move find_peak_center to find_peak_max

src/bash_slurm/RunSearchMax.sh

@@ -29,7 +29,7 @@ scriptSH="""
 #!/bin/bash -l
 source activate py27
 echo SearchMax $peak_technique peak detection for $project_name
-python $scriptFolder/src/python/find_peak_center.py -p $folder -e $project_name -t $peak_technique -s $size -g $genome_file -b $bed_name
+python $scriptFolder/src/python/find_peak_max.py -p $folder -e $project_name -t $peak_technique -s $size -g $genome_file -b $bed_name
 echo End SearchMax for $peak_technique
 """
 

src/python/find_peak_center.py → src/python/find_peak_max.py

@@ -5,6 +5,8 @@ from Bio import SeqIO
 
 def find_peak_max(path, exp_design_name, size, mouse_seq, peak_technique, bed_name):
     final_bed_name = 'MaxValues'
+    if bed_name == 'Raw':
+        final_bed_name = 'MaxValues'
     if bed_name == 'MaxValues':
         final_bed_name = 'MaxMaxValues'
     print(final_bed_name)
@@ -106,12 +108,12 @@ def main(argv):
     try:
         opts, args = getopt.getopt(argv,"hp:e:t:s:g:b:", ["path=", "expdesign=","peak_technique=","size=","genome=","bed_name"])
     except getopt.GetoptError:
-        print('Cannot run command - Help: find_peak_center.py -p <path> -e <expdesign> -t <peak_technique> '
+        print('Cannot run command - Help: find_peak_max.py -p <path> -e <expdesign> -t <peak_technique> '
               '-s <size> -g <genome> -b <bed_name>')
         sys.exit(2)
     for opt, arg in opts:
         if opt == '-h':
-            print('find_peak_center.py -p <path> -e <expdesign> -t <peak_technique> -s <size> -g <genome> -b <bed_name>')
+            print('find_peak_max.py -p <path> -e <expdesign> -t <peak_technique> -s <size> -g <genome> -b <bed_name>')
             sys.exit()
         elif opt in ("-p", "--path"):
             path = arg