Click Commands
gratools
gratools [OPTIONS] COMMAND [ARGS]...
Options
- -v, --version
Show the version and exit.
- -t, --threads <threads>
Number of threads
- Default:
1
- -vv, --verbosity <verbosity>
Set the logging verbosity level.
- Default:
'DEBUG'- Options:
DEBUG | INFO | WARNING | ERROR | CRITICAL
- -l, --log-path <log_path>
Path to the log files.
- Default:
'.'
extract_sub_graph
Extract sub GFA files
gratools extract_sub_graph [OPTIONS]
Options
- -g, --gfa <gfa>
Required GFA file
- -sn, --sample <sample>
Required Sample
- -c, --chr <chr>
Required Chromosome
- -s, --start <start>
Start
- Default:
0
- -e, --end <end>
End
- -l, --samples_list <samples_list>
Path to file with samples list (one per line)
- --build_fasta, --no-build_fasta
Build fasta file of sub graph
- Default:
False
get_fasta
Extract fasta from graph files
gratools get_fasta [OPTIONS]
Options
- -g, --gfa <gfa>
Required GFA file
- -sn, --sample <sample>
Required Sample
- -c, --chr <chr>
Required Chromosome
- -s, --start <start>
Start
- Default:
0
- -e, --end <end>
End
- -l, --samples_list <samples_list>
Path to file with samples list (one per line)
segments_info
Shared and specific nodes
gratools segments_info [OPTIONS]
Options
- -g, --gfa <gfa>
Required GFA file
- -sh, --shared_samples_min <shared_samples_min>
Required Minimum samples or percentage
- -sp, --specific_samples_max <specific_samples_max>
Required Maximum samples or percentage
- -f, --filter_len <filter_len>
Minimum segments length
- Default:
0
show_chr
Show sample names and chromosomes on GFA files
gratools show_chr [OPTIONS]
Options
- -g, --gfa <gfa>
Required GFA file
- --full, --no-full
Show all fragments of chromosomes
- Default:
False
show_samples
Show sample names on GFA files
gratools show_samples [OPTIONS]
Options
- -g, --gfa <gfa>
Required GFA file