def create_file(self):
# Expanding summits
tfbs_summit_regions = GenomicRegionSet("TFBS Summit Regions")
tfbs_summit_regions.read_bed(self.tfbs_summit_fname)
for region in iter(tfbs_summit_regions):
summit = int(region.data.split()[-1]) + region.initial
region.initial = max(summit - (self.peak_ext / 2), 0)
region.final = summit + (self.peak_ext / 2)
# Calculating intersections
mpbs_regions = GenomicRegionSet("MPBS Regions")
mpbs_regions.read_bed(self.mpbs_fname)
tfbs_summit_regions.sort()
mpbs_regions.sort()
with_overlap_regions = mpbs_regions.intersect(tfbs_summit_regions, mode=OverlapType.ORIGINAL)
without_overlap_regions = mpbs_regions.subtract(tfbs_summit_regions, whole_region=True)
tfbs_regions = GenomicRegionSet("TFBS Regions")
for region in iter(with_overlap_regions):
region.name = region.name.split(":")[0] + ":Y"
tfbs_regions.add(region)
for region in iter(without_overlap_regions):
region.name = region.name.split(":")[0] + ":N"
tfbs_regions.add(region)
tfbs_regions.sort()
tfbs_fname = os.path.join(self.output_location, "{}.bed".format(self.mpbs_name))
tfbs_regions.write_bed(tfbs_fname)
def merge_DBD_regions(path):
"""Merge all available DBD regions in BED format. """
for t in os.listdir(path):
if os.path.isdir(os.path.join(path, t)):
dbd_pool = GenomicRegionSet(t)
for rna in os.listdir(os.path.join(path,t)):
f = os.path.join(path, t, rna, "DBD_"+rna+".bed")
if os.path.exists(f):
dbd = GenomicRegionSet(rna)
dbd.read_bed(f)
for r in dbd: r.name = rna+"_"+r.name
dbd_pool.combine(dbd)
dbd_pool.write_bed(os.path.join(path, t, "DBD_"+t+".bed"))
def create_file(self):
# Expanding summits
tfbs_summit_regions = GenomicRegionSet("TFBS Summit Regions")
tfbs_summit_regions.read_bed(self.tfbs_summit_fname)
for region in iter(tfbs_summit_regions):
summit = int(region.data.split()[-1]) + region.initial
region.initial = max(summit - (self.peak_ext / 2), 0)
region.final = summit + (self.peak_ext / 2)
# Calculating intersections
mpbs_regions = GenomicRegionSet("MPBS Regions")
mpbs_regions.read_bed(self.mpbs_fname)
tfbs_summit_regions.sort()
mpbs_regions.sort()
with_overlap_regions = mpbs_regions.intersect(
tfbs_summit_regions, mode=OverlapType.ORIGINAL)
without_overlap_regions = mpbs_regions.subtract(tfbs_summit_regions,
whole_region=True)
tfbs_regions = GenomicRegionSet("TFBS Regions")
for region in iter(with_overlap_regions):
region.name = region.name.split(":")[0] + ":Y"
tfbs_regions.add(region)
for region in iter(without_overlap_regions):
region.name = region.name.split(":")[0] + ":N"
tfbs_regions.add(region)
tfbs_regions.sort()
tfbs_fname = os.path.join(self.output_location,
"{}.bed".format(self.mpbs_name))
tfbs_regions.write_bed(tfbs_fname)
class RandomTest:
def __init__(self,
rna_fasta,
rna_name,
dna_region,
organism,
showdbs=False):
self.organism = organism
genome = GenomeData(organism)
self.genome_path = genome.get_genome()
# RNA: Path to the FASTA file
self.rna_fasta = rna_fasta
self.showdbs = showdbs
rnas = SequenceSet(name="rna", seq_type=SequenceType.RNA)
rnas.read_fasta(self.rna_fasta)
if rna_name:
self.rna_name = rna_name
else:
self.rna_name = rnas[0].name
# DNA: GenomicRegionSet
self.dna_region = GenomicRegionSet(name="target")
self.dna_region.read_bed(dna_region)
self.dna_region = self.dna_region.gene_association(
organism=self.organism, show_dis=True)
self.topDBD = []
self.stat = OrderedDict(name=rna_name, genome=organism)
self.stat["target_regions"] = str(len(self.dna_region))
def get_rna_region_str(self, rna):
"""Getting the rna region from the information header with the pattern:
REGION_chr3_51978050_51983935_-_"""
self.rna_regions = get_rna_region_str(rna)
if self.rna_regions and len(self.rna_regions[0]) == 5:
self.rna_expression = float(self.rna_regions[0][-1])
else:
self.rna_expression = "n.a."
def connect_rna(self, rna, temp):
d = connect_rna(rna, temp, self.rna_name)
self.stat["exons"] = str(d[0])
self.stat["seq_length"] = str(d[1])
self.rna_len = d[1]
def target_dna(self,
temp,
remove_temp,
cutoff,
l,
e,
c,
fr,
fm,
of,
mf,
par,
obed=False):
"""Calculate the true counts of triplexes on the given dna regions"""
self.triplexator_p = [l, e, c, fr, fm, of, mf]
txp = find_triplex(rna_fasta=os.path.join(temp, "rna_temp.fa"),
dna_region=self.dna_region,
temp=temp,
organism=self.organism,
remove_temp=remove_temp,
l=l,
e=e,
c=c,
fr=fr,
fm=fm,
of=of,
mf=mf,
par=par,
genome_path=self.genome_path,
prefix="targeted_region",
dna_fine_posi=False)
txp.merge_rbs(rm_duplicate=True,
region_set=self.dna_region,
asgene_organism=self.organism,
cutoff=cutoff)
self.txp = txp
self.stat["DBSs_target_all"] = str(len(self.txp))
txp.remove_duplicates()
self.rbss = txp.merged_dict.keys()
# if len(self.rbss) == 0:
# print("ERROR: No potential binding event. Please change the parameters.")
# sys.exit(1)
txpf = find_triplex(rna_fasta=os.path.join(temp, "rna_temp.fa"),
dna_region=self.dna_region,
temp=temp,
organism=self.organism,
remove_temp=remove_temp,
l=l,
e=e,
c=c,
fr=fr,
fm=fm,
of=of,
mf=mf,
par=par,
genome_path=self.genome_path,
prefix="dbs",
dna_fine_posi=True)
txpf.remove_duplicates()
txpf.merge_rbs(rbss=self.rbss,
rm_duplicate=True,
asgene_organism=self.organism)
self.txpf = txpf
self.stat["DBSs_target_all"] = str(len(self.txpf))
self.counts_tr = OrderedDict()
self.counts_dbs = OrderedDict()
for rbs in self.rbss:
tr = len(self.txp.merged_dict[rbs])
self.counts_tr[rbs] = [tr, len(self.dna_region) - tr]
self.counts_dbs[rbs] = len(self.txpf.merged_dict[rbs])
self.region_dbd = self.txpf.sort_rbs_by_regions(self.dna_region)
self.region_dbs = self.txpf.sort_rd_by_regions(
regionset=self.dna_region)
self.region_dbsm = {}
self.region_coverage = {}
for region in self.dna_region:
self.region_dbsm[region.toString()] = self.region_dbs[
region.toString()].get_dbs().merge(w_return=True)
self.region_coverage[region.toString()] = float(self.region_dbsm[region.toString()].total_coverage()) / len \
(region)
self.stat["target_regions"] = str(len(self.dna_region))
if obed:
# btr = self.txp.get_dbs()
# btr = btr.gene_association(organism=self.organism, show_dis=True)
# btr.write_bed(os.path.join(temp, obed + "_target_region_dbs.bed"))
# dbss = txpf.get_dbs()
# dbss.write_bed(os.path.join(temp, obed + "_dbss.bed"))
# output = self.dna_region.gene_association(organism=self.organism, show_dis=True)
self.txp.write_bed(filename=os.path.join(
temp, obed + "_target_region_dbs.bed"),
dbd_tag=False,
remove_duplicates=False,
associated=self.organism)
self.txpf.write_bed(filename=os.path.join(temp,
obed + "_dbss.bed"),
remove_duplicates=False)
def random_test(self, repeats, temp, remove_temp, l, e, c, fr, fm, of, mf,
rm, par, filter_bed, alpha):
"""Perform randomization for the given times"""
self.repeats = repeats
marks = numpy.round(numpy.linspace(0, repeats - 1, num=41)).tolist()
print("random_test")
print(par)
# Prepare the input lists for multiprocessing
mp_input = []
for i in range(repeats):
mp_input.append([
str(i),
os.path.join(temp, "rna_temp.fa"), self.dna_region, temp,
self.organism, self.rbss,
str(marks.count(i)),
str(l),
str(e),
str(c),
str(fr),
str(fm),
str(of),
str(mf),
str(rm), filter_bed, self.genome_path, par
])
# Multiprocessing
print("\t\t|0% | 100%|")
print("\t\t[", end="")
pool = multiprocessing.Pool(processes=multiprocessing.cpu_count() - 2)
mp_output = pool.map(random_each, mp_input)
# print(mp_output)
pool.close()
pool.join()
print("]")
# Processing the result
self.region_matrix = []
self.dbss_matrix = []
self.data = {
"region": {
"ave": [],
"sd": [],
"p": [],
"sig_region": [],
"sig_boolean": []
},
"dbs": {
"ave": [],
"sd": [],
"p": [],
"sig_region": [],
"sig_boolean": []
}
}
region_counts = [v[0] for v in mp_output]
dbss_counts = [v[1] for v in mp_output]
for i, rbs in enumerate(self.rbss):
counts_regions = [v[i] for v in region_counts]
self.data["region"]["ave"].append(numpy.mean(counts_regions))
self.data["region"]["sd"].append(numpy.std(counts_regions))
num_sig = len(
[h for h in counts_regions if h > self.counts_tr[rbs][0]])
p_region = float(num_sig) / repeats
self.data["region"]["p"].append(p_region)
self.region_matrix.append(counts_regions)
if p_region < alpha:
self.data["region"]["sig_region"].append(rbs)
self.data["region"]["sig_boolean"].append(True)
else:
self.data["region"]["sig_boolean"].append(False)
try:
if p_region < self.topDBD[1]:
self.topDBD = [rbs.str_rna(pa=False), p_region]
except:
self.topDBD = [rbs.str_rna(pa=False), p_region]
# Analysis based on DBSs
if self.showdbs:
counts_dbss = [v[i] for v in dbss_counts]
self.data["dbs"]["ave"].append(numpy.mean(counts_dbss))
self.data["dbs"]["sd"].append(numpy.std(counts_dbss))
num_sig = len(
[h for h in counts_dbss if h > self.counts_dbs[rbs]])
p_dbs = float(num_sig) / repeats
self.data["dbs"]["p"].append(p_dbs)
self.dbss_matrix.append(counts_dbss)
if p_dbs < alpha:
self.data["dbs"]["sig_region"].append(rbs)
self.data["dbs"]["sig_boolean"].append(True)
else:
self.data["dbs"]["sig_boolean"].append(False)
try:
self.stat["p_value"] = str(min(self.data["region"]["p"]))
except:
self.stat["p_value"] = "1"
self.region_matrix = numpy.array(self.region_matrix)
if self.showdbs: self.dbss_matrix = numpy.array(self.dbss_matrix)
counts_dbss = [v[i] for v in dbss_counts]
self.stat["DBSs_random_ave"] = numpy.mean(counts_dbss)
try:
self.stat["p_value"] = str(min(self.data["region"]["p"]))
except:
self.stat["p_value"] = "1"
def dbd_regions(self, sig_region, output):
"""Generate the BED file of significant DBD regions and FASTA file of the sequences"""
dbd_regions(exons=self.rna_regions,
sig_region=sig_region,
rna_name=self.rna_name,
output=output)
self.stat["DBD_all"] = str(len(self.rbss))
self.stat["DBD_sig"] = str(len(self.data["region"]["sig_region"]))
sigDBD = GenomicRegionSet("DBD_sig")
sigDBD.sequences = self.data["region"]["sig_region"]
rbss = self.txp.get_rbs()
overlaps = rbss.intersect(y=sigDBD, mode=OverlapType.ORIGINAL)
self.stat["DBSs_target_DBD_sig"] = str(len(overlaps))
def lineplot(self, txp, dirp, ac, cut_off, log, ylabel, linelabel, showpa,
sig_region, filename):
"""Generate lineplot for RNA"""
lineplot(txp=txp,
rnalen=self.rna_len,
rnaname=self.rna_name,
dirp=dirp,
sig_region=sig_region,
cut_off=cut_off,
log=log,
ylabel=ylabel,
linelabel=linelabel,
filename=filename,
ac=ac,
showpa=showpa)
def boxplot(self, dir, matrix, sig_region, truecounts, sig_boolean, ylabel,
filename):
"""Generate the visualized plot"""
tick_size = 8
label_size = 9
f, ax = plt.subplots(1, 1, dpi=300, figsize=(6, 4))
max_y = int(max([matrix.max()] + truecounts) * 1.1) + 1
min_y = max(int(matrix.min() * 0.9) - 1, 0)
# Significant DBD
rect = patches.Rectangle(xy=(1, 0),
width=0.8,
height=max_y,
facecolor=sig_color,
edgecolor="none",
alpha=0.5,
lw=None,
label="Significant DBD")
for i, r in enumerate(sig_boolean):
if r:
rect = patches.Rectangle(xy=(i + 0.6, min_y),
width=0.8,
height=max_y,
facecolor=sig_color,
edgecolor="none",
alpha=0.5,
lw=None,
label="Significant DBD")
ax.add_patch(rect)
# Plotting
bp = ax.boxplot(matrix.transpose(),
notch=False,
sym='o',
vert=True,
whis=1.5,
positions=None,
widths=None,
patch_artist=True,
bootstrap=None)
z = 10
plt.setp(bp['boxes'], color=nontarget_color, alpha=1, edgecolor="none")
plt.setp(bp['whiskers'],
color='black',
linestyle='-',
linewidth=1,
zorder=z,
alpha=1)
plt.setp(bp['fliers'],
markerfacecolor='gray',
color='white',
alpha=0.3,
markersize=1.8,
zorder=z)
plt.setp(bp['caps'], color='white', zorder=-1)
plt.setp(bp['medians'], color='black', linewidth=1.5, zorder=z + 1)
# Plot target regions
plt.plot(range(1,
len(self.rbss) + 1),
truecounts,
markerfacecolor=target_color,
marker='o',
markersize=5,
linestyle='None',
markeredgecolor="white",
zorder=z + 5)
ax.set_xlabel(self.rna_name + " DNA Binding Domains",
fontsize=label_size)
ax.set_ylabel(ylabel, fontsize=label_size, rotation=90)
ax.set_ylim([min_y, max_y])
ax.yaxis.set_major_locator(MaxNLocator(integer=True))
ax.set_xticklabels([dbd.str_rna(pa=False) for dbd in self.rbss],
rotation=35,
ha="right",
fontsize=tick_size)
for tick in ax.yaxis.get_major_ticks():
tick.label.set_fontsize(tick_size)
for spine in ['top', 'right']:
ax.spines[spine].set_visible(False)
ax.tick_params(axis='x',
which='both',
bottom='off',
top='off',
labelbottom='on')
ax.tick_params(axis='y',
which='both',
left='on',
right='off',
labelbottom='off')
# Legend
dot_legend, = plt.plot([1, 1],
color=target_color,
marker='o',
markersize=5,
markeredgecolor="white",
linestyle='None')
bp_legend, = plt.plot([1, 1],
color=nontarget_color,
linewidth=6,
alpha=1)
ax.legend([dot_legend, bp_legend, rect],
["Target Regions", "Non-target regions", "Significant DBD"],
bbox_to_anchor=(0., 1.02, 1., .102),
loc=2,
mode="expand",
borderaxespad=0.,
prop={'size': 9},
ncol=3,
numpoints=1)
bp_legend.set_visible(False)
dot_legend.set_visible(False)
# f.tight_layout(pad=1.08, h_pad=None, w_pad=None)
f.savefig(os.path.join(dir, filename + ".png"),
facecolor='w',
edgecolor='w',
bbox_extra_artists=(plt.gci()),
bbox_inches='tight',
dpi=300)
# PDF
for tick in ax.xaxis.get_major_ticks():
tick.label.set_fontsize(12)
for tick in ax.yaxis.get_major_ticks():
tick.label.set_fontsize(12)
ax.xaxis.label.set_size(14)
ax.yaxis.label.set_size(14)
pp = PdfPages(os.path.join(dir, filename + '.pdf'))
pp.savefig(f, bbox_extra_artists=(plt.gci()), bbox_inches='tight')
pp.close()
def gen_html(self,
directory,
parameters,
obed,
align=50,
alpha=0.05,
score=False):
"""Generate the HTML file"""
dir_name = os.path.basename(directory)
html_header = "Genomic Region Test: " + dir_name
link_ds = OrderedDict()
link_ds["RNA"] = "index.html"
link_ds["Sig Target Regions"] = "starget_regions.html"
link_ds["Target Regions"] = "target_regions.html"
link_ds["Parameters"] = "parameters.html"
##################################################
# index.html
html = Html(
name=html_header,
links_dict=link_ds, # fig_dir=os.path.join(directory,"style"),
fig_rpath="../style",
RGT_header=False,
other_logo="TDF",
homepage="../index.html")
# Plots
html.add_figure("lineplot_region.png",
align="left",
width="45%",
more_images=["boxplot_regions.png"])
if self.showdbs:
html.add_figure("lineplot_dbs.png",
align="left",
width="45%",
more_images=["boxplot_dbs.png"])
if self.showdbs:
header_list = [[
"#", "DBD", "Target Regions", None, "Non-target Regions", None,
"Statistics", "Target Regions", "Non-target Regions", None,
"Statistics"
],
[
"", "", "with DBS", "without DBS",
"with DBS (average)", "s.d.", "<i>p</i>-value",
"NO. DBSs", "NO. DBSs (average)", "s.d.",
"<i>p</i>-value"
]]
header_titles = [
[
"Rank", "DNA Binding Domain",
"Given target regions on DNA", None,
"Regions from randomization", None,
"Statistics based on target regions",
"Given target regions on DNA",
"Regions from randomization", None,
"Statistics based on DNA Binding Sites"
],
[
"", "", "Number of target regions with DBS binding",
"Number of target regions without DBS binding",
"Average number of regions from randomization with DBS binding",
"Standard deviation", "P value",
"Number of related DNA Binding Sites binding to target regions",
"Average number of DNA Binding Sites binding to random regions",
"Standard deviation", "P-value"
]
]
border_list = [
" style=\"border-right:1pt solid gray\"",
" style=\"border-right:1pt solid gray\"", "",
" style=\"border-right:1pt solid gray\"", "",
" style=\"border-right:1pt solid gray\"",
" style=\"border-right:2pt solid gray\"",
" style=\"border-right:1pt solid gray\"", "",
" style=\"border-right:1pt solid gray\"",
" style=\"border-right:1pt solid gray\""
]
else:
header_list = [[
"#", "DBD", "Target Regions", None, "Non-target Regions", None,
"Statistics", None
],
[
"", "", "with DBS", "without DBS",
"with DBS (average)", "s.d.", "<i>p</i>-value",
"z-score"
]]
header_titles = [
[
"Rank", "DNA Binding Domain",
"Given target regions on DNA", None,
"Regions from randomization", None,
"Statistics based on target regions", None
],
[
"", "", "Number of target regions with DBS binding",
"Number of target regions without DBS binding",
"Average number of regions from randomization with DBS binding",
"Standard deviation", "P value", "Z-score"
]
]
border_list = [
" style=\"border-right:1pt solid gray\"",
" style=\"border-right:1pt solid gray\"", "",
" style=\"border-right:1pt solid gray\"", "",
" style=\"border-right:1pt solid gray\"",
" style=\"border-right:1pt solid gray\"", ""
]
type_list = 'ssssssssssssssss'
col_size_list = [
50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50
]
data_table = []
for i, rbs in enumerate(self.rbss):
if self.data["region"]["p"][i] < alpha:
p_region = "<font color=\"red\">" + value2str(
self.data["region"]["p"][i]) + "</font>"
else:
p_region = value2str(self.data["region"]["p"][i])
zs = (self.counts_tr[rbs][0] -
self.data["region"]["ave"][i]) / self.data["region"]["sd"][i]
new_line = [
str(i + 1),
rbs.str_rna(pa=False), '<a href="dbd_region.html#' +
rbs.str_rna() + '" style="text-align:left">' +
str(self.counts_tr[rbs][0]) + '</a>',
str(self.counts_tr[rbs][1]),
value2str(self.data["region"]["ave"][i]),
value2str(self.data["region"]["sd"][i]), p_region,
value2str(zs)
]
if self.showdbs:
if self.data["dbs"]["p"][i] < alpha:
p_dbs = "<font color=\"red\">" + value2str(
self.data["dbs"]["p"][i]) + "</font>"
else:
p_dbs = value2str(self.data["dbs"]["p"][i])
new_line += [
str(self.counts_dbs[rbs]),
value2str(self.data["dbs"]["ave"][i]),
value2str(self.data["dbs"]["sd"][i]), p_dbs
]
data_table.append(new_line)
data_table = natsort.natsorted(data_table, key=lambda x: x[6])
html.add_zebra_table(header_list,
col_size_list,
type_list,
data_table,
align=align,
cell_align="left",
auto_width=True,
header_titles=header_titles,
border_list=border_list,
sortable=True)
html.add_heading("Notes")
html.add_list([
"RNA name: " + self.rna_name,
"Randomization is performed for " + str(self.repeats) + " times.",
"DBD stands for DNA Binding Domain on RNA.",
"DBS stands for DNA Binding Site on DNA."
])
html.add_fixed_rank_sortable()
html.write(os.path.join(directory, "index.html"))
#############################################################
# RNA subpage: Profile of targeted regions for each merged DNA Binding Domain
#############################################################
header_list = [
"#", "Target Region", "Associated Gene", "No. of DBSs",
"DBS coverage"
]
header_titles = [
"Rank", "Given target regions from BED files",
"Associated genes which is overlapping with the given region or close to it (less than 50000 bp)",
"Number of DNA Binding Sites locate within the region",
"The proportion of the region covered by DBS binding"
]
#########################################################
# dbd_region.html
html = Html(
name=html_header,
links_dict=link_ds, # fig_dir=os.path.join(directory,"style"),
fig_rpath="../style",
RGT_header=False,
other_logo="TDF",
homepage="../index.html")
for rbsm in self.rbss:
html.add_heading("DNA Binding Domain: " + rbsm.str_rna(),
idtag=rbsm.str_rna())
data_table = []
for i, region in enumerate(self.txp.merged_dict[rbsm]):
# Add information
data_table.append([
str(i + 1),
'<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=' +
self.organism + "&position=" + region.chrom + "%3A" +
str(region.initial) + "-" + str(region.final) +
'" style="text-align:left">' +
region.toString(space=True) + '</a>',
split_gene_name(gene_name=region.name, org=self.organism),
str(len(self.region_dbs[region.toString()])),
value2str(self.region_coverage[region.toString()])
])
html.add_zebra_table(header_list,
col_size_list,
type_list,
data_table,
align=align,
cell_align="left",
auto_width=True,
header_titles=header_titles,
sortable=True)
html.add_fixed_rank_sortable()
html.write(os.path.join(directory, "dbd_region.html"))
#############################################################
# Targeted regions centered
#############################################################
##############################################################################################
# target_regions.html
html = Html(
name=html_header,
links_dict=link_ds, # fig_dir=os.path.join(directory,"style"),
fig_rpath="../style",
RGT_header=False,
other_logo="TDF",
homepage="../index.html")
if score:
header_list = [
"#", "Target region", "Associated Gene", "DBSs Count",
"DBS coverage", "Score", "Sum of ranks"
]
header_titles = [
"Rank", "Target regions loaded from the given BED file",
"Associated genes which is overlapping with the given region or close to it (less than 50000 bp)",
"Number of DNA Binding Sites within the region",
"The proportion of the region covered by DBS binding",
"Scores from BED file", "Sum of all the left-hand-side ranks"
]
else:
header_list = [
"#", "Target region", "Associated Gene", "DBSs Count",
"DBS coverage", "Sum of ranks"
]
header_titles = [
"Rank", "Target regions loaded from the given BED file",
"Associated genes which is overlapping with the given region or close to it (less than 50000 bp)",
"Number of DNA Binding Sites within the region",
"The proportion of the region covered by DBS binding",
"Sum of all the left-hand-side ranks"
]
html.add_heading("Target Regions")
data_table = []
if not self.dna_region.sorted: self.dna_region.sort()
# Calculate the ranking
rank_count = len(self.dna_region) - rank_array(
[len(self.region_dbs[p.toString()]) for p in self.dna_region])
rank_coverage = len(self.dna_region) - rank_array(
[self.region_coverage[p.toString()] for p in self.dna_region])
if score:
try:
score_list = [
float(p.data.split("\t")[0]) for p in self.dna_region
]
rank_score = len(self.dna_region) - rank_array(
[abs(s) for s in score_list])
rank_sum = [
x + y + z
for x, y, z in zip(rank_count, rank_coverage, rank_score)
]
# sum_rank = rank_array(rank_sum) # method='min'
except ImportError:
print(
"There is no score in BED file, please don't use '-score' argument."
)
else:
rank_sum = [x + y for x, y in zip(rank_count, rank_coverage)]
sum_rank = rank_array(rank_sum)
for i, region in enumerate(self.dna_region):
dbs_counts = str(len(self.region_dbs[region.toString()]))
dbs_cover = value2str(self.region_coverage[region.toString()])
newline = [
str(i + 1),
'<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=' +
self.organism + "&position=" + region.chrom + "%3A" +
str(region.initial) + "-" + str(region.final) +
'" style="text-align:left">' + region.toString(space=True) +
'</a>',
split_gene_name(gene_name=region.name, org=self.organism),
'<a href="region_dbs.html#' + region.toString() +
'" style="text-align:left">' + dbs_counts + '</a>', dbs_cover
]
if score:
dbs_score = value2str(score_list[i])
region.data = "\t".join(
[dbs_counts, dbs_cover, dbs_score,
str(rank_sum[i])])
newline.append(dbs_score)
newline.append(str(rank_sum[i]))
else:
region.data = "\t".join(
[dbs_counts, dbs_cover,
str(rank_sum[i])])
newline.append(str(rank_sum[i]))
data_table.append(newline)
data_table = natsort.natsorted(data_table, key=lambda x: x[-1])
# data_table = sorted(data_table, key=lambda x: x[-1])
html.add_zebra_table(header_list,
col_size_list,
type_list,
data_table,
align=align,
cell_align="left",
auto_width=True,
header_titles=header_titles,
sortable=True)
html.add_heading("Notes")
html.add_list(["All target regions without any bindings are ignored."])
html.add_fixed_rank_sortable()
html.write(os.path.join(directory, "target_regions.html"))
self.dna_region.sort_score()
self.dna_region.write_bed(
os.path.join(directory, obed + "_target_regions.bed"))
##############################################################################################
# starget_regions.html for significant target regions
stargets = GenomicRegionSet("sig_targets")
sig_dbs = {}
sig_dbs_coverage = {}
for i, r in enumerate(self.dna_region):
sig_bindings = self.region_dbs[r.toString()].overlap_rbss(
rbss=self.data["region"]["sig_region"])
dbs = sig_bindings.get_dbs()
if len(dbs) > 0:
stargets.add(r)
m_dbs = dbs.merge(w_return=True)
sig_dbs[r] = len(dbs)
# self.promoter["de"]["merged_dbs"][promoter.toString()] = len(m_dbs)
sig_dbs_coverage[r] = float(m_dbs.total_coverage()) / len(r)
html = Html(
name=html_header,
links_dict=link_ds, # fig_dir=os.path.join(directory,"style"),
fig_rpath="../style",
RGT_header=False,
other_logo="TDF",
homepage="../index.html")
# Select promoters in sig DBD
if len(self.data["region"]["sig_region"]) == 0:
html.add_heading("There is no significant DBD.")
else:
html.add_heading("Target regions bound by significant DBD")
data_table = []
# Calculate the ranking
rank_count = len(stargets) - rank_array(
[sig_dbs[p] for p in stargets])
rank_coverage = len(stargets) - rank_array(
[sig_dbs_coverage[p] for p in stargets])
if score:
score_list = [float(p.data.split("\t")[0]) for p in stargets]
rank_score = len(stargets) - rank_array(
[abs(s) for s in score_list])
rank_sum = [
x + y + z
for x, y, z in zip(rank_count, rank_coverage, rank_score)
]
sum_rank = rank_array(rank_sum) # method='min'
else:
rank_sum = [x + y for x, y in zip(rank_count, rank_coverage)]
sum_rank = rank_array(rank_sum)
for i, region in enumerate(stargets):
dbssount = '<a href="region_dbs.html#' + region.toString() + \
'" style="text-align:left">' + str(sig_dbs[region]) + '</a>'
region_link = region_link_internet(self.organism, region)
newline = [
str(i + 1), region_link,
split_gene_name(gene_name=region.name, org=self.organism),
dbssount,
value2str(sig_dbs_coverage[region])
]
if score:
dbs_score = value2str(score_list[i])
# region.data = "\t".join([dbs_counts, dbs_cover, dbs_score, str(sum_rank[i])])
newline.append(dbs_score)
newline.append(str(rank_sum[i]))
# print([dbs_score, str(sum_rank[i])])
else:
# region.data = "\t".join([dbs_counts, dbs_cover, str(sum_rank[i])])
newline.append(str(rank_sum[i]))
# newline += ["<i>" + str(rank_sum[i]) + "</i>"]
# print(newline)
data_table.append(newline)
# print(data_table)
# data_table = sorted(data_table, key=lambda x: x[-1])
data_table = natsort.natsorted(data_table, key=lambda x: x[-1])
html.add_zebra_table(header_list,
col_size_list,
type_list,
data_table,
align=align,
cell_align="left",
header_titles=header_titles,
border_list=None,
sortable=True)
html.add_heading("Notes")
html.add_list([
"DBS stands for DNA Binding Site on DNA.",
"DBS coverage is the proportion of the region where has potential to form triple helices with the given RNA."
])
html.add_fixed_rank_sortable()
html.write(os.path.join(directory, "starget_regions.html"))
############################
# Subpages for targeted region centered page
# region_dbs.html
header_list = ["RBS", "DBS", "Strand", "Score", "Motif", "Orientation"]
html = Html(
name=html_header,
links_dict=link_ds, # fig_dir=os.path.join(directory,"style"),
fig_rpath="../style",
RGT_header=False,
other_logo="TDF",
homepage="../index.html")
for i, region in enumerate(self.dna_region):
if len(self.region_dbs[region.toString()]) == 0:
continue
else:
html.add_heading(
"Associated gene: " +
split_gene_name(gene_name=region.name, org=self.organism),
idtag=region.toString())
html.add_free_content([
'<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=' +
self.organism + "&position=" + region.chrom + "%3A" +
str(region.initial) + "-" + str(region.final) +
'" style="margin-left:50">' + region.toString(space=True) +
'</a>'
])
data_table = []
for rd in self.region_dbs[region.toString()]:
rbs = rd.rna.str_rna(pa=False)
for rbsm in self.data["region"]["sig_region"]:
# rbsm = rbsm.partition(":")[2].split("-")
if rd.rna.overlap(rbsm):
rbs = "<font color=\"red\">" + rbs + "</font>"
data_table.append([
rbs,
'<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db='
+ self.organism + "&position=" + rd.dna.chrom + "%3A" +
str(rd.dna.initial) + "-" + str(rd.dna.final) +
'" style="text-align:left">' +
rd.dna.toString(space=True) + '</a>',
rd.dna.orientation, rd.score, rd.motif, rd.orient
])
html.add_zebra_table(header_list,
col_size_list,
type_list,
data_table,
align=align,
cell_align="left",
auto_width=True)
html.write(os.path.join(directory, "region_dbs.html"))
###############################################################################33
################ Parameters.html
html = Html(
name=html_header,
links_dict=link_ds, # fig_dir=os.path.join(directory,"style"),
fig_rpath="../style",
RGT_header=False,
other_logo="TDF",
homepage="../index.html")
html.add_heading("Parameters")
header_list = ["Description", "Arguments", "Value"]
data_table = [
["RNA sequence name", "-rn", parameters.rn],
["Input RNA sequence file", "-r",
os.path.basename(parameters.r)],
["Input BED file", "-bed",
os.path.basename(parameters.bed)],
["Output directory", "-o",
os.path.basename(parameters.o)],
["Organism", "-organism", parameters.organism],
["Number of repitetion of andomization", "-n",
str(parameters.n)],
["Alpha level for rejection p value", "-a",
str(parameters.a)],
[
"Cut off value for filtering out the low counts of DBSs",
"-ccf",
str(parameters.ccf)
], ["Remove temporary files", "-rt",
str(parameters.rt)],
[
"Input BED file for masking in randomization", "-f",
str(parameters.f)
], ["Input file for RNA accecibility", "-ac",
str(parameters.ac)],
[
"Cut off value for RNA accecibility", "-accf",
str(parameters.accf)
],
[
"Output the BED files for DNA binding sites.", "-obed",
str(parameters.obed)
],
[
"Show parallel and antiparallel bindings in the plot separately.",
"-showpa",
str(parameters.showpa)
], ["Minimum length", "-l",
str(self.triplexator_p[0])],
["Maximum error rate", "-e",
str(self.triplexator_p[1])],
[
"Tolerated number of consecutive errors", "-c",
str(self.triplexator_p[2])
], ["Filtering repeats", "-fr",
str(self.triplexator_p[3])],
["Filtering mode", "-fm",
str(self.triplexator_p[4])],
["Output format", "-of",
str(self.triplexator_p[5])],
["Merge features", "-mf",
str(self.triplexator_p[6])]
]
html.add_zebra_table(header_list,
col_size_list,
type_list,
data_table,
align=align,
cell_align="left",
auto_width=True)
html.add_free_content(
['<a href="summary.txt" style="margin-left:100">See details</a>'])
html.write(os.path.join(directory, "parameters.html"))
new_alignment = MultipleSeqAlignment(records=seqs)
#print(len(new_alignment))
AlignIO.write(new_alignment, "mm9_"+rg.name+".fa", "fasta")
process = subprocess.Popen(["/home/joseph/Apps/PhyloCSF/PhyloCSF",
"29mammals",
"mm9_"+rg.name+".fa",
"--removeRefGaps",
"--strategy=omega",
"--orf=StopStop3",
"--minCodons=25",
"--frames=3"],
stdout=subprocess.PIPE)
out, err = process.communicate()
print(out)
#print(out.split("\t")[2])
#print(out.split("\t")[3])
#print(out.split("\t")[4])
data = rg.data.split("\t")
score = out.split("\t")[2]
rg.data = "\t".join([score] + data[1:])
bed.write_bed(args.o)
# 29/9/2015
# python /projects/reg-gen/tools/phylocsf_check.py -i /projects/ig440396_dendriticcells/exp/RNASeq/expression/isofroms/deseq/new_bed/all_TCONs.bed -o all_TCONS_phyloCSF.bed -organism mm9 -mafdir /data/genome/mm9/multiz30way/maf/
def dbd_regions(exons, sig_region, rna_name, output,out_file=False, temp=None, fasta=True):
"""Generate the BED file of significant DBD regions and FASTA file of the sequences"""
if len(sig_region) == 0:
return
#print(self.rna_regions)
if not exons:
pass
else:
dbd = GenomicRegionSet("DBD")
dbdmap = {}
if len(exons) == 1:
print("## Warning: No information of exons in the given RNA sequence, the DBD position may be problematic. ")
for rbs in sig_region:
loop = True
if exons[0][3] == "-":
while loop:
cf = 0
for exon in exons:
#print(exon)
l = abs(exon[2] - exon[1])
tail = cf + l
if cf <= rbs.initial <= tail:
dbdstart = exon[2] - rbs.initial + cf
if rbs.final <= tail:
#print("1")
dbdend = exon[2] - rbs.final + cf
if dbdstart > dbdend: dbdstart, dbdend = dbdend, dbdstart
dbd.add( GenomicRegion(chrom=exons[0][0],
initial=dbdstart, final=dbdend,
orientation=exons[0][3],
name=str(rbs.initial)+"-"+str(rbs.final) ) )
dbdmap[str(rbs)] = dbd[-1].toString() + " strand:-"
loop = False
break
elif rbs.final > tail:
subtract = l + cf - rbs.initial
#print("2")
#print("Subtract: "+str(subtract))
if dbdstart > exon[1]: dbdstart, exon[1] = exon[1], dbdstart
dbd.add( GenomicRegion(chrom=exons[0][0],
initial=dbdstart, final=exon[1],
orientation=exons[0][3],
name=str(rbs.initial)+"-"+str(rbs.initial+subtract)+"_split1" ) )
elif rbs.initial < cf and rbs.final <= tail:
#print("3")
dbdstart = exon[2]
dbdend = exon[2] - rbs.final + rbs.initial + subtract
if dbdstart > dbdend: dbdstart, dbdend = dbdend, dbdstart
dbd.add( GenomicRegion(chrom=exons[0][0],
initial=dbdstart, final=dbdend,
orientation=exons[0][3],
name=str(cf)+"-"+str(rbs.final)+"_split2" ) )
dbdmap[str(rbs)] = dbd[-2].toString() + " & " + dbd[-1].toString() + " strand:-"
loop = False
break
elif rbs.initial > tail:
pass
cf += l
loop = False
else:
while loop:
cf = 0
for exon in exons:
#print(exon)
l = exon[2] - exon[1]
tail = cf + l
#print("cf: " + str(cf))
#print("tail: " + str(tail) )
if cf <= rbs.initial <= tail:
dbdstart = exon[1] + rbs.initial - cf
if rbs.final <= tail:
#print("1")
dbdend = exon[1] + rbs.final -cf
dbd.add( GenomicRegion(chrom=exons[0][0],
initial=dbdstart, final=dbdend,
orientation=exons[0][3],
name=str(rbs.initial)+"-"+str(rbs.final) ) )
dbdmap[str(rbs)] = dbd[-1].toString() + " strand:+"
loop = False
break
elif rbs.final > tail:
subtract = l + cf - rbs.initial
#print("2")
#print("Subtract: "+str(subtract))
dbd.add( GenomicRegion(chrom=exons[0][0],
initial=dbdstart, final=exon[2],
orientation=exons[0][3],
name=str(rbs.initial)+"-"+str(rbs.initial+subtract)+"_split1" ) )
elif rbs.initial < cf and rbs.final <= tail:
#print("3")
dbdstart = exon[1]
dbdend = exon[1] + rbs.final - rbs.initial - subtract
dbd.add( GenomicRegion(chrom=exons[0][0],
initial=dbdstart, final=dbdend,
orientation=exons[0][3],
name=str(cf)+"-"+str(rbs.final)+"_split2" ) )
dbdmap[str(rbs)] = dbd[-2].toString() + " & " + dbd[-1].toString() + " strand:+"
loop = False
break
elif rbs.initial > tail:
pass
cf += l
loop = False
if not out_file:
dbd.write_bed(filename=os.path.join(output, "DBD_"+rna_name+".bed"))
else:
# print(dbd)
# print(dbd.sequences[0])
dbd.write_bed(filename=output)
# FASTA
if fasta:
#print(dbdmap)
if not out_file:
seq = pysam.Fastafile(os.path.join(output,"rna_temp.fa"))
fasta_f = os.path.join(output, "DBD_"+rna_name+".fa")
else:
seq = pysam.Fastafile(os.path.join(temp,"rna_temp.fa"))
fasta_f = output+".fa"
with open(fasta_f, 'w') as fasta:
for rbs in sig_region:
print(">"+ rna_name +":"+str(rbs.initial)+"-"+str(rbs.final), file=fasta)
s = seq.fetch(rbs.chrom, max(0, rbs.initial), rbs.final)
for ss in [s[i:i + 80] for i in range(0, len(s), 80)]:
print(ss, file=fasta)
elif args.mode == "bed_extend":
print("input:\t" + args.i)
print("output:\t" + args.o)
bed = GenomicRegionSet("bed")
bed.read_bed(args.i)
for region in bed:
if args.oz:
if region.initial == region.final:
region.final += args.l
else:
if args.both:
region.initial -= args.l
else: pass
region.final += args.l
bed.write_bed(args.o)
############### BED get promoters #########################################
elif args.mode == "bed_get_promoters":
print("input:\t" + args.i)
print("output:\t" + args.o)
print("organism:\t" + args.organism)
gene = GenomicRegionSet("genes")
### Input BED file
if args.i.endswith(".bed"):
gene.read_bed(args.i)
promoter = GenomicRegionSet("promoter")
promoterLength = int(args.l)
for s in gene:
class RandomTest:
def __init__(self, rna_fasta, rna_name, dna_region, organism, showdbs=False):
self.organism = organism
genome = GenomeData(organism)
self.genome_path = genome.get_genome()
# RNA: Path to the FASTA file
self.rna_fasta = rna_fasta
self.showdbs = showdbs
rnas = SequenceSet(name="rna", seq_type=SequenceType.RNA)
rnas.read_fasta(self.rna_fasta)
if rna_name:
self.rna_name = rna_name
else:
self.rna_name = rnas[0].name
# DNA: GenomicRegionSet
self.dna_region = GenomicRegionSet(name="target")
self.dna_region.read_bed(dna_region)
self.dna_region = self.dna_region.gene_association(organism=self.organism, show_dis=True)
self.topDBD = []
self.stat = OrderedDict(name=rna_name, genome=organism)
self.stat["target_regions"] = str(len(self.dna_region))
def get_rna_region_str(self, rna):
"""Getting the rna region from the information header with the pattern:
REGION_chr3_51978050_51983935_-_"""
self.rna_regions = get_rna_region_str(rna)
if self.rna_regions and len(self.rna_regions[0]) == 5:
self.rna_expression = float(self.rna_regions[0][-1])
else:
self.rna_expression = "n.a."
def connect_rna(self, rna, temp):
d = connect_rna(rna, temp, self.rna_name)
self.stat["exons"] = str(d[0])
self.stat["seq_length"] = str(d[1])
self.rna_len = d[1]
def target_dna(self, temp, remove_temp, cutoff, l, e, c, fr, fm, of, mf, par, obed=False):
"""Calculate the true counts of triplexes on the given dna regions"""
self.triplexator_p = [ l, e, c, fr, fm, of, mf ]
txp = find_triplex(rna_fasta=os.path.join(temp, "rna_temp.fa"), dna_region=self.dna_region,
temp=temp, organism=self.organism, remove_temp=remove_temp,
l=l, e=e, c=c, fr=fr, fm=fm, of=of, mf=mf, par=par, genome_path=self.genome_path,
prefix="targeted_region", dna_fine_posi=False)
txp.merge_rbs(rm_duplicate=True, region_set=self.dna_region, asgene_organism=self.organism, cutoff=cutoff)
self.txp = txp
self.stat["DBSs_target_all"] = str(len(self.txp))
txp.remove_duplicates()
self.rbss = txp.merged_dict.keys()
# if len(self.rbss) == 0:
# print("ERROR: No potential binding event. Please change the parameters.")
# sys.exit(1)
txpf = find_triplex(rna_fasta=os.path.join(temp, "rna_temp.fa"), dna_region=self.dna_region,
temp=temp, organism=self.organism, remove_temp=remove_temp,
l=l, e=e, c=c, fr=fr, fm=fm, of=of, mf=mf, par=par, genome_path=self.genome_path,
prefix="dbs", dna_fine_posi=True)
txpf.remove_duplicates()
txpf.merge_rbs(rbss=self.rbss, rm_duplicate=True, asgene_organism=self.organism)
self.txpf = txpf
self.stat["DBSs_target_all"] = str(len(self.txpf))
self.counts_tr = OrderedDict()
self.counts_dbs = OrderedDict()
for rbs in self.rbss:
tr = len(self.txp.merged_dict[rbs])
self.counts_tr[rbs] = [tr, len(self.dna_region) - tr]
self.counts_dbs[rbs] = len(self.txpf.merged_dict[rbs])
self.region_dbd = self.txpf.sort_rbs_by_regions(self.dna_region)
self.region_dbs = self.txpf.sort_rd_by_regions(regionset=self.dna_region)
self.region_dbsm = {}
self.region_coverage = {}
for region in self.dna_region:
self.region_dbsm[region.toString()] = self.region_dbs[region.toString()].get_dbs().merge(w_return=True)
self.region_coverage[region.toString()] = float(self.region_dbsm[region.toString()].total_coverage()) / len \
(region)
self.stat["target_regions"] = str(len(self.dna_region))
if obed:
# btr = self.txp.get_dbs()
# btr = btr.gene_association(organism=self.organism, show_dis=True)
# btr.write_bed(os.path.join(temp, obed + "_target_region_dbs.bed"))
# dbss = txpf.get_dbs()
# dbss.write_bed(os.path.join(temp, obed + "_dbss.bed"))
# output = self.dna_region.gene_association(organism=self.organism, show_dis=True)
self.txp.write_bed(filename=os.path.join(temp, obed + "_target_region_dbs.bed"),
dbd_tag=False,
remove_duplicates=False, associated=self.organism)
self.txpf.write_bed(filename=os.path.join(temp, obed + "_dbss.bed"),
remove_duplicates=False)
def random_test(self, repeats, temp, remove_temp, l, e, c, fr, fm, of, mf, rm, par, filter_bed, alpha):
"""Perform randomization for the given times"""
self.repeats = repeats
marks = numpy.round(numpy.linspace(0, repeats - 1, num=41)).tolist()
print("random_test")
print(par)
# Prepare the input lists for multiprocessing
mp_input = []
for i in range(repeats):
mp_input.append([str(i), os.path.join(temp, "rna_temp.fa"), self.dna_region,
temp, self.organism, self.rbss, str(marks.count(i)),
str(l), str(e), str(c), str(fr), str(fm), str(of), str(mf), str(rm),
filter_bed, self.genome_path, par])
# Multiprocessing
print("\t\t|0% | 100%|")
print("\t\t[", end="")
pool = multiprocessing.Pool(processes=multiprocessing.cpu_count()-2)
mp_output = pool.map(random_each, mp_input)
# print(mp_output)
pool.close()
pool.join()
print("]")
# Processing the result
self.region_matrix = []
self.dbss_matrix = []
self.data = {"region": {"ave": [],
"sd": [],
"p": [],
"sig_region": [],
"sig_boolean": []},
"dbs": {"ave": [],
"sd": [],
"p": [],
"sig_region": [],
"sig_boolean": []}}
region_counts = [v[0] for v in mp_output]
dbss_counts = [v[1] for v in mp_output]
for i, rbs in enumerate(self.rbss):
counts_regions = [v[i] for v in region_counts]
self.data["region"]["ave"].append(numpy.mean(counts_regions))
self.data["region"]["sd"].append(numpy.std(counts_regions))
num_sig = len([h for h in counts_regions if h > self.counts_tr[rbs][0]])
p_region = float(num_sig) / repeats
self.data["region"]["p"].append(p_region)
self.region_matrix.append(counts_regions)
if p_region < alpha:
self.data["region"]["sig_region"].append(rbs)
self.data["region"]["sig_boolean"].append(True)
else:
self.data["region"]["sig_boolean"].append(False)
try:
if p_region < self.topDBD[1]: self.topDBD = [rbs.str_rna(pa=False), p_region]
except:
self.topDBD = [rbs.str_rna(pa=False), p_region]
# Analysis based on DBSs
if self.showdbs:
counts_dbss = [v[i] for v in dbss_counts]
self.data["dbs"]["ave"].append(numpy.mean(counts_dbss))
self.data["dbs"]["sd"].append(numpy.std(counts_dbss))
num_sig = len([h for h in counts_dbss if h > self.counts_dbs[rbs]])
p_dbs = float(num_sig) / repeats
self.data["dbs"]["p"].append(p_dbs)
self.dbss_matrix.append(counts_dbss)
if p_dbs < alpha:
self.data["dbs"]["sig_region"].append(rbs)
self.data["dbs"]["sig_boolean"].append(True)
else:
self.data["dbs"]["sig_boolean"].append(False)
try:
self.stat["p_value"] = str(min(self.data["region"]["p"]))
except:
self.stat["p_value"] = "1"
self.region_matrix = numpy.array(self.region_matrix)
if self.showdbs: self.dbss_matrix = numpy.array(self.dbss_matrix)
counts_dbss = [v[i] for v in dbss_counts]
self.stat["DBSs_random_ave"] = numpy.mean(counts_dbss)
try: self.stat["p_value"] = str(min(self.data["region"]["p"]))
except: self.stat["p_value"] = "1"
def dbd_regions(self, sig_region, output):
"""Generate the BED file of significant DBD regions and FASTA file of the sequences"""
dbd_regions(exons=self.rna_regions, sig_region=sig_region, rna_name=self.rna_name, output=output)
self.stat["DBD_all"] = str(len(self.rbss))
self.stat["DBD_sig"] = str(len(self.data["region"]["sig_region"]))
sigDBD = GenomicRegionSet("DBD_sig")
sigDBD.sequences = self.data["region"]["sig_region"]
rbss = self.txp.get_rbs()
overlaps = rbss.intersect(y=sigDBD, mode=OverlapType.ORIGINAL)
self.stat["DBSs_target_DBD_sig"] = str(len(overlaps))
def lineplot(self, txp, dirp, ac, cut_off, log, ylabel, linelabel, showpa, sig_region, filename):
"""Generate lineplot for RNA"""
lineplot(txp=txp, rnalen=self.rna_len, rnaname=self.rna_name, dirp=dirp, sig_region=sig_region,
cut_off=cut_off, log=log, ylabel=ylabel, linelabel=linelabel,
filename=filename, ac=ac, showpa=showpa)
def boxplot(self, dir, matrix, sig_region, truecounts, sig_boolean, ylabel, filename):
"""Generate the visualized plot"""
tick_size = 8
label_size = 9
f, ax = plt.subplots(1, 1, dpi=300, figsize=(6, 4))
max_y = int(max([matrix.max()] + truecounts) * 1.1) + 1
min_y = max(int(matrix.min() * 0.9) - 1, 0)
# Significant DBD
rect = patches.Rectangle(xy=(1, 0), width=0.8, height=max_y, facecolor=sig_color,
edgecolor="none", alpha=0.5, lw=None, label="Significant DBD")
for i, r in enumerate(sig_boolean):
if r:
rect = patches.Rectangle(xy=(i + 0.6, min_y), width=0.8, height=max_y, facecolor=sig_color,
edgecolor="none", alpha=0.5, lw=None, label="Significant DBD")
ax.add_patch(rect)
# Plotting
bp = ax.boxplot(matrix.transpose(), notch=False, sym='o', vert=True,
whis=1.5, positions=None, widths=None,
patch_artist=True, bootstrap=None)
z = 10
plt.setp(bp['boxes'], color=nontarget_color, alpha=1, edgecolor="none")
plt.setp(bp['whiskers'], color='black', linestyle='-', linewidth=1, zorder=z, alpha=1)
plt.setp(bp['fliers'], markerfacecolor='gray', color='white', alpha=0.3, markersize=1.8, zorder=z)
plt.setp(bp['caps'], color='white', zorder=-1)
plt.setp(bp['medians'], color='black', linewidth=1.5, zorder=z + 1)
# Plot target regions
plt.plot(range(1, len(self.rbss) + 1), truecounts, markerfacecolor=target_color,
marker='o', markersize=5, linestyle='None', markeredgecolor="white", zorder=z + 5)
ax.set_xlabel(self.rna_name + " DNA Binding Domains", fontsize=label_size)
ax.set_ylabel(ylabel, fontsize=label_size, rotation=90)
ax.set_ylim([min_y, max_y])
ax.yaxis.set_major_locator(MaxNLocator(integer=True))
ax.set_xticklabels([dbd.str_rna(pa=False) for dbd in self.rbss], rotation=35,
ha="right", fontsize=tick_size)
for tick in ax.yaxis.get_major_ticks(): tick.label.set_fontsize(tick_size)
for spine in ['top', 'right']:
ax.spines[spine].set_visible(False)
ax.tick_params(axis='x', which='both', bottom='off', top='off', labelbottom='on')
ax.tick_params(axis='y', which='both', left='on', right='off', labelbottom='off')
# Legend
dot_legend, = plt.plot([1, 1], color=target_color, marker='o', markersize=5, markeredgecolor="white",
linestyle='None')
bp_legend, = plt.plot([1, 1], color=nontarget_color, linewidth=6, alpha=1)
ax.legend([dot_legend, bp_legend, rect], ["Target Regions", "Non-target regions", "Significant DBD"],
bbox_to_anchor=(0., 1.02, 1., .102), loc=2, mode="expand", borderaxespad=0.,
prop={'size': 9}, ncol=3, numpoints=1)
bp_legend.set_visible(False)
dot_legend.set_visible(False)
# f.tight_layout(pad=1.08, h_pad=None, w_pad=None)
f.savefig(os.path.join(dir, filename + ".png"), facecolor='w', edgecolor='w',
bbox_extra_artists=(plt.gci()), bbox_inches='tight', dpi=300)
# PDF
for tick in ax.xaxis.get_major_ticks():
tick.label.set_fontsize(12)
for tick in ax.yaxis.get_major_ticks():
tick.label.set_fontsize(12)
ax.xaxis.label.set_size(14)
ax.yaxis.label.set_size(14)
pp = PdfPages(os.path.join(dir, filename + '.pdf'))
pp.savefig(f, bbox_extra_artists=(plt.gci()), bbox_inches='tight')
pp.close()
def gen_html(self, directory, parameters, obed, align=50, alpha=0.05, score=False):
"""Generate the HTML file"""
dir_name = os.path.basename(directory)
html_header = "Genomic Region Test: " + dir_name
link_ds = OrderedDict()
link_ds["RNA"] = "index.html"
link_ds["Sig Target Regions"] = "starget_regions.html"
link_ds["Target Regions"] = "target_regions.html"
link_ds["Parameters"] = "parameters.html"
##################################################
# index.html
html = Html(name=html_header, links_dict=link_ds, # fig_dir=os.path.join(directory,"style"),
fig_rpath="../style", RGT_header=False, other_logo="TDF", homepage="../index.html")
# Plots
html.add_figure("lineplot_region.png", align="left", width="45%", more_images=["boxplot_regions.png"])
if self.showdbs:
html.add_figure("lineplot_dbs.png", align="left", width="45%", more_images=["boxplot_dbs.png"])
if self.showdbs:
header_list = [["#", "DBD", "Target Regions", None, "Non-target Regions", None, "Statistics",
"Target Regions", "Non-target Regions", None, "Statistics"],
["", "", "with DBS", "without DBS", "with DBS (average)", "s.d.", "<i>p</i>-value",
"NO. DBSs", "NO. DBSs (average)", "s.d.", "<i>p</i>-value"]]
header_titles = [["Rank", "DNA Binding Domain", "Given target regions on DNA", None,
"Regions from randomization", None, "Statistics based on target regions",
"Given target regions on DNA", "Regions from randomization", None,
"Statistics based on DNA Binding Sites"],
["", "",
"Number of target regions with DBS binding",
"Number of target regions without DBS binding",
"Average number of regions from randomization with DBS binding",
"Standard deviation", "P value",
"Number of related DNA Binding Sites binding to target regions",
"Average number of DNA Binding Sites binding to random regions",
"Standard deviation", "P-value"]]
border_list = [" style=\"border-right:1pt solid gray\"",
" style=\"border-right:1pt solid gray\"", "",
" style=\"border-right:1pt solid gray\"", "",
" style=\"border-right:1pt solid gray\"",
" style=\"border-right:2pt solid gray\"",
" style=\"border-right:1pt solid gray\"", "",
" style=\"border-right:1pt solid gray\"",
" style=\"border-right:1pt solid gray\""]
else:
header_list = [["#", "DBD", "Target Regions", None, "Non-target Regions", None, "Statistics", None],
["", "", "with DBS", "without DBS", "with DBS (average)", "s.d.", "<i>p</i>-value",
"z-score"]]
header_titles = [["Rank", "DNA Binding Domain", "Given target regions on DNA", None,
"Regions from randomization", None, "Statistics based on target regions", None],
["", "",
"Number of target regions with DBS binding",
"Number of target regions without DBS binding",
"Average number of regions from randomization with DBS binding",
"Standard deviation", "P value", "Z-score"]]
border_list = [" style=\"border-right:1pt solid gray\"",
" style=\"border-right:1pt solid gray\"", "",
" style=\"border-right:1pt solid gray\"", "",
" style=\"border-right:1pt solid gray\"",
" style=\"border-right:1pt solid gray\"", ""]
type_list = 'ssssssssssssssss'
col_size_list = [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50]
data_table = []
for i, rbs in enumerate(self.rbss):
if self.data["region"]["p"][i] < alpha:
p_region = "<font color=\"red\">" + value2str(self.data["region"]["p"][i]) + "</font>"
else:
p_region = value2str(self.data["region"]["p"][i])
zs = (self.counts_tr[rbs][0] - self.data["region"]["ave"][i]) / self.data["region"]["sd"][i]
new_line = [str(i + 1),
rbs.str_rna(pa=False),
'<a href="dbd_region.html#' + rbs.str_rna() +
'" style="text-align:left">' + str(self.counts_tr[rbs][0]) + '</a>',
str(self.counts_tr[rbs][1]),
value2str(self.data["region"]["ave"][i]),
value2str(self.data["region"]["sd"][i]),
p_region,
value2str(zs)]
if self.showdbs:
if self.data["dbs"]["p"][i] < alpha:
p_dbs = "<font color=\"red\">" + value2str(self.data["dbs"]["p"][i]) + "</font>"
else:
p_dbs = value2str(self.data["dbs"]["p"][i])
new_line += [str(self.counts_dbs[rbs]),
value2str(self.data["dbs"]["ave"][i]),
value2str(self.data["dbs"]["sd"][i]),
p_dbs]
data_table.append(new_line)
data_table = natsort.natsorted(data_table, key=lambda x: x[6])
html.add_zebra_table(header_list, col_size_list, type_list, data_table, align=align, cell_align="left",
auto_width=True, header_titles=header_titles, border_list=border_list, sortable=True)
html.add_heading("Notes")
html.add_list(["RNA name: " + self.rna_name,
"Randomization is performed for " + str(self.repeats) + " times.",
"DBD stands for DNA Binding Domain on RNA.",
"DBS stands for DNA Binding Site on DNA."])
html.add_fixed_rank_sortable()
html.write(os.path.join(directory, "index.html"))
#############################################################
# RNA subpage: Profile of targeted regions for each merged DNA Binding Domain
#############################################################
header_list = ["#", "Target Region",
"Associated Gene",
"No. of DBSs",
"DBS coverage"]
header_titles = ["Rank", "Given target regions from BED files",
"Associated genes which is overlapping with the given region or close to it (less than 50000 bp)",
"Number of DNA Binding Sites locate within the region",
"The proportion of the region covered by DBS binding"]
#########################################################
# dbd_region.html
html = Html(name=html_header, links_dict=link_ds, # fig_dir=os.path.join(directory,"style"),
fig_rpath="../style", RGT_header=False, other_logo="TDF", homepage="../index.html")
for rbsm in self.rbss:
html.add_heading("DNA Binding Domain: " + rbsm.str_rna(),
idtag=rbsm.str_rna())
data_table = []
for i, region in enumerate(self.txp.merged_dict[rbsm]):
# Add information
data_table.append([str(i + 1),
'<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=' + self.organism +
"&position=" + region.chrom + "%3A" + str(region.initial) + "-" + str(region.final) +
'" style="text-align:left">' + region.toString(space=True) + '</a>',
split_gene_name(gene_name=region.name, org=self.organism),
str(len(self.region_dbs[region.toString()])),
value2str(self.region_coverage[region.toString()])
])
html.add_zebra_table(header_list, col_size_list, type_list, data_table, align=align, cell_align="left",
auto_width=True, header_titles=header_titles, sortable=True)
html.add_fixed_rank_sortable()
html.write(os.path.join(directory, "dbd_region.html"))
#############################################################
# Targeted regions centered
#############################################################
##############################################################################################
# target_regions.html
html = Html(name=html_header, links_dict=link_ds, # fig_dir=os.path.join(directory,"style"),
fig_rpath="../style", RGT_header=False, other_logo="TDF", homepage="../index.html")
if score:
header_list = ["#", "Target region", "Associated Gene", "DBSs Count",
"DBS coverage", "Score", "Sum of ranks"]
header_titles = ["Rank",
"Target regions loaded from the given BED file",
"Associated genes which is overlapping with the given region or close to it (less than 50000 bp)",
"Number of DNA Binding Sites within the region",
"The proportion of the region covered by DBS binding",
"Scores from BED file",
"Sum of all the left-hand-side ranks"]
else:
header_list = ["#", "Target region", "Associated Gene", "DBSs Count",
"DBS coverage", "Sum of ranks"]
header_titles = ["Rank",
"Target regions loaded from the given BED file",
"Associated genes which is overlapping with the given region or close to it (less than 50000 bp)",
"Number of DNA Binding Sites within the region",
"The proportion of the region covered by DBS binding",
"Sum of all the left-hand-side ranks"]
html.add_heading("Target Regions")
data_table = []
if not self.dna_region.sorted: self.dna_region.sort()
# Calculate the ranking
rank_count = len(self.dna_region) - rank_array([len(self.region_dbs[p.toString()]) for p in self.dna_region])
rank_coverage = len(self.dna_region) - rank_array([self.region_coverage[p.toString()] for p in self.dna_region])
if score:
try:
score_list = [float(p.data.split("\t")[0]) for p in self.dna_region]
rank_score = len(self.dna_region) - rank_array([abs(s) for s in score_list])
rank_sum = [x + y + z for x, y, z in zip(rank_count, rank_coverage, rank_score)]
# sum_rank = rank_array(rank_sum) # method='min'
except ImportError:
print("There is no score in BED file, please don't use '-score' argument.")
else:
rank_sum = [x + y for x, y in zip(rank_count, rank_coverage)]
sum_rank = rank_array(rank_sum)
for i, region in enumerate(self.dna_region):
dbs_counts = str(len(self.region_dbs[region.toString()]))
dbs_cover = value2str(self.region_coverage[region.toString()])
newline = [str(i + 1),
'<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=' + self.organism +
"&position=" + region.chrom + "%3A" + str(region.initial) + "-" + str(region.final) +
'" style="text-align:left">' + region.toString(space=True) + '</a>',
split_gene_name(gene_name=region.name, org=self.organism),
'<a href="region_dbs.html#' + region.toString() +
'" style="text-align:left">' + dbs_counts + '</a>',
dbs_cover]
if score:
dbs_score = value2str(score_list[i])
region.data = "\t".join([dbs_counts, dbs_cover, dbs_score, str(rank_sum[i])])
newline.append(dbs_score)
newline.append(str(rank_sum[i]))
else:
region.data = "\t".join([dbs_counts, dbs_cover, str(rank_sum[i])])
newline.append(str(rank_sum[i]))
data_table.append(newline)
data_table = natsort.natsorted(data_table, key=lambda x: x[-1])
# data_table = sorted(data_table, key=lambda x: x[-1])
html.add_zebra_table(header_list, col_size_list, type_list, data_table, align=align, cell_align="left",
auto_width=True, header_titles=header_titles, sortable=True)
html.add_heading("Notes")
html.add_list(["All target regions without any bindings are ignored."])
html.add_fixed_rank_sortable()
html.write(os.path.join(directory, "target_regions.html"))
self.dna_region.sort_score()
self.dna_region.write_bed(os.path.join(directory, obed + "_target_regions.bed"))
##############################################################################################
# starget_regions.html for significant target regions
stargets = GenomicRegionSet("sig_targets")
sig_dbs = {}
sig_dbs_coverage = {}
for i, r in enumerate(self.dna_region):
sig_bindings = self.region_dbs[r.toString()].overlap_rbss(rbss=self.data["region"]["sig_region"])
dbs = sig_bindings.get_dbs()
if len(dbs) > 0:
stargets.add(r)
m_dbs = dbs.merge(w_return=True)
sig_dbs[r] = len(dbs)
# self.promoter["de"]["merged_dbs"][promoter.toString()] = len(m_dbs)
sig_dbs_coverage[r] = float(m_dbs.total_coverage()) / len(r)
html = Html(name=html_header, links_dict=link_ds, # fig_dir=os.path.join(directory,"style"),
fig_rpath="../style", RGT_header=False, other_logo="TDF", homepage="../index.html")
# Select promoters in sig DBD
if len(self.data["region"]["sig_region"]) == 0:
html.add_heading("There is no significant DBD.")
else:
html.add_heading("Target regions bound by significant DBD")
data_table = []
# Calculate the ranking
rank_count = len(stargets) - rank_array([sig_dbs[p] for p in stargets])
rank_coverage = len(stargets) - rank_array([sig_dbs_coverage[p] for p in stargets])
if score:
score_list = [float(p.data.split("\t")[0]) for p in stargets]
rank_score = len(stargets) - rank_array([abs(s) for s in score_list])
rank_sum = [x + y + z for x, y, z in zip(rank_count, rank_coverage, rank_score)]
sum_rank = rank_array(rank_sum) # method='min'
else:
rank_sum = [x + y for x, y in zip(rank_count, rank_coverage)]
sum_rank = rank_array(rank_sum)
for i, region in enumerate(stargets):
dbssount = '<a href="region_dbs.html#' + region.toString() + \
'" style="text-align:left">' + str(sig_dbs[region]) + '</a>'
region_link = region_link_internet(self.organism, region)
newline = [str(i + 1), region_link,
split_gene_name(gene_name=region.name, org=self.organism),
dbssount, value2str(sig_dbs_coverage[region]) ]
if score:
dbs_score = value2str(score_list[i])
# region.data = "\t".join([dbs_counts, dbs_cover, dbs_score, str(sum_rank[i])])
newline.append(dbs_score)
newline.append(str(rank_sum[i]))
# print([dbs_score, str(sum_rank[i])])
else:
# region.data = "\t".join([dbs_counts, dbs_cover, str(sum_rank[i])])
newline.append(str(rank_sum[i]))
# newline += ["<i>" + str(rank_sum[i]) + "</i>"]
# print(newline)
data_table.append(newline)
# print(data_table)
# data_table = sorted(data_table, key=lambda x: x[-1])
data_table = natsort.natsorted(data_table, key=lambda x: x[-1])
html.add_zebra_table(header_list, col_size_list, type_list, data_table, align=align, cell_align="left",
header_titles=header_titles, border_list=None, sortable=True)
html.add_heading("Notes")
html.add_list(["DBS stands for DNA Binding Site on DNA.",
"DBS coverage is the proportion of the region where has potential to form triple helices with the given RNA."])
html.add_fixed_rank_sortable()
html.write(os.path.join(directory, "starget_regions.html"))
############################
# Subpages for targeted region centered page
# region_dbs.html
header_list = ["RBS", "DBS", "Strand", "Score", "Motif", "Orientation"]
html = Html(name=html_header, links_dict=link_ds, # fig_dir=os.path.join(directory,"style"),
fig_rpath="../style", RGT_header=False, other_logo="TDF", homepage="../index.html")
for i, region in enumerate(self.dna_region):
if len(self.region_dbs[region.toString()]) == 0:
continue
else:
html.add_heading("Associated gene: " + split_gene_name(gene_name=region.name, org=self.organism),
idtag=region.toString())
html.add_free_content(['<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=' + self.organism +
"&position=" + region.chrom + "%3A" + str(region.initial) +
"-" + str(region.final) + '" style="margin-left:50">' +
region.toString(space=True) + '</a>'])
data_table = []
for rd in self.region_dbs[region.toString()]:
rbs = rd.rna.str_rna(pa=False)
for rbsm in self.data["region"]["sig_region"]:
# rbsm = rbsm.partition(":")[2].split("-")
if rd.rna.overlap(rbsm):
rbs = "<font color=\"red\">" + rbs + "</font>"
data_table.append([rbs,
'<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=' + self.organism +
"&position=" + rd.dna.chrom + "%3A" + str(rd.dna.initial) + "-" + str(
rd.dna.final) +
'" style="text-align:left">' + rd.dna.toString(space=True) + '</a>',
rd.dna.orientation, rd.score, rd.motif, rd.orient])
html.add_zebra_table(header_list, col_size_list, type_list, data_table, align=align, cell_align="left",
auto_width=True)
html.write(os.path.join(directory, "region_dbs.html"))
###############################################################################33
################ Parameters.html
html = Html(name=html_header, links_dict=link_ds, # fig_dir=os.path.join(directory,"style"),
fig_rpath="../style", RGT_header=False, other_logo="TDF", homepage="../index.html")
html.add_heading("Parameters")
header_list = ["Description", "Arguments", "Value"]
data_table = [["RNA sequence name", "-rn", parameters.rn],
["Input RNA sequence file", "-r", os.path.basename(parameters.r)],
["Input BED file", "-bed", os.path.basename(parameters.bed)],
["Output directory", "-o", os.path.basename(parameters.o)],
["Organism", "-organism", parameters.organism],
["Number of repitetion of andomization", "-n", str(parameters.n)],
["Alpha level for rejection p value", "-a", str(parameters.a)],
["Cut off value for filtering out the low counts of DBSs", "-ccf", str(parameters.ccf)],
["Remove temporary files", "-rt", str(parameters.rt)],
["Input BED file for masking in randomization", "-f", str(parameters.f)],
["Input file for RNA accecibility", "-ac", str(parameters.ac)],
["Cut off value for RNA accecibility", "-accf", str(parameters.accf)],
["Output the BED files for DNA binding sites.", "-obed", str(parameters.obed)],
["Show parallel and antiparallel bindings in the plot separately.", "-showpa",
str(parameters.showpa)],
["Minimum length", "-l", str(self.triplexator_p[0])],
["Maximum error rate", "-e", str(self.triplexator_p[1])],
["Tolerated number of consecutive errors", "-c", str(self.triplexator_p[2])],
["Filtering repeats", "-fr", str(self.triplexator_p[3])],
["Filtering mode", "-fm", str(self.triplexator_p[4])],
["Output format", "-of", str(self.triplexator_p[5])],
["Merge features", "-mf", str(self.triplexator_p[6])]]
html.add_zebra_table(header_list, col_size_list, type_list, data_table, align=align, cell_align="left",
auto_width=True)
html.add_free_content(['<a href="summary.txt" style="margin-left:100">See details</a>'])
html.write(os.path.join(directory, "parameters.html"))