genomes
$ lexicmap utils genomes -h
View genome IDs in the index
Usage:
lexicmap utils genomes [flags]
Flags:
-e, --extra ► Show extra columns, such as where the genome is stored (genome_batch,
genome_index)
-h, --help help for genomes
-d, --index string ► Index directory created by "lexicmap index".
-o, --out-file string ► Out file, supports the ".gz" suffix ("-" for stdout). (default "-")
Global Flags:
-X, --infile-list string ► File of input file list (one file per line). If given, they are
appended to files from CLI arguments.
--log string ► Log file.
--quiet ► Do not print any verbose information. But you can write them to a file
with --log.
-j, --threads int ► Number of CPU cores to use. By default, it uses all available cores.
(default 8)
$ lexicmap utils genomes -d demo.lmi/ \
| csvtk pretty -t
ref chunked
--------------- -------
GCF_000148585.2
GCF_001457655.1
GCF_900638025.1
GCF_001096185.1
GCF_006742205.1
GCF_001544255.1
GCF_001027105.1
GCF_000392875.1
GCF_009759685.1
GCF_002949675.1
GCF_000006945.2
GCF_000017205.1
GCF_003697165.2
GCF_002950215.1
GCF_000742135.1
Extra columns
$ lexicmap utils genomes -d demo.lmi/ --extra \
| csvtk pretty -t
ref chunked genome_batch genome_index
--------------- ------- ------------ ------------
GCF_001457655.1 0 0
GCF_900638025.1 0 1
GCF_000148585.2 0 2
GCF_001096185.1 0 3
GCF_006742205.1 0 4
GCF_001027105.1 0 5
GCF_001544255.1 0 6
GCF_000392875.1 0 7
GCF_009759685.1 0 8
GCF_000006945.2 0 9
GCF_002949675.1 0 10
GCF_002950215.1 0 11
GCF_003697165.2 0 12
GCF_000742135.1 0 13
GCF_000017205.1 0 14