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Motif scripts.
Perl
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README
align_the_clusters.pl
clustering.pl
dot_plots.pl

README

********** THIS IS THE README FILE **********
***
***
*** CREATED BY: MIREYA PLASS ;)
***
***
***
********** HOW TO RUN THE SCRIPTS  **********


SCRIPT Nº 1: dot_plots.pl


*** Input files: ***

file1: file with the z-scores and the p-values for one of the sets you want to compare
file2: file with the z-scores and the p-values for the other set you want to compare
name1: name of the x-axis (for the plot. it will represent the data of file1)
name2: name of the y-axis (for the plot. it will represent the data of file2)
title: name of the title of the plot

name1,name2 and title cannot have blank spaces. use "_" instead

file1 and file2 have to contain 3 columns (tab separated)

ex:
AAAGAA  2.9164355012174 0.001770280
GAAGAA  0.709008144909659       0.2391597
AAAAGA  2.63630134311544        0.004190763

*** command: 
./dot_plots.pl R_oryzae_acceptor_z_score R_oryzae_donor_z_score name_of_x_axis name_of_y_axis title_of_the_plot

*** Output file ***

a postscript file with a dotplot of the distribution.


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SCRIPT Nº 2:  clustering.pl


*** Input files: ***

file1: file with the z-scores and the p-values for one of the sets you want to compare
file2: file with the z-scores and the p-values for the other set you want to compare
title: name of the title of the plot

name1,name2 and title cannot have blank spaces. use "_" instead

file1 and file2 have to contain 3 columns (tab separated)

ex:
AAAGAA  2.9164355012174 0.001770280
GAAGAA  0.709008144909659       0.2391597
AAAAGA  2.63630134311544        0.004190763

*** command: 
./clustering.pl R_oryzae_acceptor_z_score R_oryzae_donor_z_score title_of_the_plot

*** Output file ***

output file 1: a postscript file with a dendogram of the sequences.
output file 2: a postscript file with a dendogram of the sequences and the clusters in boxes.
output file 3: text file. Each line has the sequences that belong to a particular cluster. 
		This file will be used to run the next program


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SCRIPT Nº 3:  align_the_clusters.pl


*** Input files: ***
The output file 3 of script 2

ex:

AAAGAT:AAAAGA:AAAAAG
ATAAAA:TTAAAG:GTAAAA:TAAAAA:TAAAAG:AATAAA:ATTAAA
AGCAAA:TAACAA


*** command: 
./align_the_clusters.pl name_of_the_file

*** Output file ***+
png files, one for each cluster with more than 4 sequences
other file: information_of_the_pictograms.txt. contains information of the sequences used for each pictogram
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