gratools list_chr๏
Quickly inventory and describe genomic paths (chromosomes/contigs) within your graph.
๐งฌ Chromosome Mapping
The list_chr command scans the GFA walk lines (W-lines) to identify the contigs or chromosomes associated with each sample. It provides a quick way to check the completeness and naming consistency of your pangenome graph.
Options๏
๐ ๏ธ View Command Line Options
$ gratools list_chr
Welcome to GraTools version: '0.1.0.dev134'
@author: GraTools team's
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Please cite our gitlab: https://forge.ird.fr/diade/gratools.git\
Usage: gratools list_chr [OPTIONS]
Aliases: chr
Lists the chromosome information derived from the walks (W lines) of the
imported GFA file. By default, it shows a summary of unique chromosomes per
sample (meaning multiple fragments in the same chromosome are combined as a
single one). The --full option displays the detailed start/end positions for
each chromosome fragment. The results is displayed in the command line or in a
CSV file. This command relies on the pre-existing GraTools import.
For more details, see the full documentation:
https://gratools.readthedocs.io/en/latest/commands/list_chr.html
Chromosome Listing Options:
-g, --gfa PATH
Path to the input GFA file (e.g., myGraph.gfa or myGraph.gfa.gz).
[required]
-o, --outdir DIRECTORY
Output directory for GraTools results. If not specified, results are
typically placed in a subdirectory within the GFA file's parent directory
(e.g., 'GraTools-output_<gfa_name>').
--full / --no-full
Display the detailed chromosome fragment information (original start/end
positions from walks). [default: no-full]
--save / --no-save
Save the chromosome list (summary or full, based on --full) to a CSV file.
[default: no-save]
Logging Options:
-vv, --verbosity [DEBUG|INFO|ERROR]
Set the logging verbosity level. [default: INFO]
-l, --log-path DIRECTORY
Directory where the log files will be saved. If not specified, logs will be
placed in the main output directory (or in a default GraTools log
location).
Performance Options:
-t, --threads INTEGER
Number of threads to be used for parallelizable operations. [default: 1]
Other options:
-h, --help
Show this message and exit.
Usage Examples๏
๐ Short Format (Summary)
Get a concise list of unique chromosome names and counts per sample. Perfect for a quick overview.
$ gratools list_chr --gfa Og_cactus.gfa.gz
โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ Summary โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
Total samples: 5
Min chromosomes per sample: 2
Max chromosomes per sample: 2
5 Samples, 2-2 Unique Chromosomes/Sample (GFA: Og_cactus)
โญโโโโโโโโโโโโโโฌโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฌโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฎ
โ Sample Name โ Unique Chromosomes (Comma-separated) โ Number of Unique Chromosomes โ
โโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโค
โ CG14 โ CG14_Chr07, CG14_Chr08 โ 2 โ
โโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโค
โ Og103 โ Og103_Chr07, Og103_Chr08 โ 2 โ
โโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโค
โ Og182 โ Og182_Chr07, Og182_Chr08 โ 2 โ
โโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโค
โ Og20 โ Og20_Chr07, Og20_Chr08 โ 2 โ
โโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโค
โ Tog5681 โ Tog5681_Chr07, Tog5681_Chr08 โ 2 โ
โฐโโโโโโโโโโโโโโดโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโดโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฏ
๐ Full Format (Detailed)
Displays every chromosome fragment with its exact start and end positions. Crucial for fragmented assemblies.
$ gratools list_chr --gfa Og_cactus.gfa.gz --full
โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ Summary โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
Total samples: 5
Total unique chromosomes: 10
Total fragments: 23
Min fragment length: 1,772,164 bp
Max fragment length: 2,075,321 bp
Average fragment length: 11,330,633.22 bp
5 Samples, 2-2 Chromosomes/Sample (GFA: Og_cactus) - Full Fragment List
โญโโโโโโโโโโโโโโฌโโโโโโโโโโโโโโโโโโโโโโโโโโโฌโโโโโโโโโโโโโโโโโฌโโโโโโโโโโโโโโโฎ
โ Sample Name โ Chromosome Fragment Name โ Fragment Start โ Fragment End โ
โโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโค
โ CG14 โ CG14_Chr07 โ 0 โ 26,599,614 โ
โ โ CG14_Chr08 โ 0 โ 25,472,747 โ
โโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโค
โ Og103 โ Og103_Chr07 โ 23,875 โ 12,687,580 โ
โ โ Og103_Chr07 โ 12,866,628 โ 13,747,795 โ
โ โ Og103_Chr07 โ 13,903,795 โ 27,060,440 โ
โ โ Og103_Chr08 โ 30,268 โ 25,689,516 โ
โโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโค
โ Og182 โ Og182_Chr07 โ 16,376 โ 26,829,393 โ
โ โ Og182_Chr08 โ 11,495 โ 25,639,462 โ
โโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโค
โ Og20 โ Og20_Chr07 โ 13,644 โ 1,772,164 โ
โ โ Og20_Chr07 โ 1,890,766 โ 13,326,301 โ
โ โ Og20_Chr07 โ 13,432,358 โ 26,556,933 โ
โ โ Og20_Chr08 โ 33,688 โ 25,577,180 โ
โโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโค
โ Tog5681 โ Tog5681_Chr07 โ 22,457 โ 9,322,325 โ
โ โ Tog5681_Chr07 โ 9,748,285 โ 9,764,302 โ
โ โ Tog5681_Chr07 โ 9,907,780 โ 9,939,241 โ
โ โ Tog5681_Chr07 โ 10,023,782 โ 13,034,997 โ
โ โ Tog5681_Chr07 โ 13,211,081 โ 14,101,598 โ
โ โ Tog5681_Chr07 โ 14,241,787 โ 25,016,640 โ
โ โ Tog5681_Chr07 โ 25,052,306 โ 25,203,063 โ
โ โ Tog5681_Chr07 โ 25,411,687 โ 25,413,700 โ
โ โ Tog5681_Chr07 โ 25,481,734 โ 27,557,055 โ
โ โ Tog5681_Chr08 โ 9,084 โ 16,374,127 โ
โ โ Tog5681_Chr08 โ 16,391,988 โ 25,643,255 โ
โฐโโโโโโโโโโโโโโดโโโโโโโโโโโโโโโโโโโโโโโโโโโดโโโโโโโโโโโโโโโโโดโโโโโโโโโโโโโโโฏ
๐พ Save to File
Export the chromosome list to a tabular file for documentation or downstream parsing.
$ gratools list_chr --gfa graph.gfa --full --save
Output Formats Explained๏
Provides a summary table where each row represents one sample.
Unique Chromosomes: Comma-separated list of all path names found for that sample.
Number of Unique Chromosomes: Total count of distinct names.
Use this to verify that all samples have the expected number of chromosomes.
Provides a detailed fragment list. If a sampleโs chromosome is split into several walks (W-lines), each fragment is listed separately.
Fragment Start/End: The exact coordinates within the pangenome graph.
Fragment Statistics: The summary header will also show Min/Max/Avg fragment lengths.
Use this to diagnose fragmented assemblies or check for gaps in the graph.
๐ก Pro Tip: Fragmented Paths
In some GFA files (like those from Cactus), a single chromosome might be represented by multiple non-contiguous W lines. In Full Mode, GraTools lists every single one of these lines as a โfragmentโ, allowing you to see exactly how your assembly is structured in the graph.
โ
๐ Quick Links
Command Import: gratools import
Sample Listing: gratools list_samples
Graph Stats: gratools stats