genome
Convert Genome Assembly Data Report into TSV format
genome
Convert Genome Assembly Data Report into TSV format
Name
dataformat tsv genome - Convert Genome Assembly Data Report into TSV format
Synopsis
dataformat tsv genome [flags]
Description
Convert Genome Assembly Data Report into TSV format.
Refer to NCBI’s command line start documentation for information about getting started with the command-line tools.
Examples
dataformat tsv genome --inputfile human/ncbi_dataset/data/assembly_data_report.jsonl
dataformat tsv genome --package human.zip
Options
--elide-header Do not output header
--fields strings comma-separated list of fields
-h, --help help for genome
--inputfile string input file (default "/dev/stdin")
--package string datasets package (zip archive), inputfile parameter is relative to the root path inside the archive
Fields
| Mnemonic | Name |
|---|---|
| annotinfo-busco-complete | Annotation Info BUSCO Complete |
| annotinfo-busco-duplicated | Annotation Info BUSCO Duplicated |
| annotinfo-busco-fragmented | Annotation Info BUSCO Fragmented |
| annotinfo-busco-lineage | Annotation Info BUSCO Lineage |
| annotinfo-busco-missing | Annotation Info BUSCO Missing |
| annotinfo-busco-singlecopy | Annotation Info BUSCO Single Copy |
| annotinfo-busco-totalcount | Annotation Info BUSCO Total Count |
| annotinfo-busco-ver | Annotation Info BUSCO Version |
| annotinfo-featcount-gene-non-coding | Annotation Info Count Gene Non-coding |
| annotinfo-featcount-gene-other | Annotation Info Count Gene Other |
| annotinfo-featcount-gene-protein-coding | Annotation Info Count Gene Protein-coding |
| annotinfo-featcount-gene-pseudogene | Annotation Info Count Gene Pseudogene |
| annotinfo-featcount-gene-total | Annotation Info Count Gene Total |
| annotinfo-name | Annotation Info Name |
| annotinfo-release-date | Annotation Info Release Date |
| annotinfo-report-url | Annotation Info Report URL |
| annotinfo-source | Annotation Info Source |
| assminfo-accession | Assembly Accession |
| assminfo-atypicalis-atypical | Assembly Atypical Is Atypical |
| assminfo-atypicalwarnings | Assembly Atypical Warnings |
| assminfo-bioproject-lineage-accession | Assembly BioProject Lineage Accession |
| assminfo-bioproject-lineage-parent-accessions | Assembly BioProject Lineage Parent Accessions |
| assminfo-bioproject-lineage-title | Assembly BioProject Lineage Title |
| assminfo-biosample-accession | Assembly BioSample Accession |
| assminfo-biosample-attribute-name | Assembly BioSample Attribute Name |
| assminfo-biosample-attribute-value | Assembly BioSample Attribute Value |
| assminfo-biosample-bioproject-accession | Assembly BioSample BioProject Accession |
| assminfo-biosample-bioproject-parent-accessions | Assembly BioSample BioProject Parent Accessions |
| assminfo-biosample-bioproject-title | Assembly BioSample BioProject Title |
| assminfo-biosample-description-comment | Assembly BioSample Description Comment |
| assminfo-biosample-description-organism-common-name | Assembly BioSample Description Organism Common Name |
| assminfo-biosample-description-organism-organism-name | Assembly BioSample Description Organism Organism Name |
| assminfo-biosample-description-organism-pangolin | Assembly BioSample Description Organism Pangolin Classification |
| assminfo-biosample-description-organism-strain | Assembly BioSample Description Organism Strain |
| assminfo-biosample-description-organism-tax-id | Assembly BioSample Description Organism Taxonomic ID |
| assminfo-biosample-description-title | Assembly BioSample Description Title |
| assminfo-biosample-ids-db | Assembly BioSample Sample Identifiers Database |
| assminfo-biosample-ids-label | Assembly BioSample Sample Identifiers Label |
| assminfo-biosample-ids-value | Assembly BioSample Sample Identifiers Value |
| assminfo-biosample-last-updated | Assembly BioSample Last updated |
| assminfo-biosample-models | Assembly BioSample Models |
| assminfo-biosample-owner-contact-lab | Assembly BioSample Owner Contact Lab |
| assminfo-biosample-owner-name | Assembly BioSample Owner Name |
| assminfo-biosample-package | Assembly BioSample Package |
| assminfo-biosample-publication-date | Assembly BioSample Publication date |
| assminfo-biosample-status-status | Assembly BioSample Status Status |
| assminfo-biosample-status-when | Assembly BioSample Status When |
| assminfo-biosample-submission-date | Assembly BioSample Submission date |
| assminfo-blast-url | Assembly Blast URL |
| assminfo-current-accession | Assembly Current Accession |
| assminfo-description | Assembly Description |
| assminfo-genbank-assm-accession | Assembly GenBank Accession |
| assminfo-level | Assembly Level |
| assminfo-linked-assmaccession | Assembly Linked Assembly Accession |
| assminfo-linked-assmtype | Assembly Linked Assembly Type |
| assminfo-name | Assembly Name |
| assminfo-paired-assmaccession | Assembly Paired Assembly Accession |
| assminfo-paired-assmname | Assembly Paired Assembly Name |
| assminfo-paired-assmstatus | Assembly Paired Assembly Status |
| assminfo-paired_accession | Assembly Paired Accession |
| assminfo-refseq-assm-accession | Assembly RefSeq Accession |
| assminfo-refseq-category | Assembly Refseq Category |
| assminfo-sequencing-tech | Assembly Sequencing Tech |
| assminfo-status | Assembly Status |
| assminfo-submission-date | Assembly Submission Date |
| assminfo-submitter | Assembly Submitter |
| assminfo-type | Assembly Type |
| assminfo-ucsc-assm-name | Assembly UCSC Assembly Name |
| assmstats-contig-l50 | Assembly Stats Contig L50 |
| assmstats-contig-n50 | Assembly Stats Contig N50 |
| assmstats-gaps-between-scaffolds-count | Assembly Stats Gaps Between Scaffolds Count |
| assmstats-gc-count | Assembly Stats GC Count |
| assmstats-number-of-component-sequences | Assembly Stats Number of Component Sequences |
| assmstats-number-of-contigs | Assembly Stats Number of Contigs |
| assmstats-number-of-scaffolds | Assembly Stats Number of Scaffolds |
| assmstats-scaffold-l50 | Assembly Stats Scaffold L50 |
| assmstats-scaffold-n50 | Assembly Stats Scaffold N50 |
| assmstats-total-number-of-chromosomes | Assembly Stats Total Number of Chromosomes |
| assmstats-total-sequence-len | Assembly Stats Total Sequence Length |
| assmstats-total-ungapped-len | Assembly Stats Total Ungapped Length |
| breed | Breed |
| common-name | Common name |
| cultivar | Cultivar |
| ecotype | Ecotype |
| isolate | Isolate |
| organelle-assembly-name | Organelle Assembly Name |
| organelle-bioproject-accessions | Organelle BioProject Accessions |
| organelle-description | Organelle Description |
| organelle-infraspecific-name | Organelle Infraspecific Name |
| organelle-submitter | Organelle Submitter |
| organelle-total-seq-length | Organelle Total Seq Length |
| organism-name | Organism name |
| sex | Sex |
| strain | Strain |
| tax-id | Taxonomic ID |
| wgs-contigs-url | WGS contigs URL |
| wgs-project-accession | WGS project accession |
| wgs-url | WGS URL |