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* Create ngsDataGrabber.py This is a copy of ngsDataGrabber_V0.6.py and it has been renamed to something more generic for ngsQC protocol. * Create assemblyQC_data_grabber.py file This file is created in order to extract numbers of unspecified nucleotides from the backend. * Update assemblyQC_data_grabber.py * Bump numpy from 1.21.6 to 1.22.0 in /lib Bumps [numpy](https://github.com/numpy/numpy) from 1.21.6 to 1.22.0. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v1.21.6...v1.22.0) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Created assemblyQC_NCBI.tsv Changes to be committed: new file: data_files/assemblyQC_NCBI.tsv new file: lib/assembly_qc_ncbi_.py * Update requirements.txt Changes to be committed: modified: requirements.txt * Publish v0.9 Changes to be committed: new file: data_dictionary/v0.9/README.tsv new file: data_dictionary/v0.9/core_property_list.tsv new file: data_dictionary/v0.9/non_core_property_list.tsv new file: data_dictionary/v0.9/property_definition.tsv new file: data_dictionary/v0.9/release_notes.tsv new file: schema/v0.9/core/assemblyQC.json new file: schema/v0.9/core/biosampleMeta.json new file: schema/v0.9/core/ngsQC.json new file: schema/v0.9/core/siteQC.json new file: schema/v0.9/non-core/SRA_assemblyQC.json new file: schema/v0.9/non-core/SRA_biosample.json new file: schema/v0.9/non-core/SRA_ngsQC.json new file: schema/v0.9/non-core/ngs_ID_list.json new file: schema/v0.9/non-core/sars-cov-2_lineage_mutations.json new file: schema/v0.9/non-core/uniprot-proteome_*.json Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Jingyue Wu <[email protected]> Co-authored-by: penningtonea <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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| This page: V0.9_argos_dict | ||
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| property definition | ||
| column header data | ||
| Property consensus name for data property described in row | ||
| Name in Files Alternate names for data property in existing datasets | ||
| Data Files A `|` separated list of dataset names where this property is utilized | ||
| recommended Ther person or resource that suggested using the property | ||
| Description A definition and additional information about the property. | ||
| source/type def The data source for obtaining the property. | ||
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| core property list | ||
| column header data | ||
| Property consensus name for data property described in row | ||
| Data Object Type The dataset this property is used in | ||
| Optional/Required indicates if the property is REQUIRED to hava a valid data row | ||
| $id For JSON schema conversion | ||
| Title Human readable name for property. Default is the same as property. | ||
| Type property type as defined by JSON types | ||
| default a default value for property | ||
| examples and example for the property | ||
| pattern the regular expression evaluation for this property | ||
| description A definition and additional information about the property. | ||
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| annotation property list | ||
| column header data | ||
| Property consensus name for data property described in row | ||
| Data Object Type The dataset this property is used in | ||
| Optional/Required indicates if the property is REQUIRED to hava a valid data row | ||
| $id For JSON schema conversion | ||
| Title Human readable name for property. Default is the same as property. | ||
| Type property type as defined by JSON types | ||
| default a default value for property | ||
| examples and example for the property | ||
| pattern the regular expression evaluation for this property | ||
| description A definition and additional information about the property. | ||
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| property data_object required id title type default examples pattern description | ||
| sra_experiment_id SRA_ngsQC.tsv required #root/sra_experiment_id sra_experiment_id string - SRR9107811 ^.*$ - | ||
| sra_run_id SRA_ngsQC.tsv required #root/sra_run_id sra_run_id string - SRX5882434 ^.*$ - | ||
| bioproject SRA_ngsQC.tsv required #root/bioproject bioproject string - PRJNA231221 ^.*$ - | ||
| biosample SRA_ngsQC.tsv optional #root/biosample biosample string - SAMN11077980 ^.*$ - | ||
| num_of_bases SRA_ngsQC.tsv required #root/num_of_bases num_of_bases string - 400293278 ^.*$ - | ||
| file_size SRA_ngsQC.tsv required #root/file_size file_size string - 195921414 ^.*$ - | ||
| published SRA_ngsQC.tsv required #root/published published string - ########## ^.*$ - | ||
| source SRA_ngsQC.tsv required #root/source source string - VIRAL RNA (Genomic DNA|GENOMIC|TRANSCRIPTOMIC|METAGENOMIC|METATRANSCRIPTOMIC|SYNTHETIC|VIRAL RNA|OTHER) - | ||
| strategy SRA_ngsQC.tsv required #root/strategy strategy string - WGS (WGA|WGS|WXS|RNA-Seq|miRNA-Seq|WCS|CLONE|POOLCLONE|AMPLICON|CLONEEND|FINISHING|ChIP-Seq|MNase-Seq|DNase-Hypersensitivity|Bisulfite-Seq|Tn-Seq|EST|FL-cDNA|CTS|MRE-Seq|MeDIP-Seq|MBD-Seq|Synthetic-Long-Read|ATAC-seq|ChIA-PET|FAIRE-seq|Hi-C|ncRNA-Seq|RAD-Seq|RIP-Seq|SELEX|ssRNA-seq|Targeted-Capture|Tethered Chromatin Conformation Capture|OTHER) - | ||
| layout SRA_ngsQC.tsv required #root/layout layout string - PAIRED ^.*$ - | ||
| library_name SRA_ngsQC.tsv optional #root/library_name library_name string - IL100100209 ^.*$ - | ||
| selection SRA_ngsQC.tsv optional #root/selection selection string - cDNA (RANDOM|PCR|RANDOM PCR|RT-PCR|HMPR|MF|CF-S|CF-M|CF-H|CF-T|MDA|MSLL|cDNA|ChIP|MNase|DNAse|Hybrid Selection|Reduced Representation|Restriction Digest|5-methylcytidine antibody|MBD2 protein methyl-CpG binding domain|CAGE|RACE|size fractionation|Padlock probes capture method|other|unspecified|cDNA_oligo_dT|cDNA_randomPriming|Inverse rRNA|Oligo-dT|PolyA|repeat fractionation) - | ||
| instrument SRA_ngsQC.tsv optional #root/instrument instrument string - Illumina MiSeq ^.*$ - | ||
| file_type SRA_ngsQC.tsv required #root/file_type file_type string - fastq ^.*$ - | ||
| reads_unaligned SRA_ngsQC.tsv optional #root/reads_unaligned reads_unaligned string - 61059 ^[2-9]|[1-9]\d+$ - | ||
| identified_reads SRA_ngsQC.tsv optional #root/identified_reads identified_reads string - 603880 ^[2-9]|[1-9]\d+$ - | ||
| taxonomy_id SRA_ngsQC.tsv optional #root/taxonomy_id taxonomy_id string - 64320 ^[2-9]|[1-9]\d+$ - | ||
| lineage SRA_ngsQC.tsv optional #root/lineage lineage string - Viruses|Riboviria|Orthornavirae|Kitrinoviricota|Flasuviricetes|Amarillovirales|Flaviviridae|Flavivirus|Zika virus ^.*$ - | ||
| percent_identified SRA_ngsQC.tsv optional #root/percent_identified percent_identified string - 0.90817353 ^[+-]?([0]+\.?[0-9]*|\.[0-9]+)$ - | ||
| ngs_gc_content SRA_ngsQC.tsv optional #root/gc_content gc_content string - 0.45566968 ^[+-]?([0]+\.?[0-9]*|\.[0-9]+)$ - | ||
| genome_assembly_id SRA_assemblyQC.tsv required #root/genome_assembly_id genome_assembly_id string - GCA_013267415.1 ^.*$ - | ||
| level SRA_assemblyQC.tsv required #root/level level string - Complete genome ^.*$ - | ||
| assembly_level SRA_assemblyQC.tsv required #root/assembly_level assembly_level string - undefined ^.*$ - | ||
| num_chromosomes SRA_assemblyQC.tsv required #root/num_chromosomes num_chromosomes string - 1 ^.*$ - | ||
| biosample SRA_assemblyQC.tsv required #root/biosample biosample string - SAMN11056500 ^.*$ - | ||
| strain SRA_assemblyQC.tsv required #root/strain strain string - FDAARGOS_785 ^.*$ - | ||
| organism_name SRA_assemblyQC.tsv required #root/Taxonomy Name Taxonomy Name string - Abiotrophia defectiva ^.*$ - | ||
| bioproject SRA_assemblyQC.tsv required #root/BioPproject BioPproject string - PRJNA231221 ^.*$ - | ||
| taxonomy_id SRA_assemblyQC.tsv required #root/taxonomy_id taxonomy_id string - 46125 ^[2-9]|[1-9]\d+$ - | ||
| lineage SRA_assemblyQC.tsv required #root/lineage lineage string - cellular organisms; Bacteria; Terrabacteria group; Firmicutes; Bacilli; Lactobacillales; Aerococcaceae; Abiotrophia ^.*$ - | ||
| uniprotkb_canonical_ac sars-cov-2_lineage_mutations.tsv required #root/uniprotkb_canonical_ac uniprotkb_canonical_ac string - P0DTC2-1 ^.*$ - | ||
| found_in sars-cov-2_lineage_mutations.tsv required #root/found_in found_in string - "Omicron (21K, BA.1)" ^.*$ - | ||
| gene_name sars-cov-2_lineage_mutations.tsv required #root/gene_name gene_name string - S ^.*$ - | ||
| protein_name sars-cov-2_lineage_mutations.tsv required #root/protein_name protein_name string - Spike glycoprotein ^.*$ - | ||
| evidence_ECO0000313 sars-cov-2_lineage_mutations.tsv required #root/evidence_ECO0000313 evidence_ECO0000313 string - CoVariants ^.*$ - | ||
| begin_aa_pos sars-cov-2_lineage_mutations.tsv required #root/begin_aa_pos begin_aa_pos string - 67 ^.*$ - | ||
| end_aa_pos sars-cov-2_lineage_mutations.tsv required #root/end_aa_pos end_aa_pos string - 67 ^.*$ - | ||
| mutation_type sars-cov-2_lineage_mutations.tsv required #root/mutation_type mutation_type string - missense ^.*$ - | ||
| is_known_glycoprotein sars-cov-2_lineage_mutations.tsv required #root/is_known_glycoprotein is_known_glycoprotein string - yes ^.*$ - | ||
| motif_start sars-cov-2_lineage_mutations.tsv required #root/motif_start motif_start string - 67 ^.*$ - | ||
| ref_motif sars-cov-2_lineage_mutations.tsv required #root/ref_motif ref_motif string - A ^.*$ - | ||
| alt_motif sars-cov-2_lineage_mutations.tsv required #root/alt_motif alt_motif string - V ^.*$ - | ||
| effect sars-cov-2_lineage_mutations.tsv required #root/effect effect string - - ^.*$ - | ||
| note sars-cov-2_lineage_mutations.tsv required #root/note note string - - ^.*$ - | ||
| organism_name ngs_ID_list.tsv required #root/note organism_name string - Severe acute respiratory syndrome coronavirus 3 ^.*$ - | ||
| leaf_node ngs_ID_list.tsv required #root/note Leaf Node string - B.1.1.529/Omicron isolate ^.*$ - | ||
| genome_assembly_id ngs_ID_list.tsv required #root/genome_assembly_id genome_assembly_id string - GCA_013267415.1 ^.*$ - | ||
| taxonomy_id ngs_ID_list.tsv required #root/taxonomy_id taxonomy_id string - 2697049 ^[2-9]|[1-9]\d+$ - | ||
| sra_run_id ngs_ID_list.tsv required #root/note SRA Run ID string - SRR17309642 ^\+SRR.+ - | ||
| selection_notes ngs_ID_list.tsv required #root/note Selection Notes string - "For omicron, we are selecting EPI_ISL_6913953. Sequencing was conducted on Illumina MiSeq, has high coverage, and a consistent quality score across all base calls above 30. Raw reads are available at https://www.ncbi.nlm.nih.gov/sra/SRX13486794, and a full description of the patient harboring the virus is supplied with the following publication https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciab1072/6494531?login=true. The patient was one of the first two known COVID-19 cases classified as omicron in Japan. To put the collection date of 28 November 2021 in perspective, the first known omicron sample was collected on 8 November 2021. Raw reads from South Africa are available, but the average phred quality score is much lower for those samples." ^.*$ - | ||
| lab_name ngs_ID_list.tsv required #root/note Lab Name string - Pond Lab (Pond Lab|Crandall Lab|HIVE Lab) - | ||
| files_processed ngs_ID_list.tsv required #root/processed processed string - ngsQC_HL|assemblyQC_HL|siteQC_HL|biosampleMeta_HL (ngsQC_HL|assemblyQC_HL|siteQC_HL|biosampleMeta_HL) - | ||
| biosample SRA_biosample required #root/biosample biosample string - SAMN16357302 ^.*$ - | ||
| organism_name SRA_biosample required #root/organism_name organism_name string - Pediococcus acidilactici ^.*$ - | ||
| strain SRA_biosample required #root/strain strain string - FDAARGOS_1133 ^.*$ - | ||
| sample_name SRA_biosample required #root/sample_name sample_name string - FDAARGOS_1133 ^.*$ - | ||
| taxonomy_id SRA_biosample required #root/taxonomy_id taxonomy_id string - 1254 ^.*$ - | ||
| isolate SRA_biosample required #root/isolate isolate string - Not applicable ^.*$ - | ||
| collected_by SRA_biosample required #root/collected_by collected_by string - DSMZ ^.*$ - | ||
| collection_date SRA_biosample required #root/collection_date collection_date string - Unknown ^.*$ - | ||
| geo_loc_name SRA_biosample required #root/geo_loc_name geo_loc_name string - Germany: Braunschweig ^.*$ - | ||
| isolation_source SRA_biosample required #root/isolation_source isolation_source string - missing ^.*$ - | ||
| lat_lon SRA_biosample required #root/lat_lon lat_lon string - Not applicable ^.*$ - | ||
| culture_collection SRA_biosample required #root/culture_collection culture_collection string - DSM:20284 ^.*$ - | ||
| host SRA_biosample required #root/host host string - missing ^.*$ - | ||
| host_age SRA_biosample required #root/host_age host_age string - Unknown ^.*$ - | ||
| host_description SRA_biosample required #root/host_description host_description string - Not applicable ^.*$ - | ||
| host_disease SRA_biosample required #root/host_disease host_disease string - Unknown ^.*$ - | ||
| host_disease_outcome SRA_biosample required #root/host_disease_outcome host_disease_outcome string - Unknown ^.*$ - | ||
| host_disease_stage SRA_biosample required #root/host_disease_stage host_disease_stage string - Unknown ^.*$ - | ||
| host_health_state SRA_biosample required #root/host_health_state host_health_state string - Unknown ^.*$ - | ||
| host_sex SRA_biosample required #root/host_sex host_sex string - Unknown ^.*$ - | ||
| id_method SRA_biosample required #root/id_method id_method string - Phenotypic and Molecular Methods ^.*$ - | ||
| type_material SRA_biosample required #root/type_material type_material string - neotype strain of Pediococcus acidilactici ^.*$ - | ||
| uniprotkb_ac uniprot-proteome_*.csv required #root/uniprotkb_ac uniprotkb_ac string - P03466 ^.*$ - | ||
| entry_name uniprot-proteome_*.csv required #root/entry_name entry_name string - RDRP_I34A1 ^.*$ - | ||
| status uniprot-proteome_*.csv required #root/status status string - reviewed ^.*$ - | ||
| protein_names uniprot-proteome_*.csv required #root/protein_names protein_names string - RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) (Polymerase basic protein 1) (PB1) (RNA-directed RNA polymerase subunit P1) ^.*$ - | ||
| gene_names uniprot-proteome_*.csv required #root/gene_names gene_names string - PB1 ^.*$ - | ||
| organism_name uniprot-proteome_*.csv required #root/organism organism string - Influenza A virus (strain A/Puerto Rico/8/1934 H1N1) ^.*$ - | ||
| length uniprot-proteome_*.csv required #root/length length string - 498 ^.*$ - |
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