def main(argv):
parser = OptionParser()
parser.add_option("-s", "--species", action="store", type="string",
dest="species", help="species under consideration", metavar="<str>")
parser.add_option("-b", "--raw_bam_file", action="store", type="string",
dest="bam_file", help="raw bam file", metavar="<file>")
parser.add_option("-t", "--threshold", action="store", type="int",
dest="threshold", help="threshold for copy number", metavar="<int>")
parser.add_option("-o", "--output_file_name", action="store", type="string",
dest="out_file", help="output file name", metavar="<file>")
(opt, args) = parser.parse_args(argv)
if len(argv) < 8:
parser.print_help()
sys.exit(1)
if opt.species in GenomeData.species_chroms.keys():
chroms = GenomeData.species_chroms[opt.species];
else:
print "This species is not recognized, exiting";
sys.exit(1);
SeparateByChrom.separateByChromBamToBed(chroms, opt.bam_file, '.bed1')
for chrom in chroms:
if (Utility.fileExists(chrom + ".bed1")):
strand_broken_remove(chrom, opt.threshold)
SeparateByChrom.combineAllGraphFilesBedToBam(chroms, '.bed2', opt.bam_file, opt.out_file)
SeparateByChrom.cleanup(chroms, '.bed1')
SeparateByChrom.cleanup(chroms, '.bed2')
def main(argv):
"""
Note the window_size and the fragment_size are both input as strings, as they are used in
a shell script in makeGraphFile.
"""
parser = OptionParser()
parser.add_option("-s", "--species", action="store", type="string",
dest="species", help="mm8,hg18,dm2,etc", metavar="<str>")
parser.add_option("-b", "--bed_file", action="store", type="string",
dest="bamfile", help="bed file to make graph file of",
metavar="<file>")
parser.add_option("-w", "--window_size", action="store", type="int",
dest="window_size", help="window size", metavar="<int>")
parser.add_option("-i", "--fragment_size", action="store", type="int",
dest="fragment_size",
help="size of fragments after CHIP experiment",
metavar="<int>")
parser.add_option("-o", "--outfile", action="store", type="string",
dest="outfile", help="output bed summary file name",
metavar="<file>")
(opt, args) = parser.parse_args(argv)
#if len(argv) < 10:
# sys.stderr.write(str(len(argv)) + '\n')
# parser.print_help()
# sys.exit(1)
#
#if opt.species in GenomeData.species_chroms.keys():
# chroms = GenomeData.species_chroms[opt.species];
#
#chrom_lengths = GenomeData.species_chrom_lengths[opt.species];
chromsDict= SeparateByChrom.getChromsFromBam(opt.bamfile)
SeparateByChrom.separateByChromBamToBed(chromsDict.keys(), opt.bamfile, '.bed');
makeGraphFile(chromsDict.keys(), chromsDict, opt.window_size, opt.fragment_size);
final_output_file = opt.outfile;
final_output_file = SeparateByChrom.combineAllGraphFiles(chromsDict.keys(), ".graph", final_output_file);
SeparateByChrom.cleanup(chromsDict.keys(), ".bed");
SeparateByChrom.cleanup(chromsDict.keys(), ".graph");
def main(argv):
parser = OptionParser()
parser.add_option("-s", "--species", action="store", type="string",
dest="species", help="species under consideration", metavar="<str>")
parser.add_option("-b", "--raw_bam_file", action="store", type="string",
dest="bam_file", help="raw bam file", metavar="<file>")
parser.add_option("-t", "--threshold", action="store", type="int",
dest="threshold", help="threshold for copy number", metavar="<int>")
parser.add_option("-o", "--output_file_name", action="store", type="string",
dest="out_file", help="output file name", metavar="<file>")
## Add options to filter reads
parser.add_option("-f", "--requiredFlag", type= 'int', help="Required bit in sam flag. Same as samtools view -f")
parser.add_option("-F", "--filterFlag", type= 'int', help="Filter out bit in sam flag, Same as samtools view -F")
parser.add_option("-q", "--mapq", type= 'int', help="minimum mapq for a read to be kept")
(opt, args) = parser.parse_args(argv)
if len(argv) < 8:
parser.print_help()
sys.exit(1)
#if opt.species in GenomeData.species_chroms.keys():
# chroms = GenomeData.species_chroms[opt.species];
#else:
# sys.stderr.write("\nThis species is not recognized, exiting\n");
# sys.exit(1);
chroms= SeparateByChrom.getChromsFromBam(opt.bam_file)
SeparateByChrom.separateByChromBamToBed(chroms, opt.bam_file, '.bed1', requiredFlag= opt.requiredFlag, filterFlag= opt.filterFlag, mapq= opt.mapq)
if opt.threshold > 0:
for chrom in chroms:
if (Utility.fileExists(chrom + ".bed1")):
strand_broken_remove(chrom, opt.threshold)
SeparateByChrom.combineAllGraphFilesBedToBam(chroms, '.bed2', opt.bam_file, opt.out_file)
else:
SeparateByChrom.combineAllGraphFilesBedToBam(chroms, '.bed1', opt.bam_file, opt.out_file)
SeparateByChrom.cleanup(chroms, '.bed1')
SeparateByChrom.cleanup(chroms, '.bed2')
def main(argv):
"""
Note the window_size and the fragment_size are both input as strings, as they are used in
a shell script in makeGraphFile.
"""
parser = OptionParser()
parser.add_option("-s",
"--species",
action="store",
type="string",
dest="species",
help="mm8,hg18,dm2,etc",
metavar="<str>")
parser.add_option("-b",
"--bed_file",
action="store",
type="string",
dest="bamfile",
help="bed file to make graph file of",
metavar="<file>")
parser.add_option("-w",
"--window_size",
action="store",
type="int",
dest="window_size",
help="window size",
metavar="<int>")
parser.add_option("-i",
"--fragment_size",
action="store",
type="int",
dest="fragment_size",
help="size of fragments after CHIP experiment",
metavar="<int>")
parser.add_option("-o",
"--outfile",
action="store",
type="string",
dest="outfile",
help="output bed summary file name",
metavar="<file>")
(opt, args) = parser.parse_args(argv)
#if len(argv) < 10:
# sys.stderr.write(str(len(argv)) + '\n')
# parser.print_help()
# sys.exit(1)
#
#if opt.species in GenomeData.species_chroms.keys():
# chroms = GenomeData.species_chroms[opt.species];
#
#chrom_lengths = GenomeData.species_chrom_lengths[opt.species];
chromsDict = SeparateByChrom.getChromsFromBam(opt.bamfile)
SeparateByChrom.separateByChromBamToBed(chromsDict.keys(), opt.bamfile,
'.bed')
makeGraphFile(chromsDict.keys(), chromsDict, opt.window_size,
opt.fragment_size)
final_output_file = opt.outfile
final_output_file = SeparateByChrom.combineAllGraphFiles(
chromsDict.keys(), ".graph", final_output_file)
SeparateByChrom.cleanup(chromsDict.keys(), ".bed")
SeparateByChrom.cleanup(chromsDict.keys(), ".graph")
def main(argv):
parser = OptionParser()
parser.add_option("-s",
"--species",
action="store",
type="string",
dest="species",
help="species under consideration",
metavar="<str>")
parser.add_option("-b",
"--raw_bam_file",
action="store",
type="string",
dest="bam_file",
help="raw bam file",
metavar="<file>")
parser.add_option("-t",
"--threshold",
action="store",
type="int",
dest="threshold",
help="threshold for copy number",
metavar="<int>")
parser.add_option("-o",
"--output_file_name",
action="store",
type="string",
dest="out_file",
help="output file name",
metavar="<file>")
## Add options to filter reads
parser.add_option(
"-f",
"--requiredFlag",
type='int',
help="Required bit in sam flag. Same as samtools view -f")
parser.add_option(
"-F",
"--filterFlag",
type='int',
help="Filter out bit in sam flag, Same as samtools view -F")
parser.add_option("-q",
"--mapq",
type='int',
help="minimum mapq for a read to be kept")
(opt, args) = parser.parse_args(argv)
if len(argv) < 8:
parser.print_help()
sys.exit(1)
#if opt.species in GenomeData.species_chroms.keys():
# chroms = GenomeData.species_chroms[opt.species];
#else:
# sys.stderr.write("\nThis species is not recognized, exiting\n");
# sys.exit(1);
chroms = SeparateByChrom.getChromsFromBam(opt.bam_file)
SeparateByChrom.separateByChromBamToBed(chroms,
opt.bam_file,
'.bed1',
requiredFlag=opt.requiredFlag,
filterFlag=opt.filterFlag,
mapq=opt.mapq)
if opt.threshold > 0:
for chrom in chroms:
if (Utility.fileExists(chrom + ".bed1")):
strand_broken_remove(chrom, opt.threshold)
SeparateByChrom.combineAllGraphFilesBedToBam(chroms, '.bed2',
opt.bam_file,
opt.out_file)
else:
SeparateByChrom.combineAllGraphFilesBedToBam(chroms, '.bed1',
opt.bam_file,
opt.out_file)
SeparateByChrom.cleanup(chroms, '.bed1')
SeparateByChrom.cleanup(chroms, '.bed2')
def main(argv):
parser = OptionParser()
parser.add_option("-s", "--species", action="store", type="string", dest="species", help="species, mm8, hg18", metavar="<str>")
parser.add_option("-a", "--rawchipreadfile", action="store", type="string", dest="chipreadfile", metavar="<file>", help="raw read file from chip in bed format")
parser.add_option("-b", "--rawcontrolreadfile", action="store", type="string", dest="controlreadfile", metavar="<file>", help="raw read file from control in BAM format")
parser.add_option("-f", "--fragment_size", action="store", type="int", dest="fragment_size", metavar="<int>", help="average size of a fragment after CHIP experiment")
parser.add_option("-d", "--islandfile", action="store", type="string", dest="islandfile", metavar="<file>", help="island file in BED format")
parser.add_option("-o", "--outfile", action="store", type="string", dest="out_file", metavar="<file>", help="island read count summary file")
parser.add_option("-t", "--mappable_fraction_of_genome_size ", action="store", type="float", dest="fraction", help="mapable fraction of genome size", metavar="<float>")
(opt, args) = parser.parse_args(argv)
if len(argv) < 14:
parser.print_help()
sys.exit(1)
if opt.species in GenomeData.species_chroms.keys():
chroms = GenomeData.species_chroms[opt.species];
genomesize = sum (GenomeData.species_chrom_lengths[opt.species].values());
genomesize = opt.fraction * genomesize;
else:
print "This species is not recognized, exiting";
sys.exit(1);
chip_library_size=get_total_tag_counts.get_total_tag_counts_bam(opt.chipreadfile);
control_library_size=get_total_tag_counts.get_total_tag_counts_bam(opt.controlreadfile);
print "chip library size ", chip_library_size
print "control library size ", control_library_size
totalchip = 0;
totalcontrol = 0;
islands = BED.BED(opt.species, opt.islandfile, "BED3", 0);
# separate by chrom the chip library
if Utility.fileExists(opt.chipreadfile):
SeparateByChrom.separateByChromBamToBed(chroms, opt.chipreadfile, '.bed1');
else:
print opt.chipreadfile, " not found";
sys.exit(1)
# separate by chrom the control library
if Utility.fileExists(opt.controlreadfile):
SeparateByChrom.separateByChromBamToBed(chroms, opt.controlreadfile, '.bed2');
else:
print opt.controlreadfile, " not found";
sys.exit(1)
island_chip_readcount = {};
island_control_readcount = {};
for chrom in chroms:
if chrom in islands.keys():
if len(islands[chrom]) != 0:
island_list = islands[chrom];
if Utility.is_bed_sorted(island_list) == 0:
island_list.sort(key=operator.attrgetter('start'));
island_start_list = []
island_end_list = []
for item in island_list:
island_start_list.append(item.start)
island_end_list.append(item.end)
island_chip_readcount_list=[0]*len(island_list);
read_file = chrom + ".bed1";
f = open(read_file,'r')
for line in f:
if not re.match("#", line):
line = line.strip()
sline = line.split()
position = associate_tags_with_regions.tag_position(sline, opt.fragment_size)
index =associate_tags_with_regions.find_readcount_on_islands(island_start_list, island_end_list, position);
if index >= 0:
island_chip_readcount_list[index] += 1;
totalchip += 1;
f.close();
island_chip_readcount[chrom] = island_chip_readcount_list;
island_control_readcount_list=[0]*len(island_list);
read_file = chrom + ".bed2";
f = open(read_file,'r')
for line in f:
if not re.match("#", line):
line = line.strip()
sline = line.split()
position = associate_tags_with_regions.tag_position(sline, opt.fragment_size)
index = associate_tags_with_regions.find_readcount_on_islands(island_start_list, island_end_list, position);
if index >= 0:
island_control_readcount_list[index] += 1;
totalcontrol += 1;
f.close();
island_control_readcount[chrom] = island_control_readcount_list;
chip_background_read = chip_library_size - totalchip;
control_background_read = control_library_size - totalcontrol;
#scaling_factor = chip_background_read*1.0/control_background_read;
scaling_factor = chip_library_size*1.0/control_library_size;
print "Total number of chip reads on islands is: ", totalchip;
print "Total number of control reads on islands is: ", totalcontrol;
#print "chip_background_read ", chip_background_read
#print "control_background_read ", control_background_read
out = open(opt.out_file, 'w');
pvalue_list = [];
result_list = [];
for chrom in chroms:
if chrom in islands.keys():
if len(islands[chrom]) != 0:
island_list = islands[chrom];
for index in xrange(len(island_list)):
item = island_list[index];
observation = (island_chip_readcount[chrom])[index];
control_tag = (island_control_readcount[chrom])[index];
if (island_control_readcount[chrom])[index] > 0:
#average = (island_control_readcount[chrom])[index] * scaling_factor;
average = control_tag * scaling_factor
fc = float(observation)/float(average);
else:
length = item.end - item.start + 1;
average = length * control_library_size *1.0/genomesize;
average = min(0.25, average)* scaling_factor;
fc = float(observation)/float(average);
if observation > average:
pvalue = scipy.stats.poisson.sf((island_chip_readcount[chrom])[index], average)[()];
else:
pvalue = 1;
pvalue_list.append(pvalue);
item_dic = {}
item_dic['chrom'] = item.chrom
item_dic['start'] = item.start
item_dic['end'] = item.end
item_dic['chip'] = observation
item_dic['control'] = control_tag
item_dic['pvalue'] = pvalue
item_dic['fc'] = fc
result_list.append(item_dic)
pvaluearray=scipy.array(pvalue_list);
pvaluerankarray=scipy.stats.rankdata(pvaluearray);
totalnumber = len(result_list);
for i in range(totalnumber):
item = result_list[i];
alpha = pvalue_list[i] * totalnumber/pvaluerankarray[i];
if alpha > 1:
alpha = 1;
outline = item['chrom'] + "\t" + str(item['start']) + "\t" + str(item['end']) + "\t" + str(item['chip']) + "\t" + str(item['control']) + "\t" + str(item['pvalue']) + "\t" + str(item['fc']) + "\t" + str(alpha) + "\n";
out.write(outline);
#pvalue_list.sort()
#for item in result_list:
#pvalue = float(item['pvalue'])
#alpha = pvalue * len(result_list) / (pvalue_list.index(pvalue) + 1)
#if alpha > 1:
#alpha = 1;
#outline = item['chrom'] + "\t" + str(item['start']) + "\t" + str(item['end']) + "\t" + str(item['chip']) + "\t" + str(item['control']) + "\t" + str(item['pvalue']) + "\t" + str(item['fc']) + "\t" + str(alpha) + "\n";
#out.write(outline);
out.close();
SeparateByChrom.cleanup(chroms, '.bed1');
SeparateByChrom.cleanup(chroms, '.bed2');
def main(argv):
parser = OptionParser()
# parser.add_option("-s", "--species", action="store", type="string", dest="species", help="species, mm8, hg18", metavar="<str>")
parser.add_option("-a",
"--rawchipreadfile",
action="store",
type="string",
dest="chipreadfile",
metavar="<file>",
help="raw read file from chip in bed format")
parser.add_option("-b",
"--rawcontrolreadfile",
action="store",
type="string",
dest="controlreadfile",
metavar="<file>",
help="raw read file from control in BAM format")
parser.add_option("-f",
"--fragment_size",
action="store",
type="int",
dest="fragment_size",
metavar="<int>",
help="average size of a fragment after CHIP experiment")
parser.add_option("-d",
"--islandfile",
action="store",
type="string",
dest="islandfile",
metavar="<file>",
help="island file in BED format")
parser.add_option("-o",
"--outfile",
action="store",
type="string",
dest="out_file",
metavar="<file>",
help="island read count summary file")
parser.add_option("-t",
"--mappable_fraction_of_genome_size ",
action="store",
type="float",
dest="fraction",
help="mapable fraction of genome size",
metavar="<float>")
(opt, args) = parser.parse_args(argv)
#if len(argv) < 14:
# parser.print_help()
# sys.exit(1)
#
#if opt.species in GenomeData.species_chroms.keys():
# chroms = GenomeData.species_chroms[opt.species];
# genomesize = sum (GenomeData.species_chrom_lengths[opt.species].values());
# genomesize = opt.fraction * genomesize;
#else:
# sys.stderr.write("This species is not recognized, exiting\n")
# sys.exit(1)
chromsDict = SeparateByChrom.getChromsFromBam(opt.chipreadfile)
genomesize = sum(chromsDict.values()) * opt.fraction
chip_library_size = get_total_tag_counts.get_total_tag_counts_bam(
opt.chipreadfile)
control_library_size = get_total_tag_counts.get_total_tag_counts_bam(
opt.controlreadfile)
sys.stderr.write("chip library size %s\n" % (chip_library_size))
sys.stderr.write("control library size %s\n" % (control_library_size))
totalchip = 0
totalcontrol = 0
islands = BED.BED(chromsDict.keys(), opt.islandfile, "BED3", 0)
# separate by chrom the chip library
if Utility.fileExists(opt.chipreadfile):
SeparateByChrom.separateByChromBamToBed(chromsDict.keys(),
opt.chipreadfile, '.bed1')
else:
sys.stderr.write(opt.chipreadfile + " not found")
sys.exit(1)
# separate by chrom the control library
if Utility.fileExists(opt.controlreadfile):
SeparateByChrom.separateByChromBamToBed(chromsDict.keys(),
opt.controlreadfile, '.bed2')
else:
sys.stderr.write(opt.controlreadfile + " not found")
sys.exit(1)
island_chip_readcount = {}
island_control_readcount = {}
for chrom in chromsDict:
if chrom in islands.keys():
if len(islands[chrom]) != 0:
island_list = islands[chrom]
if Utility.is_bed_sorted(island_list) == 0:
island_list.sort(key=operator.attrgetter('start'))
island_start_list = []
island_end_list = []
for item in island_list:
island_start_list.append(item.start)
island_end_list.append(item.end)
island_chip_readcount_list = [0] * len(island_list)
read_file = chrom + ".bed1"
f = open(read_file, 'r')
for line in f:
if not re.match("#", line):
line = line.strip()
sline = line.split()
position = associate_tags_with_regions.tag_position(
sline, opt.fragment_size)
index = associate_tags_with_regions.find_readcount_on_islands(
island_start_list, island_end_list, position)
if index >= 0:
island_chip_readcount_list[index] += 1
totalchip += 1
f.close()
island_chip_readcount[chrom] = island_chip_readcount_list
island_control_readcount_list = [0] * len(island_list)
read_file = chrom + ".bed2"
f = open(read_file, 'r')
for line in f:
if not re.match("#", line):
line = line.strip()
sline = line.split()
position = associate_tags_with_regions.tag_position(
sline, opt.fragment_size)
index = associate_tags_with_regions.find_readcount_on_islands(
island_start_list, island_end_list, position)
if index >= 0:
island_control_readcount_list[index] += 1
totalcontrol += 1
f.close()
island_control_readcount[chrom] = island_control_readcount_list
chip_background_read = chip_library_size - totalchip
control_background_read = control_library_size - totalcontrol
#scaling_factor = chip_background_read*1.0/control_background_read;
scaling_factor = chip_library_size * 1.0 / control_library_size
print "Total number of chip reads on islands is: ", totalchip
print "Total number of control reads on islands is: ", totalcontrol
#print "chip_background_read ", chip_background_read
#print "control_background_read ", control_background_read
out = open(opt.out_file, 'w')
pvalue_list = []
result_list = []
for chrom in sorted(chromsDict.keys()):
if chrom in islands.keys():
if len(islands[chrom]) != 0:
island_list = islands[chrom]
for index in xrange(len(island_list)):
item = island_list[index]
observation = (island_chip_readcount[chrom])[index]
control_tag = (island_control_readcount[chrom])[index]
if (island_control_readcount[chrom])[index] > 0:
#average = (island_control_readcount[chrom])[index] * scaling_factor;
average = control_tag * scaling_factor
fc = float(observation) / float(average)
else:
length = item.end - item.start + 1
average = length * control_library_size * 1.0 / genomesize
average = min(0.25, average) * scaling_factor
fc = float(observation) / float(average)
if observation > average:
pvalue = scipy.stats.poisson.sf(
(island_chip_readcount[chrom])[index], average)[()]
else:
pvalue = 1
pvalue_list.append(pvalue)
item_dic = {}
item_dic['chrom'] = item.chrom
item_dic['start'] = item.start
item_dic['end'] = item.end
item_dic['chip'] = observation
item_dic['control'] = control_tag
item_dic['pvalue'] = pvalue
item_dic['fc'] = fc
result_list.append(item_dic)
pvaluearray = scipy.array(pvalue_list)
pvaluerankarray = scipy.stats.rankdata(pvaluearray)
totalnumber = len(result_list)
for i in range(totalnumber):
item = result_list[i]
alpha = pvalue_list[i] * totalnumber / pvaluerankarray[i]
if alpha > 1:
alpha = 1
outline = item['chrom'] + "\t" + str(item['start']) + "\t" + str(
item['end']) + "\t" + str(item['chip']) + "\t" + str(
item['control']) + "\t" + str(item['pvalue']) + "\t" + str(
item['fc']) + "\t" + str(alpha) + "\n"
out.write(outline)
#pvalue_list.sort()
#for item in result_list:
#pvalue = float(item['pvalue'])
#alpha = pvalue * len(result_list) / (pvalue_list.index(pvalue) + 1)
#if alpha > 1:
#alpha = 1;
#outline = item['chrom'] + "\t" + str(item['start']) + "\t" + str(item['end']) + "\t" + str(item['chip']) + "\t" + str(item['control']) + "\t" + str(item['pvalue']) + "\t" + str(item['fc']) + "\t" + str(alpha) + "\n";
#out.write(outline);
out.close()
SeparateByChrom.cleanup(chromsDict.keys(), '.bed1')
SeparateByChrom.cleanup(chromsDict.keys(), '.bed2')
