anvi-import-protein-profile

This program imports protein abundance data into a profile database..

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Authors

Samuel Miller
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Requires

profile-db

Provides

This program does not seem to provide any artifacts. Such programs usually print out some information for you to see or alter some anvi’o artifacts without producing any immediate outputs.

Usage

This program imports a protein abundance profile, such as from proteomic experiments, into a profile-db.

This program takes as input a tab-delimited file of protein abundance data and a profile-db. The tabular file must have four columns with the following names: “source”, “accession”, “sample”, and “abundance”. Each row of the table corresponds to a distinct protein abundance measurement.

  • “source” is the source of the protein accessions. It must be a gene function annotation source stored in the anvi’o profile-db (available sources can be found with the program, anvi-db-info).
  • “accession” is the protein ID in the annotation source. A contigs database built from a GenBank file, for example, could contain the source, “NCBI_PGAP”, and the accession, “WP_011862028.1”.
  • “sample” is the name of the sample in which the measurement was made. It need not be the same as any nucleotide sequence samples stored in the profile database.
  • “abundance” is the protein abundance value, however defined.

Once protein abundances are stored in a profile database, they can be loaded into a metabolic reaction-network for analysis in the context of biochemical pathways.

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-import-protein-profile.

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-import-protein-profile [-h] --protein-profile-table PROTEIN_PROFILE_TABLE -p PROFILE_DB

Parameters and their descriptions

options
--protein-profile-table PROTEIN_PROFILE_TABLE required
This tab-delimited table contains protein abundance data from different samples. It should have the following named columns: 'source', 'accession', 'sample', and 'abundance'. Each row corresponds to a distinct protein abundance measurement. 'source' is the source of the protein accessions, and must be a gene function annotation source stored in the anvi'o profile database (available sources can be found with the program, `anvi-db-info`). 'accession' is the protein ID in the annotation source. A contigs database built from a GenBank file, for example, could contain the source, 'NCBI_PGAP', and the accession, 'WP_011862028.1'. 'sample' is the name of the sample in which the measurement was made. It need not be the same as any nucleotide sequence samples stored in the profile database. 'abundance' is the protein abundance value itself.
-p, --profile-db PROFILE_DB required
Anvi'o profile database

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