anvi-get-split-coverages

Export splits and the coverage table from database.

🔙 To the main page of anvi’o programs and artifacts.

Authors

A. Murat Eren (Meren)
WebEmailTwitterGithub

Requires

profile-db

Can use

contigs-db collection bin

Provides

coverages-txt

Usage

This program returns the nucleotide-level coverage data for a specific set of the splits or gene in your profile-db.

If you want to get the coverage data for all splits in your profile-db, run anvi-export-splits-and-coverages with the flag --splits-mode.

Simply provide a profile-db and contigs-db pair and specify which splits, or gene, you want to look at. You have three ways to do this:

  1. Provide a single split name. (You can list all splits available with --list-splits)

anvi-get-split-coverages -p profile-db \ -c contigs-db \ -o coverages-txt \ --split-name Day17a_QCcontig9_split_00003

  1. Provide both the name of a bin and the collection it is contained in.

anvi-get-split-coverages -p profile-db \ -c contigs-db \ -o coverages-txt \ -b bin \ -C collection

You can list all collections available with --list-collections or all bins in a collection with --list-bins. Alternatively, you could run anvi-show-collections-and-bins on your profile-db to get a more comprehensive overview.

  1. Provide a gene caller id and a flanking size (bp).

anvi-get-split-coverages -p profile-db \ -c contigs-db \ -o coverages-txt \ --gene-caller-id 25961 \ --flank-length 500

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-get-split-coverages.

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

anvi-get-split-coverages [-h] -p PROFILE_DB [-c CONTIGS_DB] [--split-name SPLIT_NAME] [--contig-name CONTIG_NAME] [-C COLLECTION_NAME] [-b BIN_NAME] [--gene-caller-id GENE_CALLER_ID] [--flank-length INT] [-o FILE_PATH] [--list-splits] [--list-collections] [--list-bins]

Parameters and their descriptions

ESSENTIAL ANVI'O DBs You need to provide a profile database, but whether you will need to provide a contigs database will depend on which input option you want to go with.
-p, --profile-db PROFILE_DB required
Anvi'o profile database
-c, --contigs-db CONTIGS_DB
Anvi'o contigs database generated by 'anvi-gen-contigs-database'
INPUT OPTION #1: SPLIT or CONTIG NAME You want nothing but the coverage values in a single split .. or a contig. FINE.
--split-name SPLIT_NAME
Split name.
--contig-name CONTIG_NAME
Contig name.
INPUT OPTION #2: COLLECTION + BIN You want nucletide-level coverage values for all splits in a bin. FANCY.
-C, --collection-name COLLECTION_NAME
Collection name.
-b, --bin-id BIN_NAME
Bin name you are interested in.
INPUT OPTION #3: GENE CALL You want nucletide-level coverage values for a given gene call. PRO.
--gene-caller-id GENE_CALLER_ID
A single gene id.
--flank-length INT
Extend sequences for gene calls with additional nucleotides from both ends. If the seqeunce for a target gene is between nucleotide positions START and STOP, using a flank lenght of M will give you a sequence that starts at START - M and ends at STOP + M. Default: 0
BORING STUFF The output file and all.
-o, --output-file FILE_PATH
File path to store results.
--list-splits
When declared, the program will list split names in the profile database and quite
--list-collections
Show available collections and exit.
--list-bins
List available bins in a collection and exit.

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.

Copyleft, The anvi'o Project