Command line tools
ProCope provides a collection of command line tools which provide
fast access to many methods and functions in a way suitable for
automated computations and batch jobs. In this part of the
documentation you find general information on how to access these tools
as well as descriptions and example calls for each single tool.
Note: All tools detect GZIPed input files and automatically decompress them.
Calling from the command line
All tools are called using a single script file which can be found in
the root directory of the package:
cmdline.sh
- for systems with
a bash-shell (e.g. Linux)
cmdline.bat
- for Microsoft
Windows Systems
The first argument you pass to the script is the name of the command
line tool you want to use. Specifiy no parameters to get a list of
available tool names (or consult this documentation). Each command line
tool itself will print usage information when called without any
further parameters.
Note: All examples in this documentation use the cmdline.sh
script for bash shells. Windows users simply replace this command with cmdline.bat
.
Example:
cmdline.sh colocalization
- starts the colocalization tool and shows usage information as no further parameters are passed
Memory
By default 256MB of memory will be available for the Java VM when using
a command line tool. If you want to change this amount, specificy -Xmx000m
as the first argument where 000
is the amount of megabytes which will be available. (Note: the -Xmx
parameter is directly passed to the Java virtual machine, syntax errors will cause error messages of the Java interpreter).
Example:
cmdline.sh -Xmx1024m generatescores
... - starts the scores generator with 1GB of available memory
Return codes
All command line tools return
- 0 - if everything worked fine
- 1 - if invalid or no command line arguments where specified
- 2 - if an error occured during the program execution (e.g. file not found)
Name mapping
All tools support the argument -namemap
. See also: Name mapping
Tools
The following command line tools are provided with this package:
btsampler
- randomly samples purification data, needed to calculate Bootstrap scores
btclusterer
- cluster bootstrap samples
btfinisher
- integrate clustering results to calculate final bootstrap network
clusterer
- clusters score networks to derive complex sets
colocalization
- calculates colocalization scores or PPVs for a given complex set
complexcompare
- compares given sets of complexes
complexmanipulate
- contains different methods to manipulate complex sets
complexscores
- calculates scores for complex sets using a given scores network
generatescores
- generates score networks from purification data
gosim
- calculates semantic similarities based on GO annotations
roc
- plots a ROC curve for a given set of networks and a reference complex set