gratools
A tool for analyzing and manipulating pangenome graphs
gratools [OPTIONS] COMMAND [ARGS]...
Options
- -v, --version
Show the version and exit.
extract_sub_graph
Extract sub GFA files
gratools extract_sub_graph [OPTIONS]
Options
- -g, --gfa <gfa>
Required Path to the GFA file (gfa or .gfa.gz)
- -t, --threads <threads>
Number of threads to use
- Default:
1
- -vv, --verbosity <verbosity>
Log verbosity level
- Default:
'DEBUG'- Options:
DEBUG | INFO | WARNING | ERROR | CRITICAL
- -l, --log-path <log_path>
Directory path of log files
- Default:
'.'
- -su, --suffix <suffix>
Prefix added to output filename
- Default:
''
- -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
Extracts a specific sequence region from a sample within a GFA file and saves it in a FASTA file
gratools get_fasta [OPTIONS]
Options
- -g, --gfa <gfa>
Required Path to the GFA file (gfa or .gfa.gz)
- -t, --threads <threads>
Number of threads to use
- Default:
1
- -vv, --verbosity <verbosity>
Log verbosity level
- Default:
'DEBUG'- Options:
DEBUG | INFO | WARNING | ERROR | CRITICAL
- -l, --log-path <log_path>
Directory path of log files
- Default:
'.'
- -su, --suffix <suffix>
Prefix added to output filename
- Default:
''
- -sn, --sample <sample>
Required Sample name used as reference genome
- -c, --chr <chr>
Required Chromosome name
- -s, --start <start>
Start position on the reference genome
- Default:
0
- -e, --end <end>
End position on the reference genome
- -l, --samples_list <samples_list>
Path to a file with a list of samples (one per line)
segments_info
Shared and specific nodes
gratools segments_info [OPTIONS]
Options
- -g, --gfa <gfa>
Required Path to the GFA file (gfa or .gfa.gz)
- -t, --threads <threads>
Number of threads to use
- Default:
1
- -vv, --verbosity <verbosity>
Log verbosity level
- Default:
'DEBUG'- Options:
DEBUG | INFO | WARNING | ERROR | CRITICAL
- -l, --log-path <log_path>
Directory path of log files
- Default:
'.'
- -su, --suffix <suffix>
Prefix added to output filename
- Default:
''
- -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
Lists the chromosomes per samples in a GFA file
gratools show_chr [OPTIONS]
Options
- -g, --gfa <gfa>
Required Path to the GFA file (gfa or .gfa.gz)
- -t, --threads <threads>
Number of threads to use
- Default:
1
- -vv, --verbosity <verbosity>
Log verbosity level
- Default:
'DEBUG'- Options:
DEBUG | INFO | WARNING | ERROR | CRITICAL
- -l, --log-path <log_path>
Directory path of log files
- Default:
'.'
- -su, --suffix <suffix>
Prefix added to output filename
- Default:
''
- --full, --no-full
Provides detailed information, including chromosome start and end positions
- Default:
False
show_samples
Lists samples available in a GFA file
gratools show_samples [OPTIONS]
Options
- -g, --gfa <gfa>
Required Path to the GFA file (gfa or .gfa.gz)
- -t, --threads <threads>
Number of threads to use
- Default:
1
- -vv, --verbosity <verbosity>
Log verbosity level
- Default:
'DEBUG'- Options:
DEBUG | INFO | WARNING | ERROR | CRITICAL
- -l, --log-path <log_path>
Directory path of log files
- Default:
'.'
- -su, --suffix <suffix>
Prefix added to output filename
- Default:
''