Commits

Davide Cittaro  committed 3b6275a

added rmdupid

  • Participants
  • Parent commits 18efeb1

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Files changed (3)

File bwa_submit.sh

 
 experiment_name=$name
 
-LOCAL_SCRATCH=/lustre2/scratch/${experiment_name}
-mkdir $LOCAL_SCRATCH
+LOCAL_SCRATCH=/lustre2/scratch/${RANDOM}/${experiment_name}
+mkdir -p $LOCAL_SCRATCH
 
 echo $experiment_name
 #------------------------------------------------------------------------#
 	# write the first job script
 	SCRIPT=job.$R1_final
 	cat <<__EOF__> $SCRIPT
-#PBS -l select=1:ncpus=2:mem=16g
+#PBS -l select=1:ncpus=2:mem=16g:app=java
 #PBS -N ${job_nameR1:0:15}
 #PBS -M cittaro.davide@hsr.it
 #PBS -P ${experiment_name}
 
 	SCRIPT=job.$R2_final
 	cat <<__EOF__> $SCRIPT
-#PBS -l select=1:ncpus=2:mem=16g
+#PBS -l select=1:ncpus=2:mem=16g:app=java
 #PBS -N ${job_nameR2:0:15}
 #PBS -M cittaro.davide@hsr.it
 #PBS -P ${experiment_name}
 
 	SCRIPT=job.final.$R_final
 	cat <<__EOF__> $SCRIPT
-#PBS -l select=1:ncpus=2:mem=24g
+#PBS -l select=1:ncpus=2:mem=24g:app=java
 #PBS -W depend=afterok:$job_id1:$job_id2
 #PBS -N ${job_nameR:0:15}
 #PBS -M cittaro.davide@hsr.it
+#!/usr/bin/env python2.7
+
+import sys
+
+if len(sys.argv) > 1:
+  stream = open(sys.argv[1])
+else:
+  stream = sys.stdin
+
+for line in stream:
+  if line.startswith('#'):
+    sys.stdout.write(line)
+  else:
+    f = line.strip().split()
+    ids = set(f[2].split(';'))
+    f[2] = ';'.join(ids)
+    sys.stdout.write('\t'.join(f) + '\n')

File stats2gtable.py

 print sep
 print '   |                                    |   number   |  %         |'
 print sep
-for line in content[5:17]:
+for line in content[5:19]:
   f = line.split(':')
   v = f[1].split()
   if len(v) == 1: