Merge pull request #79 from stjude/peaksnil

correction when no peaks

scripts/peaksanno.py

@@ -473,9 +473,14 @@ def main():
  gtf_to_genes(options.chrom_sizes, options.gtf)
 
  # Turn 4 column bed to 5 (for SICER peaks: include unique id)
- command = "awk -F'\\t' '{print NF; exit}' " + options.macs_peaks
- numberofcolumns = int(subprocess.check_output(command,shell=True).strip())
-
+ command = "wc -l " + options.macs_peaks + " | awk -F' ' '{print $1}'"
+ checkcolumns = int(subprocess.check_output(command,shell=True).strip())
+ if checkcolumns > 0:
+ command = "awk -F'\\t' '{print NF; exit}' " + options.macs_peaks
+ numberofcolumns = int(subprocess.check_output(command,shell=True).strip())
+ else:
+ sys.exit("ERROR :\tNo peaks were identified\n")
+
  command = "head -n 1 " + options.macs_peaks + ' | cut -f5 '
  fifthcol_value = (str(subprocess.check_output(command,shell=True).strip()).split("'"))[1] #FDRisland from SICER produce a fifth empty column