SimiTriX-SimiTetra Files

#---------------------1 prepare data--------------------------
This is a script to get data for BioERCP GUI application.
You can use it to run blast and parse its result.
This script is useful for SimiTri and SimiTetra, you can run
it use options to get what you want.
#----------------------------------
INSTALLTATION:

This software is based on Perl script, you do not need to
download other modules.


#----------------------------------
RUN IT

It is very simple to run this script ,just like this:

usage: perl PrepareData.pl -m <method BS or BSR> -l <list of id file> -a <blast tab file of datasetA> -b <blast tab file of datasetB> -c <blast tab file of datasetC>
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required:
-m --method=
                        method: BS(Blast Score) or BSR(Blast Scroe Ratio)(default BS)
-l --list= 
                        file of ID's list in Reference data file
-i --input=
                        input file(reference blast to reference itself)(only used in BSR method)
-a --seta=
                        blast tab result of Reference against to datasetA(blastall -i reference -d datastA -m 8)
-b --setb=
                        blast tab result of Reference against to datasetB(blastall -i reference -d datastB -m 8)
-c --setc=
                        blast tab result of Reference against to datasetC(blastall -i reference -d datastC -m 8)

options:
-d --setd=
                        blast tab result of Reference against to datasetD(blastall -i reference -d datastD -m 8)
-t --thershold =
            threshold of blast score(or blast scroe ratio),if the value is smaller than the threshold
            the value will be setted to 0.(default 0)
-o output file of result(default STDOUT)



#---------------------------2  clustering analysis-------------------------
Offer two functions to cluster the points in object (trinagle or tetrahedron).
For SimiTriX:

>source("CalcDistanceCluster1.R") ;
>result <- runcluster1(filename="SimiTriX-For-Clustering.txt",x0=250,y0=250,dis=174) ;

parameters
filename: the file contains contents: each line in it is "item xcoord ycoord".
x0: the x coord of center point in triangle.
y0: the y coord of center point in triangle.
dis: the distance from center point to vertex in triangle.

There will generate a clustering-result colored image and a csv format file to define the classification of each item.


For SimiTetra:
This script uses the package "scatterplot3d", so if you do not install it, please run install.packages("scatterplot3d") first.

>source("CalcDistanceCluster2.R") ;
>result <- runcluster2("SimiTetra-For-Clustering.txt",dis=4) ;

parameters
filename: the file contains contents: each line in it is "item xcoord ycoord zcoord".
dis: the distance from center point to vertex in tetrahedron.

There will generate a clustering-result colored image and a csv format file to define the classification of each item too.