genome-seq
Convert Genome Assembly Sequence Report into TSV format
genome-seq
Convert Genome Assembly Sequence Report into TSV format
Name
dataformat tsv genome-seq - Convert Genome Assembly Sequence Report into TSV format
Synopsis
dataformat tsv genome-seq [flags]
Description
Convert Genome Assembly Sequence Report into TSV format.
Refer to NCBI’s download and install documentation for information about getting started with the command-line tools.
Examples
dataformat tsv genome-seq --inputfile human_package/ncbi_dataset/data/GCF_000001405.40/sequence_report.jsonl
dataformat tsv genome-seq --package human.zip --inputfile GCF_000001405.40/sequence_report.jsonl
Options
--elide-header Do not output header
--fields strings Comma-separated list of fields
--force Force dataformat to run without type check prompt
-h, --help help for genome-seq
--inputfile string Input file (default "/dev/stdin")
--package string Data package (zip archive), inputfile parameter is relative to the root path inside the archive
Fields
| Mnemonic | Name |
|---|---|
| accession | Assembly Accession |
| assembly-unplaced-count | Assembly Unplaced Count |
| assm-unit-acc | Assembly-unit accession |
| chr-name | Chromosome name |
| gc-count | GC Count |
| gc-percent | GC Percent |
| genbank-seq-acc | GenBank seq accession |
| mol-type | Molecule type |
| ordering | Ordering |
| refseq-seq-acc | RefSeq seq accession |
| role | Role |
| seq-length | Seq length |
| ucsc-style-name | UCSC style name |
| unlocalized-count | Unlocalized Count |