "Comment[umi barcode size]",
"source": "10.0"
},
{
"name": "Comment[cell barcode read]",
"source": "Read 1"
},
{
"name": "Comment[cell barcode offset]",
"source": "0.0"
},
{
"name": "Comment[cell barcode size]",
"source": "16.0"
},
{
"name": "Comment[sample barcode read]",
"source": ""
},
{
"name": "Comment[sample barcode offset]",
"source": "0"
},
{
"name": "Comment[sample barcode size]",
"source": "8"
},
{
"name": "Comment[single cell isolation]",
"source": "magnetic affinity cell sorting"
},
{
"name": "Comment[cDNA read]",
"source": "read2"
},
{
"name": "Comment[cDNA read offset]",
"source": "0"
},
{
"name": "Comment[cDNA read size]",
"source": "98"
},
{
"name": "Comment[LIBRARY_LAYOUT]",
"source": "PAIRED"
},
{
"name": "Comment[LIBRARY_SOURCE]",
"source": "TRANSCRIPTOMIC SINGLE CELL"
},
{
"name": "Comment[LIBRARY_STRATEGY]",
"source": "RNA-Seq"
},
{
"name": "Comment[LIBRARY_SELECTION]",
"source": "cDNA"
},
{
"name": "Technology Type",
"source": "sequencing assay"
},
{
"name": "Scan Name",
"type": "column",
"source": [
"cell_suspension.biomaterial_core.biomaterial_id",
"cell_suspension.biomaterial_core.biosamples_accession",
"donor_organism.biomaterial_core.biomaterial_id",
"donor_organism.biomaterial_core.biosamples_accession",
"specimen_from_organism.biomaterial_core.biomaterial_id",
"specimen_from_organism.biomaterial_core.biosamples_accession"
]
},
{
"name": "Comment[RUN]",
"type": "column",
"source": [
"cell_suspension.biomaterial_core.biomaterial_id",
"cell_suspension.biomaterial_core.biosamples_accession",
"donor_organism.biomaterial_core.biomaterial_id",
"donor_organism.biomaterial_core.biosamples_accession",
"specimen_from_organism.biomaterial_core.biomaterial_id",
"specimen_from_organism.biomaterial_core.biosamples_accession"
]
}
]
}
updated_project_details.json
{
"accession": "2",
"curators": [
"AD",
"JFG"
],
"protocol_columns": {
"collection_protocol": [
"collection_protocol.protocol_core.protocol_id"
],
"library_preparation_protocol": [
"library_preparation_protocol.protocol_core.protocol_id"
],
"sequencing_protocol": [
"sequencing_protocol.protocol_core.protocol_id"
],
"dissociation_protocol": [
"dissociation_protocol.protocol_core.protocol_id_0"
]
},
"protocol_map": {
"collection_protocol": {
"collection_protocol_1": {
"scea_id": "P-HCAD2-1",
"hca_ids": [
"collection_protocol_1"
],
"description": "Wild-type, timed pregnant CD1 mice were acquired from Jackson Laboratory (Sacramento, CA, USA). Embryonic day 16.5 (E16.5), wild-type CD1 mice were obtained from pregnant mice. Embryonic mouse hearts were harvested, and 3 zones of microdissection were isolated based on anatomic landmarks and entailed: Zone I—SAN region (superior vena cava/right atrial junction), Zone II—AVN/His region (crux of heart), and Zone III—BB/PF region (luminal side of ventricles). Specifically, Zone II was dissected as a large area at the crux of the heart from the base of the interatrial sep- tum (including the triangle of Koch) to below the plane of the mitral annulus, from the posterior-most aspect of the heart to the anterior-most. Tissues from a total of 6 different embryos were pooled for each zone of dissection."
}
},
"dissociation_protocol": {
"dissociation_protocol_1": {
"scea_id": "P-HCAD2-2",
"hca_ids": [
"dissociation_protocol_1"
],
"description": "Dissected tissues were dissociated into single cells in a microcentrifuge tube with 100ul of 0.25% trypsin and incubated at 37 degrees celcius for 10 min. Subsequently, 1.4 mL of collagenase A/B (10 mg/ml) and 20% FBS serum in HBSS was added to the micfocentrifuge tubes and tissue samples were returned to 37 degrees celcius in a waterbath for an additional 20 min. Cells were then spun down at 1000 RPM for 5 min, supernatant was removed and cells werw washed in 20% FBS in HBSS. After suspension, cells were resuspended to around 600 cell/ul with 0.04% FBS/HBSS solution for processing on the 10X platform."
}
},
"enrichment_protocol": {},
"library_preparation_protocol": {
"library_protocol_1": {
"scea_id": "P-HCAD2-3",
"hca_ids": [
"library_protocol_1"
],
"description": "Prepared cells were captured with 10X Chromium by following the Chromium single-cell 3' reagent kits v2 user guide. Briefly, single cells were partitioned into nanoliter-scale Gel Bread-In-Emulsions in the Chromium controller. After dissolution of the Gel beads in GEMS, the primers were released, and mRNA were reverse transcribed into a barcoded cDNA library. After further clean-up and amplification, the cDNA was enzymatically fragmented and 3' end fragments were selected for library preparation. After further end repair, A-tailing, adaptor ligation and PCR amplification, sample index, UMI sequences, barcode sequences and sequencing primer P5 and P7 on both ends were added to cDNA."
}
},
"sequencing_protocol": {
"sequencing_protocol_1": {
"scea_id": "P-HCAD2-4",
"hca_ids": [
"sequencing_protocol_1"
],
"description": "Libraries were sequenced using the Illumina HiSeq 4000 instrument.",
"hardware": "Illumina HiSeq 4000"
}
}
},
"project_uuid": "",
"configurable_fields": [
{
"name": "Source Name",
"type": "column",
"source": [
"cell_suspension.biomaterial_core.biomaterial_id",
"cell_suspension.biomaterial_core.biosamples_accession",
"donor_organism.biomaterial_core.biomaterial_id",
"donor_organism.biomaterial_core.biosamples_accession",
"specimen_from_organism.biomaterial_core.biomaterial_id",
"specimen_from_organism.biomaterial_core.biosamples_accession"
],
"value": "cell_suspension.biomaterial_core.biomaterial_id"
},
{
"name": "Comment[biomaterial name]",
"type": "column",
"source": [
"cell_suspension.biomaterial_core.biomaterial_id",
"cell_suspension.biomaterial_core.biosamples_accession",
"donor_organism.biomaterial_core.biomaterial_id",
"donor_organism.biomaterial_core.biosamples_accession",
"specimen_from_organism.biomaterial_core.biomaterial_id",
"specimen_from_organism.biomaterial_core.biosamples_accession"
],
"value": "cell_suspension.biomaterial_core.biomaterial_id"
},
{
"name": "Material Type_1",
"type": "dropdown",
"source": [
"whole organism",
"organism part",
"cell"
],
"value": "whole organism"
},
{
"name": "Extract Name",
"type": "column",
"source": [
"cell_suspension.biomaterial_core.biomaterial_id",
"cell_suspension.biomaterial_core.biosamples_accession",
"donor_organism.biomaterial_core.biomaterial_id",
"donor_organism.biomaterial_core.biosamples_accession",
"specimen_from_organism.biomaterial_core.biomaterial_id",
"specimen_from_organism.biomaterial_core.biosamples_accession"
],
"value": "cell_suspension.biomaterial_core.biomaterial_id"
},
{
"name": "Material Type_2",
"source": "RNA",
"value": "RNA"
},
{
"name": "Comment[primer]",
"source": "oligo-DT",
"value": "oligo-DT"
},
{
"name": "Comment[umi barcode read]",
"source": "read1",
"value": "read1"
},
{
"name": "Comment[umi barcode offset]",
"source": "16",
"value": "16"
},
{
"name": "Comment[umi barcode size]",
"source": "10",
"value": "10"
},
{
"name": "Comment[cell barcode read]",
"source": "Read 1",
"value": "Read 1"
},
{
"name": "Comment[cell barcode offset]",
"source": "0",
"value": "0"
},
{
"name": "Comment[cell barcode size]",
"source": "16",
"value": "16"
},
{
"name": "Comment[sample barcode read]",
"source": "",
"value": ""
},
{
"name": "Comment[sample barcode offset]",
"source": "0",
"value": "0"
},
{
"name": "Comment[sample barcode size]",
"source": "8",
"value": "8"
},
{
"name": "Comment[single cell isolation]",
"source": "magnetic affinity cell sorting",
"value": "magnetic affinity cell sorting"
},
{
"name": "Comment[cDNA read]",
"source": "read2",
"value": "read2"
},
{
"name": "Comment[cDNA read offset]",
"source": "0",
"value": "0"
},
{
"name": "Comment[cDNA read size]",
"source": "98",
"value": "98"
},
{
"name": "Comment[LIBRARY_LAYOUT]",
"source": "PAIRED",
"value": "PAIRED"
},
{
"name": "Comment[LIBRARY_SOURCE]",
"source": "TRANSCRIPTOMIC SINGLE CELL",
"value": "TRANSCRIPTOMIC SINGLE CELL"
},
{
"name": "Comment[LIBRARY_STRATEGY]",
"source": "RNA-Seq",
"value": "RNA-Seq"
},
{
"name": "Comment[LIBRARY_SELECTION]",
"source": "cDNA",
"value": "cDNA"
},
{
"name": "Technology Type",
"source": "sequencing assay",
"value": "sequencing assay"
},
{
"name": "Scan Name",
"type": "column",
"source": [
"cell_suspension.biomaterial_core.biomaterial_id",
"cell_suspension.biomaterial_core.biosamples_accession",
"donor_organism.biomaterial_core.biomaterial_id",
"donor_organism.biomaterial_core.biosamples_accession",
"specimen_from_organism.biomaterial_core.biomaterial_id",
"specimen_from_organism.biomaterial_core.biosamples_accession"
],
"value": "cell_suspension.biomaterial_core.biomaterial_id"
},
{
"name": "Comment[RUN]",
"type": "column",
"source": [
"cell_suspension.biomaterial_core.biomaterial_id",
"cell_suspension.biomaterial_core.biosamples_accession",
"donor_organism.biomaterial_core.biomaterial_id",
"donor_organism.biomaterial_core.biosamples_accession",
"specimen_from_organism.biomaterial_core.biomaterial_id",
"specimen_from_organism.biomaterial_core.biosamples_accession"
],
"value": "cell_suspension.biomaterial_core.biomaterial_id"
}
],
"submission_date": "",
"last_update_date": "",
"geo_accessions": []
}
big_table.csv,project_details.json, and the idf and sdrf files in the directory pathbackend/script_spreadsheets/<name of the the supplied spreadsheet as folder name>/project_details.jsonandupdated_project_details.jsonhereproject_details.json
updated_project_details.json