Usage
To run the command line version first the archive must be
downloaded
here
and executed in a terminal with
java [-Xmx512m] -jar tintcmd.jar [-conf filename] [-in filename-or-http] [-out filename] [-type b|c|d|m] [-size size] [-check cr1|sine]
The parameter -Xmx is not neccessary and sets the memory maximum for
the java environment (in this case to 512MB). If the application
hangs while processing data, it could be neccessary to encrease this
parameter.
Error Messages
Error messages are written (added) into a file called tintcmd.log in
the folder $HOME/.bioinf (on unix machines) or the appropriate
folder .bioinf in your user's directory in Windows. In case of
failure please send this file along with a failure description.
Configuration File
In addition to the (default) configuration file of the graphical
application, the command line version has 2 new sections and 5
additional parameters to specify input, the type and destination of
output and transpositions of interest. The first 5 parameters may
be overwritten by the command line parameters -input, -output,
-type, -size and -check.
[CmdParams]
in=filename-or-http
out=filename
type=b|c|d|m
size=1000x1000
check=cr1
[Tran Selection]
Alu1
SINE12
-
in: a local filename or a http address where the input
data can be obtained.
-
out: a local filename where the output data will be
written.
-
type: the type of output. It may only specified one of
the following values: [b]ar graph, [c]umulative graph,
[d]istribution graph, [m]atrix
-
size: the size of the generated graphics, width "x"
height size (like 1000x1000).
-
check: the method to calulate the insertions ("cr1" or
"sine").
-
[Tran Selection] specifies the transposition names of
interest. If this section is ommitted all transposition names
read from the input file are taken to be selected. Otherwise
the input file is evaluated against the names given in this
section.
Note: If filenames and http addresses contain blanks, you have to
enclose the address or the filename in inverted commas!
2015-05-06 08:44