README
¶
Module name: organelle-sharedregion
Takes two lists of proteins and outputs metrics on the regions (domains/motifs) shared between common preys.
| parameters | definition | default |
|---|---|---|
| compartmentFile | JSON file with lists of proteins to compare | |
| minPreyOccurrence | The minimum number of baits that a prey must be found with in each compartment | 1 |
| outFile | output file name | organelle-shared.txt |
| regionFile | text file with protein name and domains/motifs | |
| saintFile | SAINT file |
Example file formats
compartmentFile
[
{
"name": "compartment 1",
"proteins": ["a", "b" ,"c"]
},
{
"name": "compartment 2",
"proteins": ["d", "e" ,"f"]
}
]
regionFile (tab-separated, no header)
A1BG disorder
A1BG sig_p
A1CF disorder
A1CF low_complexity
A2M disorder
A2M low_complexity
A2M sig_p
A2ML1 disorder
A2ML1 low_complexity
A2ML1 sig_p
A3GALT2 low_complexity
A3GALT2 transmembrane
Output (example)
region no. preys preys preys not containing region
- 4 a, b, c, d
regionC 4 a, b, c, d
regionD 3 a, c, d b
regionA 2 a, b c, d
regionB 1 b a, c, d
Documentation
Source Files
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