input = open(filename,'rt')

fwtS = open(outfile,'wb')

region = options.ex/2

posS = ""

negS = ""

posnoS = ""

negnoS = ""

allS = ""

countS = 0

countnoS = 0

tagS = []

tagnoS = []

std = []

for line in input:

if line.startswith("#"):

fwtS.write(line)

continue

if(len(line.split("\t")) == 9):

chrom,junk,junk,start,end,tag,strand,junk,attr = line.split("\t")

if float(get_std(attr.rstrip())) == 0:

tagS.append(int(tag))

if strand == "+":

posS = posS+line

else:

negS = negS+line

else:

countnoS +=1

std.append(float(get_std(attr.rstrip())))

tagnoS.append(int(tag))

allS = allS+line

if strand == "+":

posnoS = posnoS+line

else:

negnoS = negnoS+line

#posS_int_negnoS = pybedtools.BedTool(posS,from_string=True).slop(g=sg07,l=10,r=10).intersect(pybedtools.BedTool(negnoS,from_string=True),u=True) # add half the exclusion zone to start and end coordinate

#negS_int_posnoS = pybedtools.BedTool(negS,from_string=True).slop(g=sg07,l=10,r=10).intersect(pybedtools.BedTool(posnoS,from_string=True),u=True)

try:

posS_int_negnoS = pybedtools.BedTool(posS,from_string=True).intersect(pybedtools.BedTool(negnoS,from_string=True).slop(g=sg07,l=region,r=region),u=True) # add half the exclusion zone to start and end coordinate

negS_int_posnoS = pybedtools.BedTool(negS,from_string=True).intersect(pybedtools.BedTool(posnoS,from_string=True).slop(g=sg07,l=region,r=region),u=True)

fullFile = allS+str(posS_int_negnoS)+str(negS_int_posnoS) # merging singletons and non singletons together

countS = posS_int_negnoS.count() + negS_int_posnoS.count() # Couting all the singletongs

fwtS.write(str(pybedtools.BedTool(fullFile,from_string=True).sort()))

except pybedtools.helpers.BEDToolsError:

# if the peak call file had no singletons in it.

print "The file had no singletons"

countS = 0

fullFile = allS

fwtS.write(str(pybedtools.BedTool(fullFile,from_string=True).sort()))

ratio = signal2noise(tagnoS,tagS) # calculating the signal to noise ratio.

#fullFile = allS+str(posS_int_negnoS)+str(negS_int_posnoS) # merging singletons and non singletons together

#countS = posS_int_negnoS.count() + negS_int_posnoS.count() # Couting all the singletongs

#fwtS.write(str(pybedtools.BedTool(fullFile,from_string=True).sort()))

#ratio = signal2noise(tagnoS,tagS) # calculating the signal to noise ratio.

if not ";" in attr:

return(attr.split("=")[1])

else:

list1 = attr.split(";")

for at in list1:

if at.split("=")[0] == "stddev":

fstats = open(stats,'wb')

header = "Filename\tMapped_reads\tUniquely_mapped_reads\tPeaks\tSingletons\tPeak_median_excluding_singletons\tPeak_mean_exclusing_singletons\tMedian_std_excluding_singeltons\tMean_std_excluding_singletons\tSignal2Nose"

fstats.write(header)

fstats.write("\n")

for k,v in allInfo.items():

fstats.write(k+"\t"+v)

if sum(Stags) == 0:

return(1) # instead of returning Nan I want to see those values with no singletons, hence the value 1

else:

input_paths may be:

- a directory to run on all files in them

- a single file.

REQUIREMENT:

1) a file with chromosome lengths in it, in the format: chr1 1 1000000.

This file should be in the same folder as the script. Do not remove it. The

file name is sg07.txt. Change it for other organism.

example usages:

python create_weighted_singletons_from_peaks.py /usr/local/peaks/genetrack_peaks.gff

python create_weighted_singletons_from_peaks.py /usr/local/peaks/genetrack_s5e10/

parser = OptionParser(usage='%prog [options] input_paths', description=usage, formatter=CustomHelpFormatter())

parser.add_option('-e', action='store', type='int', dest='ex',default=20,

help='Exclusion zone used during peak calling.Default 20')

#parser.add_option('-d', action='store', type='int', dest='down_distance',default=50,

# help='Downstream distance to go from the peak-pair mid_point, Default=50')

#parser.add_option('-i', action='store', type='int', dest='iter',default=100,

# help='Number of iterations to do for shuffling')

(options, args) = parser.parse_args()

# Check if all the required arguments are provided, else exit

if not args:

parser.print_help()

sys.exit(1)

try:

from scipy.stats import stats

import pybedtools

except ImportError:

print "You need to install Scipy(http://www.scipy.org/Download) before you can run this script."

print "If you have Scipy installed, then you should check if you have pybedtools installed"

sys.exit(1)

sg07 = os.path.join(os.path.dirname(os.path.abspath(__file__)),"sg07.txt") # location of the chromosome length file. Located with the scripts. DO NOT change

if not os.path.isdir(args[0]):

# Create dir names for wtS folders

outdir_wtS = os.path.join(os.path.dirname(args[0]),"_wtS")

# Check if wtS dir exists else create them

if not os.path.exists(outdir_wtS) :

os.mkdir(outdir_wtS)

outfile_wtS = os.path.join(outdir_wtS,os.path.splitext(os.path.basename(args[0]))[0]+"wtS.gff")

stats = os.path.join(outdir_wtS,"peak_stats.txt")

process_file(args[0],outfile_wtS,sg07,options)

print_stats(stats)

else:

if not os.path.exists(args[0]):

parser.error('Path %s does not exist.' % args[0])

# Create dir names for noS and onlyS folders

outdir_wtS = os.path.join(args[0],"_wtS")

if not os.path.exists(outdir_wtS):

os.mkdir(outdir_wtS)

stats = os.path.join(outdir_wtS,"peak_stats.txt")

for name in os.listdir(args[0]):

if name.endswith('.gff'):

fname = os.path.join(args[0], name)

outfile_wtS = os.path.join(outdir_wtS,os.path.splitext(name)[0]+"wtS.gff")

process_file(fname,outfile_wtS,sg07,options)