def permuteMatrix(matrix_file, file_format, destination_path,
permutation_number):
destination_files = []
for index in range(permutation_number):
# compose the destination file path
destination_file = os.path.join(
destination_path,
os.path.basename(matrix_file) + "_" + str(index))
# Compose the permute-matrix command
cmd = os.path.join(RSATUtils.RSAT_PATH,
"perl-scripts/permute-matrix")
cmd += " -i '" + matrix_file + "'"
cmd += " -in_format " + file_format
cmd += " -o " + destination_file
cmd += " -out_format " + file_format
# Execute the command
cmd_result = commands.getstatusoutput(cmd)
if cmd_result[0] != 0:
Log.log("RSATUtils.permuteMatrix : status returned is :" +
str(cmd_result[0]) + " for command '" + cmd + "'")
Log.log(" permute-matrix output is = \n" + str(cmd_result[1]))
return None
destination_files.append(destination_file)
return destination_files
def outputHistogramFormat(table, histogram_interval, dir_path, prefix,
title1, title2, legendx, legendy, other_columns,
fhisto, out_format):
# save the stats to a tabbed file for classfreq command
input_path = os.path.join(dir_path, prefix + ".tab")
RSATUtils.outputTable(table, input_path)
# execute the classfreq command
histo_path = os.path.join(dir_path, prefix + "_histogram.tab")
cmd = os.path.join(RSATUtils.RSAT_PATH, "perl-scripts/classfreq")
cmd += " -v 1"
cmd += " -i '" + input_path + "'"
cmd += " -col 1"
cmd += " -ci " + str(histogram_interval)
cmd += " -o '" + histo_path + "'"
cmd_result = commands.getstatusoutput(cmd)
if cmd_result[0] != 0:
Log.log("RSATUtils.outputHistogram : status returned is :" +
str(cmd_result[0]) + " for command '" + cmd + "'")
Log.log(" classfreq output is = \n" + str(cmd_result[1]))
return
# Build the graph corresponding to the histogram using RSAT XYGraph command
graph_path = os.path.join(dir_path, prefix + "." + out_format)
cmd = os.path.join(RSATUtils.RSAT_PATH, "perl-scripts/XYgraph")
cmd += " -i '" + histo_path + "'"
cmd += " -title1 '" + title1 + "'"
cmd += " -title2 '" + title2 + "'"
cmd += " -xcol 3 -ycol 4"
if other_columns != None and len(other_columns) > 0:
cmd += "," + ",".join(other_columns)
cmd += " -xleg1 '" + legendx + "'"
cmd += " -yleg1 '" + legendy + "'"
cmd += " -legend -header -format " + out_format
if fhisto:
cmd += " -fhisto"
else:
cmd += " -lines"
cmd += " -o '" + graph_path + "'"
cmd_result = commands.getstatusoutput(cmd)
if cmd_result[0] != 0:
Log.log("RSATUtils.outputHistogram : status returned is :" +
str(cmd_result[0]) + " for command '" + cmd + "'")
Log.log(" XYgraph output is = \n" + str(cmd_result[1]))
return (histo_path, graph_path)
def createLogoFromTF(input_path, input_file, motif_name):
# /home/rsat/rsa-tools/perl-scripts/convert-matrix -logo_dir /home/rsat/rsa-tools/public_html/tmp -v 1 -return logo -o /home/rsat/rsa-tools/public_html/tmp/convert-matrix_2011_09_29.124903_OtxJEc.res
matrix_path = os.path.join(input_path, input_file)
logo_path = os.path.join(input_path, motif_name)
cmd = os.path.join(RSATUtils.RSAT_PATH, "perl-scripts/convert-matrix")
cmd += " -i '" + matrix_path + "'"
cmd += " -from transfac"
cmd += " -logo_format png"
cmd += " -logo_file '" + logo_path + "'"
cmd += " -logo_opt '-e' -logo_opt '-M'"
cmd += " -logo_dir " + input_path
cmd += " -return logo"
cmd_result = commands.getstatusoutput(cmd)
if cmd_result[0] != 0:
Log.log("RSATUtils.createLogoFromTF : status returned is :" +
str(cmd_result[0]) + " for command '" + cmd + "'")
Log.log(" convert-matrix output is = \n" + str(cmd_result[1]))
# Try to remove the reverse complement logo
rc_logo_path = os.path.join(input_path, motif_name + "_m1_rc.png")
if os.path.exists(rc_logo_path):
FileUtils.removeFile(rc_logo_path)
def executeChi2Test(histogram_filepath, data_col, homogen_col):
cmd = "grep -v '^#' " + histogram_filepath
cmd += " | cut -f " + str(data_col) + "," + str(homogen_col)
cmd += " | " + os.path.join(RSATUtils.RSAT_PATH,
"perl-scripts/transpose-table")
cmd += " | cut -f 2-10000"
cmd += " | " + os.path.join(RSATUtils.RSAT_PATH,
"perl-scripts/chi-square -test goodness")
cmd_result = commands.getstatusoutput(cmd)
if cmd_result[0] != 0:
Log.log("RSATUtils.executeChi2Test : status returned is :" +
str(cmd_result[0]) + " for command '" + cmd + "'")
Log.log(" chi-square output is = \n" + str(cmd_result[1]))
return None
output = str(cmd_result[1])
index_chi2 = output.find('#chi2')
if index_chi2 >= 0:
final_header = 'Sgroup'
index_pval = output.find(final_header, index_chi2)
if index_pval >= 0:
results_string = output[index_pval + len(final_header):]
results = results_string.split()
if len(results) >= 3:
chi2 = results[0]
pvalue = results[2]
return (chi2, pvalue)
Log.log(
"RSATUtils.executeChi2Test : chi-square output does not contains desired results :"
+ str(output))
return None
