Table 1.
Utilities in the ProdMX tool.
| Category/Utility | Description | Utility type | Input | Output |
|---|---|---|---|---|
| Build matrix | ||||
| prodmx-buildDomain | Build a folder containing a compressed sparse matrix of protein functional domains and index files | Command-line | [1] | [7] |
| prodmx-buildArchitecture | Build a folder containing a compressed sparse matrix of domain architectures and index files | Command-line | [1] | [7] |
| Load matrix | ||||
| loadMatrix | Load a compressed sparse matrix into an object variable | Package | [2] | [8] |
| loadBinMatrix | Load a binary compressed sparse matrix into an object variable | Package | [2] | [9] |
| Analysis | ||||
| getRow | Get a list of all row labels of the matrix | Package | – | [10] |
| getColumn | Get a list of all column labels of the matrix | Package | – | [11] |
| getProteinId | Get all protein id associated with given domain functional domains or domain architectures | Package | [3] (list_row), [4] (list_col), [5] (output) | [12] |
| sumRow | Summation of presence and absence values in row wise | Package | [3] (list_row), [4] (list_col) | [13] |
| sumColumn | Summation of presence and absence values in column wise | Package | [3] (list_row), [4] (list_col) | [14] |
| calCore | Calculate core protein functional domains or domain architectures | Package | [3] (list_row), [4] (list_col), [6] (counservation) | [15] |
[1] a tab-delimited file of unique genome ids and hmmsearch result file paths, [2] a path to folder containing matrices and database from Prodmx's build matrix command,
[3] a list of genome ids, [4] a list of functional domains or domain architectures, [5] a result file path, [6] a conservation cut-off with a default at 95%,
[7] a folder containing compressed matrices and indexes of functional domains, [8] a ProdMX object for a count matrix, [9] a ProdMX object for a binary matrix,
[10] a list variable of all row labels (genome ids), [11] a list variable of all column labels (functional domain or domain architecture ids),
[12] a tab-delimited file of genome ids and protein ids,
[13] a Pandas dataframe of the count of domains or domain architectures for each genome,
[14] a Pandas dataframe of the count of genome for each domain or domain architecture,
[15] a pandas dataframe of the genome count for each core functinal domain or domain architecture.