anvi-export-gene-calls
Table of Contents
Export gene calls from an anvi'o contigs database.
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Authors
Requires
Provides
Usage
The purpose of this program is to exports your gene calls in a given contigs-db and a gene caller, in the form of a gene-calls-txt.
To see the gene callers available in your contigs database, you can use anvi-db-info or use this program with the following flag:
anvi-export-gene-calls -c contigs-db \ --list-gene-callers
Running this will export all of your gene calls identified by the gene caller pyrodigal-gv (assuming it is in your contigs-db:
anvi-export-gene-calls -c contigs-db \ --gene-caller Prodigal \ -o gene-calls-txt
You can export genes from more gene callers by providing a comma-separated list of gene caller names.
If you don’t want to display the amino acid sequences of each gene (they can crowd the file very quickly if you don’t want to see them), you can add the following flag:
anvi-export-gene-calls -c contigs-db \ --gene-caller Prodigal \ --skip-sequence-reporting \ -o gene-calls-txt
Advanced uses
This program can take a lot of time and memory when working with very large contigs-db files (such as those that are more than 10 Gb in file size or more than 10 million contigs).
In that case you can export your gene calls the following way within minutes and a small memory space.
First open your contigs-db:
sqlite3 contigs-db
Then run these lines,
.mode csv .headers on .out gene-calls-txt select gene_callers_id, contig, start, stop, direction, partial from genes_in_contigs;
You can also continue with these lines to get the amino acid sequences for them:
.mode csv .headers on .out AMINO-ACID-SEQUENCES.txt select * from genes_in_contigs;
Edit this file to update this information.
Command line interface
The following is the list of parameters and their descriptions in the latest version of anvi-export-gene-calls.
The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).
Command line usage
Parameters and their descriptions
-c, --contigs-dbCONTIGS_DBrequired- Anvi'o contigs database generated by 'anvi-gen-contigs-database'
--gene-callerGENE-CALLER- Which gene caller(s) would you like to export gene calls for? If providing multiple they should be comma-separated (no spaces). If you don't know, use --list-gene-callers.
--list-gene-callers- List available gene callers in the contigs database and quit.
-o, --output-fileFILE_PATH- File path to store results.
--skip-sequence-reporting- By default, exported gene calls have an amino acid sequences column in the output. Turn this behavior off with this flag
Additional Resources
Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.