gratools get_segments_by_depth 

This command lists or saves segments (nodes) that are shared by a number of samples falling within a specific range (e.g., core segments shared by >95% of samples, or private segments found in only one sample). The range can be defined either by absolute numbers of samples or by percentages.

Options 

Usage Examples 

List segments shared by a number of individuals and save to a file

This example finds all segments shared by 2 or fewer individuals and saves the list to a CSV file (which is the default behavior).

$ gratools get_segments_by_depth -g Og_cactus.gfa.gz \
    --input-as-number --lower-bound 0 --upper-bound 2

|  INFO     | Parameters: lower=0; upper=2; filter_len=0
|  INFO     | Generate CSV file Og_cactus_segment_by_depth_between_0-2_individuals.csv
|  INFO     | Number of segments found: 891345 between 0 and 2 individuals

List core segments (by percentage) and display them in the terminal

This example identifies core segments, defined as those present in 95% to 100% of the samples, and prints the list directly to the terminal instead of saving it to a file.

$ gratools get_segments_by_depth -g Og_cactus.gfa.gz \
    --input-as-percentage --lower-bound 95% --upper-bound 100% --display-to-terminal

|  INFO     | Parameters: lower=95.0%; upper=100.0%; filter_len=0
|  INFO     | Segments found: 660741
Segment
5
6
7
...

Illustrated Example 

Understanding the Process

Input Mode: The user must specify whether the bounds are numbers or percentages. - With --input-as-percentage, you can specify --lower-bound 0% --upper-bound 20% to get a list of segments found in 20% or fewer of the samples. - With --input-as-number, you specify the exact lower and upper bounds for the number of individuals sharing the segments.
Get Core Genome Segments: The command get_segments_by_depth --input-as-number --lower-bound 4 --upper-bound 5 will extract a list of segments shared by exactly 4 or 5 individuals.
Get Dispensable Genome Segments: The command get_segments_by_depth --input-as-number --lower-bound 0 --upper-bound 2 will extract segments shared by 0, 1, or 2 individuals.
Length Filter: The --filter-len (-fl) option applies a filter to only include segments that are longer than the specified integer value.

gratools get_segments_by_depth

Options

Usage Examples