Given a .tsv file with a column containing Uniprot protein IDs, scrape annotations for subcellular location from Uniprot.org
The simplest way to install locScrape is to download one of the precompiled binaries under the releases tab. Binaries are available for OSX and CentOS.
You can also clone this repository with the command.
git clone https://github.com/ajmaurais/locScrape
usage: locScrape [-h] [-i IDCOL] [--columns {sl,go,all}] [--locCol LOCCOL]
[--goCol GOCOL] [--allCol ALLCOL] [--nThread NTHREAD]
[-o OFNAME] [--inPlace]
input_file [input_file ...]
Get subcellular location annotations for a list of Uniprot protein IDs. A
column in input_file should contain Uniprot IDs. After locScrape runs,
columns will be added for Unipriot location annotations, GO cellular component
annotations.
positional arguments:
input_file .tsv or .csv files to process.
optional arguments:
-h, --help show this help message and exit
-i IDCOL, --idCol IDCOL
Name of column containing Uniprot IDs.
--columns {sl,go,all}
Which new columns should be added?
sl : Uniprot annotation for subcellular location
go : GO annotation for cellular component
all : both sl and go
Default is all.
--locCol LOCCOL Name of new column to add with subcellular location.
--goCol GOCOL Name of new column to add with GO cellular component
annotation.
--allCol ALLCOL Name of new column to add with GO and Uniprot
annotations combined.
--nThread NTHREAD Number of threads to use to lookup Uniprot
annotations. Default is the number of logical cores on
your system.
-o OFNAME, --ofname OFNAME
Name of output file. Default is <input_file>_loc.tsv.
If multiple input files are given, this argument is
ignored.
--inPlace Overwrite input files with output files. This option
overrides the --ofname option.