def main(argv=sys.argv):
parser = E.OptionParser(version="%prog version: $Id: mali2mali.py 2782 2009-09-10 11:40:29Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-i", "--input-format", dest="input_format", type="choice",
choices=(
"plain", "fasta", "clustal", "stockholm", "phylip"),
help="input format of multiple alignment [default=%default].")
parser.add_option("-o", "--output-format", dest="output_format", type="choice",
choices=(
"plain", "fasta", "stockholm", "phylip", "nexus", "plain-fasta"),
help="output format of multiple alignment [default=%default].")
parser.add_option("--with-ranges", dest="with_ranges", action="store_true",
help="output alignment ranges (suffix /from-to after identifier) [default=%default].")
parser.add_option("--without-ranges", dest="with_ranges", action="store_false",
help="do not output alignment ranges (suffix /from-to after identifier) [default=%default].")
parser.add_option("-u", "--allow-duplicates", dest="allow_duplicates", action="store_true",
help="permit duplicate entries [default=%default].")
parser.add_option("-m", "--method", dest="methods", type="string",
help="""methods to apply. Several methods can be specified in a ','-separated list [default=%default].""" )
parser.add_option("-p", "--parameters", dest="parameters", type="string",
help="parameter stack for methods that require one [default=%default].")
parser.add_option("-a", "--mask-char", dest="mask_char", type="string",
help="character to identify/set masked characters [default=%default].")
parser.set_defaults(
input_format="fasta",
output_format="fasta",
methods="",
parameters="",
mask_char="x",
gap_chars="-.nN",
with_ranges=True,
allow_duplicates=False,
)
(options, args) = E.Start(parser)
options.methods = options.methods.split(",")
options.parameters = options.parameters.split(",")
# 1. read multiple alignment in various formats
if options.allow_duplicates:
mali = Mali.SequenceCollection()
else:
mali = Mali.Mali()
t1 = time.time()
mali.readFromFile(options.stdin, format=options.input_format)
E.info("read mali with %i entries in %i seconds." %
(len(mali), time.time() - t1))
if len(mali) == 0:
raise ValueError("empty multiple alignment")
for method in options.methods:
t1 = time.time()
if method == "remove-unaligned-ends":
mali.removeUnalignedEnds()
elif method == "remove-end-gaps":
mali.removeEndGaps()
elif method == "remove-all-gaps":
mali.removeGaps(minimum_gaps=len(mali))
elif method == "remove-any-gaps":
mali.removeGaps(minimum_gaps=1)
elif method == "remove-some-gaps":
minimum_gaps = int(options.parameters[0])
del options.parameters[0]
mali.removeGaps(minimum_gaps=minimum_gaps)
elif method == "remove-empty-sequences":
mali.removeEmptySequences()
elif method == "upper":
mali.upperCase()
elif method == "lower":
mali.lowerCase()
elif method == "mark-codons":
mali.markCodons()
elif method == "remove-stops":
mali.removePattern(lambda x: x.upper() in ("TAG", "TAA", "TGA"),
allowed_matches=0,
minimum_matches=1,
delete_frame=3,
search_frame=3)
elif method == "shift-alignment":
map_id2offset = IOTools.ReadMap(open(options.parameters[0], "r"),
map_functions=(str, int))
del options.parameters[0]
mali.shiftAlignment(map_id2offset)
elif method == "propagate-masks":
mali.propagateMasks(mask_char=options.mask_char)
elif method == "recount":
mali.recount()
elif method in ("mark-transitions", "filter-odd-transitions", "filter-even-transitions",
"keep-even-segments", "keep-odd-segments"):
if os.path.exists(options.parameters[0]):
map_id2transitions = IOTools.readMultiMap(open(options.parameters[0], "r"),
map_functions=(str, int))
else:
map_id2transitions = {}
r = map(int, options.parameters[0].split(':'))
r.sort()
map_id2transitions["mali"] = r
del options.parameters[0]
if method == "mark-transitions":
mali.markTransitions(map_id2transitions)
elif method in ("filter-odd-transitions", "keep-even-segments"):
mali.markTransitions(map_id2transitions, mode="keep-odd")
elif method in ("filter-even-transitions", "keep-odd-segments"):
mali.markTransitions(map_id2transitions, mode="keep-even")
elif method == "propagate-transitions":
mali.propagateTransitions()
elif method == "map-annotation":
# map annotations in one mali (stockholm-format) to the annotations in another.
# Note: the first two sequence identifiers must be shared and the sequence of the
# same length
other_mali = Mali.Mali()
other_mali.readFromFile(
open(options.parameters[0], "r"), format="stockholm")
del options.parameters[0]
mali.copyAnnotations(other_mali)
elif method == "add-annotation":
annotation_type, annotation_file = options.parameters[:2]
del options.parameters[:2]
AddAnnotation(mali, annotation_type, annotation_file)
elif method == "mask-columns":
annotation_type, annotation_file = options.parameters[:2]
del options.parameters[:2]
maskColumns(mali, annotation_type, annotation_file)
elif method == "remove-unaligned-pairs":
removeUnalignedPairs(mali, options)
elif method == "filter-3rd":
filterMali(mali, "3rd")
elif method == "filter-4d":
filterMali(mali, "4d")
elif method in ("mask-seg", "mask-bias"):
a, b = method.split("-")
maskMali(mali, b)
elif method == "exclude-with-stop":
mali.filter(method="with-stop")
elif method == "exclude-with-stop":
mali.filter(method="with-frameshift")
E.info("applied method %s in %i seconds." % (method, time.time() - t1))
mali.writeToFile(options.stdout,
format=options.output_format,
write_ranges=options.with_ranges)
E.Stop()
options.section,
outfile_synonyms = outfile_synonyms,
max_length = options.max_length,
remove_regex = options.remove_regex )
if outfile_synonyms:
outfile_synonyms.close()
elif options.section == "annotations-go":
assert options.input_filename_map, "please supply option --input-filename-map"
iterator = GTF.iterator_filtered( GTF.iterator( options.stdin ),
feature=options.feature )
geneid2categories = IOTools.readMultiMap( open( options.input_filename_map, "r") )
category2segments = collections.defaultdict( list )
for contig, gffs in GTF.readAsIntervals( iterator, with_gene_id = True ).items():
if options.remove_regex and options.remove_regex.search( contig ): continue
for start, end, geneid in gffs:
if geneid not in geneid2categories: continue
for category in geneid2categories[geneid]:
category2segments[category].append(nsegments)
options.stdout.write( "%s\t%i\t%s\t(%i,%i)\n" % (prefix, nsegments, contig, start, end ) )
nsegments += 1
for category, segments in category2segments.iteritems():
def main(argv=sys.argv):
parser = E.OptionParser(
version=
"%prog version: $Id: mali2mali.py 2782 2009-09-10 11:40:29Z andreas $",
usage=globals()["__doc__"])
parser.add_option(
"-i",
"--input-format",
dest="input_format",
type="choice",
choices=("plain", "fasta", "clustal", "stockholm", "phylip"),
help="input format of multiple alignment [default=%default].")
parser.add_option(
"-o",
"--output-format",
dest="output_format",
type="choice",
choices=("plain", "fasta", "stockholm", "phylip", "nexus",
"plain-fasta"),
help="output format of multiple alignment [default=%default].")
parser.add_option(
"--with-ranges",
dest="with_ranges",
action="store_true",
help=
"output alignment ranges (suffix /from-to after identifier) [default=%default]."
)
parser.add_option(
"--without-ranges",
dest="with_ranges",
action="store_false",
help=
"do not output alignment ranges (suffix /from-to after identifier) [default=%default]."
)
parser.add_option("-u",
"--allow-duplicates",
dest="allow_duplicates",
action="store_true",
help="permit duplicate entries [default=%default].")
parser.add_option(
"-m",
"--method",
dest="methods",
type="string",
help=
"""methods to apply. Several methods can be specified in a ','-separated list [default=%default]."""
)
parser.add_option(
"-p",
"--parameters",
dest="parameters",
type="string",
help="parameter stack for methods that require one [default=%default]."
)
parser.add_option(
"-a",
"--mask-char",
dest="mask_char",
type="string",
help="character to identify/set masked characters [default=%default].")
parser.set_defaults(
input_format="fasta",
output_format="fasta",
methods="",
parameters="",
mask_char="x",
gap_chars="-.nN",
with_ranges=True,
allow_duplicates=False,
)
(options, args) = E.Start(parser)
options.methods = options.methods.split(",")
options.parameters = options.parameters.split(",")
# 1. read multiple alignment in various formats
if options.allow_duplicates:
mali = Mali.SequenceCollection()
else:
mali = Mali.Mali()
t1 = time.time()
mali.readFromFile(options.stdin, format=options.input_format)
E.info("read mali with %i entries in %i seconds." %
(len(mali), time.time() - t1))
if len(mali) == 0:
raise ValueError("empty multiple alignment")
for method in options.methods:
t1 = time.time()
if method == "remove-unaligned-ends":
mali.removeUnalignedEnds()
elif method == "remove-end-gaps":
mali.removeEndGaps()
elif method == "remove-all-gaps":
mali.removeGaps(minimum_gaps=len(mali))
elif method == "remove-any-gaps":
mali.removeGaps(minimum_gaps=1)
elif method == "remove-some-gaps":
minimum_gaps = int(options.parameters[0])
del options.parameters[0]
mali.removeGaps(minimum_gaps=minimum_gaps)
elif method == "remove-empty-sequences":
mali.removeEmptySequences()
elif method == "upper":
mali.upperCase()
elif method == "lower":
mali.lowerCase()
elif method == "mark-codons":
mali.markCodons()
elif method == "remove-stops":
mali.removePattern(lambda x: x.upper() in ("TAG", "TAA", "TGA"),
allowed_matches=0,
minimum_matches=1,
delete_frame=3,
search_frame=3)
elif method == "shift-alignment":
map_id2offset = IOTools.ReadMap(open(options.parameters[0], "r"),
map_functions=(str, int))
del options.parameters[0]
mali.shiftAlignment(map_id2offset)
elif method == "propagate-masks":
mali.propagateMasks(mask_char=options.mask_char)
elif method == "recount":
mali.recount()
elif method in ("mark-transitions", "filter-odd-transitions",
"filter-even-transitions", "keep-even-segments",
"keep-odd-segments"):
if os.path.exists(options.parameters[0]):
map_id2transitions = IOTools.readMultiMap(
open(options.parameters[0], "r"), map_functions=(str, int))
else:
map_id2transitions = {}
r = map(int, options.parameters[0].split(':'))
r.sort()
map_id2transitions["mali"] = r
del options.parameters[0]
if method == "mark-transitions":
mali.markTransitions(map_id2transitions)
elif method in ("filter-odd-transitions", "keep-even-segments"):
mali.markTransitions(map_id2transitions, mode="keep-odd")
elif method in ("filter-even-transitions", "keep-odd-segments"):
mali.markTransitions(map_id2transitions, mode="keep-even")
elif method == "propagate-transitions":
mali.propagateTransitions()
elif method == "map-annotation":
# map annotations in one mali (stockholm-format) to the annotations in another.
# Note: the first two sequence identifiers must be shared and the sequence of the
# same length
other_mali = Mali.Mali()
other_mali.readFromFile(open(options.parameters[0], "r"),
format="stockholm")
del options.parameters[0]
mali.copyAnnotations(other_mali)
elif method == "add-annotation":
annotation_type, annotation_file = options.parameters[:2]
del options.parameters[:2]
AddAnnotation(mali, annotation_type, annotation_file)
elif method == "mask-columns":
annotation_type, annotation_file = options.parameters[:2]
del options.parameters[:2]
maskColumns(mali, annotation_type, annotation_file)
elif method == "remove-unaligned-pairs":
removeUnalignedPairs(mali, options)
elif method == "filter-3rd":
filterMali(mali, "3rd")
elif method == "filter-4d":
filterMali(mali, "4d")
elif method in ("mask-seg", "mask-bias"):
a, b = method.split("-")
maskMali(mali, b)
elif method == "exclude-with-stop":
mali.filter(method="with-stop")
elif method == "exclude-with-stop":
mali.filter(method="with-frameshift")
E.info("applied method %s in %i seconds." % (method, time.time() - t1))
mali.writeToFile(options.stdout,
format=options.output_format,
write_ranges=options.with_ranges)
E.Stop()
def main(argv=sys.argv):
parser = E.OptionParser(
version="%prog version: $Id: annotator_distance.py 2861 2010-02-23 17:36:32Z andreas $", usage=globals()["__doc__"])
parser.add_option("-a", "--filename-annotations", dest="filename_annotations", type="string",
help="filename mapping gene ids to annotations (a tab-separated table with two-columns) [default=%default].")
parser.add_option("-r", "--resolution", dest="resolution", type="int",
help="resolution of count vector [default=%default].")
parser.add_option("-b", "--num-bins", dest="num_bins", type="int",
help="number of bins in count vector [default=%default].")
parser.add_option("-i", "--num-samples", dest="num_samples", type="int",
help="sample size to compute [default=%default].")
parser.add_option("-w", "--workspace", dest="filename_workspace", type="string",
help="filename with workspace information [default=%default].")
parser.add_option("--workspace-builder", dest="workspace_builder", type="choice",
choices=(
"gff", "gtf-intergenic", "gtf-intronic", "gtf-genic"),
help="given a gff/gtf file build a workspace [default=%default].")
parser.add_option("--workspace-labels", dest="workspace_labels", type="choice",
choices=("none", "direction", "annotation"),
help="labels to use for the workspace workspace [default=%default].")
parser.add_option("--sampler", dest="sampler", type="choice",
choices=("permutation", "gaps"),
help="sampler to use. The sampler determines the null model of how segments are distributed in the workspace [default=%default]")
parser.add_option("--counter", dest="counters", type="choice", action="append",
choices=(
"transcription", "closest-distance", "all-distances"),
help="counter to use. The counter computes the quantity of interest [default=%default]")
parser.add_option("--analysis", dest="analysis", type="choice", action="append",
choices=("proximity", "area-under-curve"),
help="analysis to perform [default=%default]")
parser.add_option("--transform-counts", dest="transform_counts", type="choice",
choices=("raw", "cumulative"),
help="cumulate counts [default=%default].")
parser.add_option("-s", "--segments", dest="filename_segments", type="string",
help="filename with segment information [default=%default].")
parser.add_option("--xrange", dest="xrange", type="string",
help="xrange to plot [default=%default]")
parser.add_option("-o", "--logscale", dest="logscale", type="string",
help="use logscale on x, y or xy [default=%default]")
parser.add_option("-p", "--plot", dest="plot", action="store_true",
help="output plots [default=%default]")
parser.add_option("--hardcopy", dest="hardcopy", type="string",
help="output hardcopies to file [default=%default]")
parser.add_option("--no-fdr", dest="do_fdr", action="store_false",
help="do not compute FDR rates [default=%default]")
parser.add_option("--segments-format", dest="segments_format", type="choice",
choices=("gtf", "bed"),
help="format of segments file [default=%default].")
parser.add_option("--truncate", dest="truncate", action="store_true",
help="truncate segments extending beyond a workspace [default=%default]")
parser.add_option("--remove-overhangs", dest="remove_overhangs", action="store_true",
help="remove segments extending beyond a workspace[default=%default]")
parser.add_option("--keep-ambiguous", dest="keep_ambiguous", action="store_true",
help="keep segments extending to more than one workspace [default=%default]")
parser.set_defaults(
filename_annotations=None,
filename_workspace="workspace.gff",
filename_segments="FastDown.gtf",
filename_annotations_gtf="../data/tg1_territories.gff",
workspace_builder="gff",
workspace_labels="none",
sampler="permutation",
truncate=False,
num_bins=10000,
num_samples=10,
resolution=100,
plot_samples=False,
plot_envelope=True,
counters=[],
transform_counts="raw",
xrange=None,
plot=False,
logscale=None,
output_all=False,
do_test=False,
analysis=[],
do_fdr=True,
hardcopy="%s.png",
segments_format="gtf",
remove_overhangs=False,
)
(options, args) = E.Start(parser, argv=argv, add_output_options=True)
###########################################
# setup options
if options.sampler == "permutation":
sampler = SamplerPermutation
elif options.sampler == "gaps":
sampler = SamplerGaps
if options.xrange:
options.xrange = map(float, options.xrange.split(","))
if len(options.counters) == 0:
raise ValueError("please specify at least one counter.")
if len(options.analysis) == 0:
raise ValueError("please specify at least one analysis.")
if options.workspace_labels == "annotation" and not options.filename_annotations:
raise ValueError(
"please specify --filename-annotations is --workspace-labels=annotations.")
###########################################
# read data
if options.workspace_labels == "annotation":
def constant_factory(value):
return itertools.repeat(value).next
def dicttype():
return collections.defaultdict(constant_factory(("unknown",)))
map_id2annotations = IOTools.readMultiMap(open(options.filename_annotations, "r"),
dtype=dicttype)
else:
map_id2annotations = {}
workspace = readWorkspace(open(options.filename_workspace, "r"),
options.workspace_builder,
options.workspace_labels,
map_id2annotations)
E.info("read workspace for %i contigs" % (len(workspace)))
indexed_workspace = indexIntervals(workspace, with_values=True)
segments = readSegments(open(options.filename_segments, "r"), indexed_workspace,
format=options.segments_format,
keep_ambiguous=options.keep_ambiguous,
truncate=options.truncate,
remove_overhangs=options.remove_overhangs)
nsegments = 0
for contig, vv in segments.iteritems():
nsegments += len(vv)
E.info("read %i segments for %i contigs" % (nsegments, len(workspace)))
indexed_segments = indexIntervals(segments, with_values=False)
if nsegments == 0:
E.warn("no segments read - no computation done.")
E.Stop()
return
# build labels
labels = collections.defaultdict(int)
for contig, vv in workspace.iteritems():
for start, end, v in vv:
for l in v[0]:
labels[l] += 1
for l in v[1]:
labels[l] += 1
E.info("found %i workspace labels" % len(labels))
###########################################
# setup counting containers
counters = []
for cc in options.counters:
if cc == "transcription":
counter = CounterTranscription
elif cc == "closest-distance":
counter = CounterClosestDistance
elif cc == "all-distances":
counter = CounterAllDistances
if nsegments < 256:
dtype = numpy.uint8
elif nsegments < 65536:
dtype = numpy.uint16
elif nsegments < 4294967296:
dtype = numpy.uint32
else:
dtype = numpy.int
E.debug("choosen dtype %s" % str(dtype))
E.info("samples space is %i bases: %i bins at %i resolution" %
(options.num_bins * options.resolution,
options.num_bins,
options.resolution,
))
E.info("allocating counts: %i bytes (%i labels, %i samples, %i bins)" %
(options.num_bins * len(labels) * dtype().itemsize * (options.num_samples + 1),
len(labels),
options.num_samples,
options.num_bins,
))
c = CountingResults(labels)
c.mObservedCounts = counter(
labels, options.num_bins, options.resolution, dtype=dtype)
simulated_counts = []
for x in range(options.num_samples):
simulated_counts.append(
counter(labels, options.num_bins, options.resolution, dtype=dtype))
c.mSimulatedCounts = simulated_counts
c.mName = c.mObservedCounts.mName
counters.append(c)
E.info("allocated memory successfully")
segments_per_workspace = []
segment_sizes = []
segments_per_label = collections.defaultdict(int)
workspaces_per_label = collections.defaultdict(int)
############################################
# get observed and simpulated counts
nworkspaces, nempty_workspaces, nempty_contigs, nmiddle = 0, 0, 0, 0
iteration2 = 0
for contig, vv in workspace.iteritems():
iteration2 += 1
E.info("counting %i/%i: %s %i segments" %
(iteration2,
len(workspace),
contig,
len(vv)))
if len(vv) == 0:
continue
iteration1 = 0
for work_start, work_end, v in vv:
left_labels, right_labels = v[0], v[1]
iteration1 += 1
# ignore empty segments
if contig not in indexed_segments:
nempty_contigs += 1
continue
r = indexed_segments[contig].find(work_start, work_end)
segments_per_workspace.append(len(r))
if not r:
nempty_workspaces += 1
continue
# collect segments and stats
nworkspaces += 1
observed = [(x.start, x.end) for x in r]
observed.sort()
segments_per_workspace.append(len(observed))
segment_sizes.extend([x[1] - x[0] for x in observed])
# collect basic counts
for label in list(left_labels) + list(right_labels):
workspaces_per_label[label] += 1
segments_per_label[label] += len(observed)
# add observed counts
for counter in counters:
counter.mObservedCounts.addCounts(
observed, work_start, work_end, left_labels, right_labels)
# create sampler
s = sampler(observed, work_start, work_end)
# add simulated counts
for iteration in range(options.num_samples):
simulated = s.sample()
for counter in counters:
counter.mSimulatedCounts[iteration].addCounts(
simulated, work_start, work_end, left_labels, right_labels)
E.info("counting finished")
E.info("nworkspaces=%i, nmiddle=%i, nempty_workspaces=%i, nempty_contigs=%i" %
(nworkspaces, nmiddle, nempty_workspaces, nempty_contigs))
######################################################
# transform counts
if options.transform_counts == "cumulative":
transform = cumulative_transform
elif options.transform_counts == "raw":
transform = normalize_transform
####################################################
# analysis
if "proximity" in options.analysis:
outfile_proximity = E.openOutputFile("proximity")
outfile_proximity.write("\t".join(("label", "observed", "pvalue",
"expected", "CIlower", "CIupper", "qvalue", "segments", "workspaces")) + "\n")
else:
outfile_proximity = None
if "area-under-curve" in options.analysis:
outfile_auc = E.openOutputFile("auc")
outfile_auc.write("label\tobserved\texpected\tCIlower\tCIupper\n")
else:
outfile_auc = None
# qvalue: expected false positives at p-value
# qvalue = expected false positives /
if options.do_fdr:
E.info("computing pvalues for fdr")
for counter in counters:
for label in labels:
E.info("working on counter:%s label:%s" % (counter, label))
# collect all P-Values of simulated results to compute FDR
sim_pvalues = []
medians = counter.getMedians(label)
for median in medians:
pvalue = float(
scipy.stats.percentileofscore(medians, median)) / 100.0
sim_pvalues.append(pvalue)
sim_pvalues.sort()
else:
sim_pvalues = []
# compute observed p-values
for counter in counters:
counter.update()
obs_pvalues = []
for counter in counters:
for label in labels:
obs_pvalues.append(counter.mStats[label].pvalue)
obs_pvalues.sort()
# compute observed p-values
if options.do_fdr:
for counter in counters:
counter.updateFDR(obs_pvalues, sim_pvalues)
for counter in counters:
outofbounds_sim, totals_sim = 0, 0
outofbounds_obs, totals_obs = 0, 0
for label in labels:
for sample in range(options.num_samples):
if counter.mSimulatedCounts[sample].mOutOfBounds[label]:
E.debug("out of bounds: sample %i, label %s, counts=%i" %
(sample, label, counter.mSimulatedCounts[sample].mOutOfBounds[label]))
outofbounds_sim += counter.mSimulatedCounts[
sample].mOutOfBounds[label]
totals_sim += counter.mSimulatedCounts[sample].mTotals[label]
outofbounds_obs += counter.mObservedCounts.mOutOfBounds[label]
totals_obs += counter.mObservedCounts.mTotals[label]
E.info("out of bounds observations: observed=%i/%i (%5.2f%%), simulations=%i/%i (%5.2f%%)" %
(outofbounds_obs, totals_obs,
100.0 * outofbounds_obs / totals_obs,
outofbounds_sim, totals_sim,
100.0 * outofbounds_sim / totals_sim,
))
for label in labels:
if outfile_auc:
mmin, mmax, mmean = counter.getEnvelope(
label, transform=normalize_transform)
obs = normalize_transform(
counter.mObservedCounts[label], counter.mObservedCounts.mOutOfBounds[label])
def block_iterator(a1, a2, a3, num_bins):
x = 0
while x < num_bins:
while x < num_bins and a1[x] <= a2[x]:
x += 1
start = x
while x < options.num_bins and a1[x] > a2[x]:
x += 1
end = x
total_a1 = a1[start:end].sum()
total_a3 = a3[start:end].sum()
if total_a1 > total_a3:
yield (total_a1 - total_a3, start, end, total_a1, total_a3)
blocks = list(
block_iterator(obs, mmax, mmean, options.num_bins))
if options.output_all:
for delta, start, end, total_obs, total_mean in blocks:
if end - start <= 1:
continue
outfile_auc.write("%s\t%i\t%i\t%i\t%f\t%f\t%f\t%f\t%f\n" %
(label,
start * options.resolution,
end * options.resolution,
(end - start) * options.resolution,
total_obs,
total_mean,
delta,
total_obs / total_mean,
100.0 * (total_obs / total_mean - 1.0)))
# output best block
blocks.sort()
delta, start, end, total_obs, total_mean = blocks[-1]
outfile_auc.write("%s\t%i\t%i\t%i\t%f\t%f\t%f\t%f\t%f\n" %
(label,
start * options.resolution,
end * options.resolution,
(end - start) * options.resolution,
total_obs,
total_mean,
delta,
total_obs / total_mean,
100.0 * (total_obs / total_mean - 1.0)))
if outfile_proximity:
# find error bars at median
st = counter.mStats[label]
outfile_proximity.write("%s\t%i\t%f\t%i\t%i\t%i\t%s\t%i\t%i\n" %
(label,
st.observed *
options.resolution,
st.pvalue,
st.expected *
options.resolution,
st.ci95lower *
options.resolution,
st.ci95upper *
options.resolution,
IOTools.prettyFloat(st.qvalue),
segments_per_label[label],
workspaces_per_label[label],
))
if options.plot:
for counter in counters:
plotCounts(counter, options, transform)
# plot summary stats
plt.figure()
plt.title("distribution of workspace length")
data = []
for contig, segs in workspace.iteritems():
if len(segs) == 0:
continue
data.extend([x[1] - x[0] for x in segs])
vals, bins = numpy.histogram(
data, bins=numpy.arange(0, max(data), 100), new=True)
t = float(sum(vals))
plt.plot(bins[:-1], numpy.cumsum(vals) / t)
plt.gca().set_xscale('log')
plt.legend()
t = float(sum(vals))
plt.xlabel("size of workspace")
plt.ylabel("cumulative relative frequency")
if options.hardcopy:
plt.savefig(
os.path.expanduser(options.hardcopy % "workspace_size"))
plt.figure()
plt.title("segments per block")
vals, bins = numpy.histogram(segments_per_workspace, bins=numpy.arange(
0, max(segments_per_workspace), 1), new=True)
plt.plot(bins[:-1], vals)
plt.xlabel("segments per block")
plt.ylabel("absolute frequency")
if options.hardcopy:
plt.savefig(
os.path.expanduser(options.hardcopy % "segments_per_block"))
plt.figure()
plt.title("workspaces per label")
plt.barh(
range(0, len(labels)), [workspaces_per_label[x] for x in labels], height=0.5)
plt.yticks(range(0, len(labels)), labels)
plt.ylabel("workspaces per label")
plt.xlabel("absolute frequency")
plt.gca().set_xscale('log')
if options.hardcopy:
plt.savefig(
os.path.expanduser(options.hardcopy % "workspaces_per_label"))
plt.figure()
plt.title("segments per label")
plt.barh(range(0, len(labels)), [segments_per_label[x]
for x in labels], height=0.5)
plt.yticks(range(0, len(labels)), labels)
plt.ylabel("segments per label")
plt.xlabel("absolute frequency")
plt.xticks(range(0, len(labels)), labels)
if options.hardcopy:
plt.savefig(
os.path.expanduser(options.hardcopy % "segments_per_label"))
if not options.hardcopy:
plt.show()
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version=
"%prog version: $Id: gff2annotator2tsv.py 2861 2010-02-23 17:36:32Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-g",
"--genome-file",
dest="genome_file",
type="string",
help="filename with genome.")
parser.add_option("-f",
"--features",
dest="features",
type="string",
help="feature to collect [default=None].")
parser.add_option("-i",
"--files",
dest="files",
action="append",
help="use multiple annotations [default=None].")
parser.add_option(
"-a",
"--annotations",
dest="annotations",
type="string",
help=
"aggregate name for annotations if only single file is provided from STDIN [default=None]."
)
parser.add_option(
"--input-filename-map",
dest="input_filename_map",
type="string",
help="filename with a map of gene_ids to categories [default=None].")
parser.add_option(
"--output-filename-synonyms",
dest="output_filename_synonyms",
type="string",
help=
"output filename for synonyms. For workspace building, the gff source will be used as the id (instead of the contig) [default=None]."
)
parser.add_option("-m",
"--max-length",
dest="max_length",
type="string",
help="maximum segment length [default=None].")
parser.add_option("-s",
"--section",
dest="section",
type="choice",
choices=("segments", "annotations", "annotations-genes",
"annotations-go", "workspace",
"annotations-gff"),
help="annotator section [default=None].")
parser.add_option(
"--subset",
dest="subsets",
type="string",
action="append",
help=
"add filenames to delimit subsets within the gff files. The syntax is filename.gff,label,filename.ids [default=None]."
)
parser.add_option(
"--remove-regex",
dest="remove_regex",
type="string",
help="regular expression of contigs to remove [default=None].")
parser.set_defaults(
genome_file=None,
feature=None,
section="segments",
annotations="annotations",
max_length=100000,
files=[],
subsets=[],
input_filename_map=None,
output_filename_synonyms=None,
input_format="gff",
remove_regex=None,
)
(options, args) = E.Start(parser)
options.files += args
if len(options.files) == 0:
options.files.append("-")
options.files = list(
itertools.chain(*[re.split("[,; ]+", x) for x in options.files]))
if options.subsets:
subsets = collections.defaultdict(list)
for s in options.subsets:
filename_gff, label, filename_ids = s.split(",")
subsets[filename_gff].append((label, filename_ids))
options.subsets = subsets
if options.genome_file:
fasta = IndexedFasta.IndexedFasta(options.genome_file)
else:
fasta = None
if options.section == "segments":
prefix = "##Segs"
elif options.section.startswith("annotations"):
prefix = "##Id"
elif options.section == "workspace":
prefix = "##Work"
else:
raise ValueError("unknown section %s" % options.section)
ninput, ncontigs, nsegments, ndiscarded = 0, 0, 0, 0
if options.remove_regex:
options.remove_regex = re.compile(options.remove_regex)
if options.section in ("segments", "workspace"):
iterator = GTF.iterator_filtered(GFF.iterator(options.stdin),
feature=options.feature)
if options.output_filename_synonyms:
outfile_synonyms = open(options.output_filename_synonyms, "w")
with_records = True
else:
outfile_synonyms = None
with_records = False
intervals = GTF.readAsIntervals(iterator, with_records=with_records)
ninput, nsegments, ndiscarded, ncontigs = \
PipelineEnrichment.outputSegments(options.stdout,
intervals,
options.section,
outfile_synonyms=outfile_synonyms,
max_length=options.max_length,
remove_regex=options.remove_regex)
if outfile_synonyms:
outfile_synonyms.close()
elif options.section == "annotations-go":
assert options.input_filename_map, "please supply option --input-filename-map"
iterator = GTF.iterator_filtered(GTF.iterator(options.stdin),
feature=options.feature)
geneid2categories = IOTools.readMultiMap(
open(options.input_filename_map, "r"))
category2segments = collections.defaultdict(list)
for contig, gffs in GTF.readAsIntervals(iterator,
with_gene_id=True).items():
if options.remove_regex and options.remove_regex.search(contig):
continue
for start, end, geneid in gffs:
if geneid not in geneid2categories:
continue
for category in geneid2categories[geneid]:
category2segments[category].append(nsegments)
options.stdout.write("%s\t%i\t%s\t(%i,%i)\n" %
(prefix, nsegments, contig, start, end))
nsegments += 1
for category, segments in category2segments.iteritems():
options.stdout.write(
"##Ann\t%s\t%s\n" %
(category, "\t".join(["%i" % x for x in segments])))
E.info("set %s annotated with %i segments" %
(category, len(segments)))
elif options.section == "annotations":
for filename in options.files:
E.info("adding filename %s" % filename)
start = nsegments
is_gtf = False
if filename == "-":
iterator = GTF.iterator_filtered(GFF.iterator(sys.stdin),
feature=options.feature)
filename = options.annotations
elif filename.endswith(".gtf"):
is_gtf = True
with open(filename, "r") as infile:
iterator = GTF.iterator_filtered(GTF.iterator(infile),
feature=options.feature)
else:
with open(filename, "r") as infile:
iterator = GTF.iterator_filtered(GFF.iterator(infile),
feature=options.feature)
E.debug("processing %s" % (filename))
if not options.subsets or filename not in options.subsets:
for contig, gffs in GTF.readAsIntervals(iterator).items():
if options.remove_regex and options.remove_regex.search(
contig):
continue
for x in gffs:
options.stdout.write(
"%s\t%i\t%s\t(%i,%i)\n" %
(prefix, nsegments, contig, x[0], x[1]))
nsegments += 1
options.stdout.write("##Ann\t%s\t%s\n" % (filename, "\t".join(
["%i" % x for x in range(start, nsegments)])))
E.info("set %s annotated with %i segments" %
(filename, nsegments - start))
else:
raise ValueError("don't know how to filter %s" % filename)
elif options.section == "annotations-gff":
for filename in options.files:
if filename == "-":
iterator = GTF.iterator(sys.stdin)
else:
iterator = GTF.iterator_filtered(
GFF.iterator(open(filename, "r")))
segments = collections.defaultdict(list)
for gff in iterator:
segments[":".join((gff.source, gff.feature))].append(
(gff.contig, gff.start, gff.end))
feature2segments = {}
for feature, s in segments.iteritems():
s.sort()
s1 = nsegments
for contig, start, end in s:
if options.remove_regex and options.remove_regex.search(
contig):
continue
options.stdout.write(
"%s\t%i\t%s\t(%i,%i)\n" %
(prefix, nsegments, contig, start, end))
nsegments += 1
feature2segments[feature] = (s1, nsegments)
for feature, id_range in feature2segments.iteritems():
start, end = id_range
options.stdout.write(
"##Ann\t%s\t%s\n" %
(feature, "\t".join(["%i" % x for x in xrange(start, end)])))
E.info("set %s annotated with %i segments" %
(feature, end - start))
elif options.section == "annotations-genes":
for filename in options.files:
E.info("adding filename %s" % filename)
start = nsegments
assert filename.endswith(".gtf") or filename.endswith(".gtf.gz"), \
"requiring .gtf files for gene list filtering, received %s" % filename
infile = IOTools.openFile(filename)
iterator = GTF.iterator_filtered(GTF.iterator(infile),
feature=options.feature)
E.debug("processing %s" % (filename))
if not options.subsets or filename not in options.subsets:
# output all
for contig, gffs in GTF.readAsIntervals(iterator).items():
if options.remove_regex and options.remove_regex.search(
contig):
continue
for x in gffs:
options.stdout.write(
"%s\t%i\t%s\t(%i,%i)\n" %
(prefix, nsegments, contig, x[0], x[1]))
nsegments += 1
options.stdout.write("##Ann\t%s\t%s\n" % (filename, "\t".join(
["%i" % x for x in range(start, nsegments)])))
E.info("set %s annotated with %i segments" %
(filename, nsegments - start))
else:
# create subsets
E.debug("applying subsets for %s" % filename)
geneid2label, label2segments = collections.defaultdict(
list), {}
for label, filename_ids in options.subsets[filename]:
gene_ids = IOTools.readList(open(filename_ids, "r"))
for gene_id in gene_ids:
geneid2label[gene_id].append(label)
label2segments[label] = []
for contig, gffs in GTF.readAsIntervals(
iterator, with_gene_id=True).items():
if options.remove_regex and options.remove_regex.search(
contig):
continue
for start, end, gene_id in gffs:
if gene_id not in geneid2label:
continue
for label in geneid2label[gene_id]:
label2segments[label].append(nsegments)
options.stdout.write(
"%s\t%i\t%s\t(%i,%i)\n" %
(prefix, nsegments, contig, start, end))
nsegments += 1
for label, segments in label2segments.iteritems():
options.stdout.write(
"##Ann\t%s\t%s\n" %
(label, "\t".join(["%i" % x for x in segments])))
E.info("set %s (%s) annotated with %i segments" %
(label, filename, len(segments)))
E.info("ninput=%i, ncontigs=%i, nsegments=%i, ndiscarded=%i" %
(ninput, ncontigs, nsegments, ndiscarded))
E.Stop()
def main(argv=sys.argv):
parser = E.OptionParser(
version=
"%prog version: $Id: annotator_distance.py 2861 2010-02-23 17:36:32Z andreas $",
usage=globals()["__doc__"])
parser.add_option(
"-a",
"--annotations-tsv-file",
dest="filename_annotations",
type="string",
help=
"filename mapping gene ids to annotations (a tab-separated table with two-columns) [default=%default]."
)
parser.add_option("-r",
"--resolution",
dest="resolution",
type="int",
help="resolution of count vector [default=%default].")
parser.add_option(
"-b",
"--num-bins",
dest="num_bins",
type="int",
help="number of bins in count vector [default=%default].")
parser.add_option("-i",
"--num-samples",
dest="num_samples",
type="int",
help="sample size to compute [default=%default].")
parser.add_option(
"-w",
"--workspace-bed-file",
dest="filename_workspace",
type="string",
help="filename with workspace information [default=%default].")
parser.add_option(
"--workspace-builder",
dest="workspace_builder",
type="choice",
choices=("gff", "gtf-intergenic", "gtf-intronic", "gtf-genic"),
help="given a gff/gtf file build a workspace [default=%default].")
parser.add_option(
"--workspace-labels",
dest="workspace_labels",
type="choice",
choices=("none", "direction", "annotation"),
help="labels to use for the workspace workspace [default=%default].")
parser.add_option(
"--sampler",
dest="sampler",
type="choice",
choices=("permutation", "gaps"),
help=
"sampler to use. The sampler determines the null model of how segments are distributed in the workspace [default=%default]"
)
parser.add_option(
"--counter",
dest="counters",
type="choice",
action="append",
choices=("transcription", "closest-distance", "all-distances"),
help=
"counter to use. The counter computes the quantity of interest [default=%default]"
)
parser.add_option("--analysis",
dest="analysis",
type="choice",
action="append",
choices=("proximity", "area-under-curve"),
help="analysis to perform [default=%default]")
parser.add_option("--transform-counts",
dest="transform_counts",
type="choice",
choices=("raw", "cumulative"),
help="cumulate counts [default=%default].")
parser.add_option(
"-s",
"--segments",
dest="filename_segments",
type="string",
help="filename with segment information [default=%default].")
parser.add_option("--xrange",
dest="xrange",
type="string",
help="xrange to plot [default=%default]")
parser.add_option("-o",
"--logscale",
dest="logscale",
type="string",
help="use logscale on x, y or xy [default=%default]")
parser.add_option("-p",
"--plot",
dest="plot",
action="store_true",
help="output plots [default=%default]")
parser.add_option("--hardcopy",
dest="hardcopy",
type="string",
help="output hardcopies to file [default=%default]")
parser.add_option("--no-fdr",
dest="do_fdr",
action="store_false",
help="do not compute FDR rates [default=%default]")
parser.add_option("--segments-format",
dest="segments_format",
type="choice",
choices=("gtf", "bed"),
help="format of segments file [default=%default].")
parser.add_option(
"--truncate",
dest="truncate",
action="store_true",
help="truncate segments extending beyond a workspace [default=%default]"
)
parser.add_option(
"--remove-overhangs",
dest="remove_overhangs",
action="store_true",
help="remove segments extending beyond a workspace[default=%default]")
parser.add_option(
"--keep-ambiguous",
dest="keep_ambiguous",
action="store_true",
help=
"keep segments extending to more than one workspace [default=%default]"
)
parser.set_defaults(
filename_annotations=None,
filename_workspace="workspace.gff",
filename_segments="FastDown.gtf",
filename_annotations_gtf="../data/tg1_territories.gff",
workspace_builder="gff",
workspace_labels="none",
sampler="permutation",
truncate=False,
num_bins=10000,
num_samples=10,
resolution=100,
plot_samples=False,
plot_envelope=True,
counters=[],
transform_counts="raw",
xrange=None,
plot=False,
logscale=None,
output_all=False,
do_test=False,
analysis=[],
do_fdr=True,
hardcopy="%s.png",
segments_format="gtf",
remove_overhangs=False,
)
(options, args) = E.Start(parser, argv=argv, add_output_options=True)
###########################################
# setup options
if options.sampler == "permutation":
sampler = SamplerPermutation
elif options.sampler == "gaps":
sampler = SamplerGaps
if options.xrange:
options.xrange = map(float, options.xrange.split(","))
if len(options.counters) == 0:
raise ValueError("please specify at least one counter.")
if len(options.analysis) == 0:
raise ValueError("please specify at least one analysis.")
if options.workspace_labels == "annotation" and not options.filename_annotations:
raise ValueError(
"please specify --annotations-tsv-file is --workspace-labels=annotations."
)
###########################################
# read data
if options.workspace_labels == "annotation":
def constant_factory(value):
return itertools.repeat(value).next
def dicttype():
return collections.defaultdict(constant_factory(("unknown", )))
map_id2annotations = IOTools.readMultiMap(open(
options.filename_annotations, "r"),
dtype=dicttype)
else:
map_id2annotations = {}
workspace = readWorkspace(open(options.filename_workspace,
"r"), options.workspace_builder,
options.workspace_labels, map_id2annotations)
E.info("read workspace for %i contigs" % (len(workspace)))
indexed_workspace = indexIntervals(workspace, with_values=True)
segments = readSegments(open(options.filename_segments, "r"),
indexed_workspace,
format=options.segments_format,
keep_ambiguous=options.keep_ambiguous,
truncate=options.truncate,
remove_overhangs=options.remove_overhangs)
nsegments = 0
for contig, vv in segments.iteritems():
nsegments += len(vv)
E.info("read %i segments for %i contigs" % (nsegments, len(workspace)))
indexed_segments = indexIntervals(segments, with_values=False)
if nsegments == 0:
E.warn("no segments read - no computation done.")
E.Stop()
return
# build labels
labels = collections.defaultdict(int)
for contig, vv in workspace.iteritems():
for start, end, v in vv:
for l in v[0]:
labels[l] += 1
for l in v[1]:
labels[l] += 1
E.info("found %i workspace labels" % len(labels))
###########################################
# setup counting containers
counters = []
for cc in options.counters:
if cc == "transcription":
counter = CounterTranscription
elif cc == "closest-distance":
counter = CounterClosestDistance
elif cc == "all-distances":
counter = CounterAllDistances
if nsegments < 256:
dtype = numpy.uint8
elif nsegments < 65536:
dtype = numpy.uint16
elif nsegments < 4294967296:
dtype = numpy.uint32
else:
dtype = numpy.int
E.debug("choosen dtype %s" % str(dtype))
E.info("samples space is %i bases: %i bins at %i resolution" % (
options.num_bins * options.resolution,
options.num_bins,
options.resolution,
))
E.info("allocating counts: %i bytes (%i labels, %i samples, %i bins)" %
(
options.num_bins * len(labels) * dtype().itemsize *
(options.num_samples + 1),
len(labels),
options.num_samples,
options.num_bins,
))
c = CountingResults(labels)
c.mObservedCounts = counter(labels,
options.num_bins,
options.resolution,
dtype=dtype)
simulated_counts = []
for x in range(options.num_samples):
simulated_counts.append(
counter(labels,
options.num_bins,
options.resolution,
dtype=dtype))
c.mSimulatedCounts = simulated_counts
c.mName = c.mObservedCounts.mName
counters.append(c)
E.info("allocated memory successfully")
segments_per_workspace = []
segment_sizes = []
segments_per_label = collections.defaultdict(int)
workspaces_per_label = collections.defaultdict(int)
############################################
# get observed and simpulated counts
nworkspaces, nempty_workspaces, nempty_contigs, nmiddle = 0, 0, 0, 0
iteration2 = 0
for contig, vv in workspace.iteritems():
iteration2 += 1
E.info("counting %i/%i: %s %i segments" %
(iteration2, len(workspace), contig, len(vv)))
if len(vv) == 0:
continue
iteration1 = 0
for work_start, work_end, v in vv:
left_labels, right_labels = v[0], v[1]
iteration1 += 1
# ignore empty segments
if contig not in indexed_segments:
nempty_contigs += 1
continue
r = indexed_segments[contig].find(work_start, work_end)
segments_per_workspace.append(len(r))
if not r:
nempty_workspaces += 1
continue
# collect segments and stats
nworkspaces += 1
observed = [(x.start, x.end) for x in r]
observed.sort()
segments_per_workspace.append(len(observed))
segment_sizes.extend([x[1] - x[0] for x in observed])
# collect basic counts
for label in list(left_labels) + list(right_labels):
workspaces_per_label[label] += 1
segments_per_label[label] += len(observed)
# add observed counts
for counter in counters:
counter.mObservedCounts.addCounts(observed, work_start,
work_end, left_labels,
right_labels)
# create sampler
s = sampler(observed, work_start, work_end)
# add simulated counts
for iteration in range(options.num_samples):
simulated = s.sample()
for counter in counters:
counter.mSimulatedCounts[iteration].addCounts(
simulated, work_start, work_end, left_labels,
right_labels)
E.info("counting finished")
E.info(
"nworkspaces=%i, nmiddle=%i, nempty_workspaces=%i, nempty_contigs=%i" %
(nworkspaces, nmiddle, nempty_workspaces, nempty_contigs))
######################################################
# transform counts
if options.transform_counts == "cumulative":
transform = cumulative_transform
elif options.transform_counts == "raw":
transform = normalize_transform
####################################################
# analysis
if "proximity" in options.analysis:
outfile_proximity = E.openOutputFile("proximity")
outfile_proximity.write("\t".join(
("label", "observed", "pvalue", "expected", "CIlower", "CIupper",
"qvalue", "segments", "workspaces")) + "\n")
else:
outfile_proximity = None
if "area-under-curve" in options.analysis:
outfile_auc = E.openOutputFile("auc")
outfile_auc.write("label\tobserved\texpected\tCIlower\tCIupper\n")
else:
outfile_auc = None
# qvalue: expected false positives at p-value
# qvalue = expected false positives /
if options.do_fdr:
E.info("computing pvalues for fdr")
for counter in counters:
for label in labels:
E.info("working on counter:%s label:%s" % (counter, label))
# collect all P-Values of simulated results to compute FDR
sim_pvalues = []
medians = counter.getMedians(label)
for median in medians:
pvalue = float(
scipy.stats.percentileofscore(medians, median)) / 100.0
sim_pvalues.append(pvalue)
sim_pvalues.sort()
else:
sim_pvalues = []
# compute observed p-values
for counter in counters:
counter.update()
obs_pvalues = []
for counter in counters:
for label in labels:
obs_pvalues.append(counter.mStats[label].pvalue)
obs_pvalues.sort()
# compute observed p-values
if options.do_fdr:
for counter in counters:
counter.updateFDR(obs_pvalues, sim_pvalues)
for counter in counters:
outofbounds_sim, totals_sim = 0, 0
outofbounds_obs, totals_obs = 0, 0
for label in labels:
for sample in range(options.num_samples):
if counter.mSimulatedCounts[sample].mOutOfBounds[label]:
E.debug(
"out of bounds: sample %i, label %s, counts=%i" %
(sample, label,
counter.mSimulatedCounts[sample].mOutOfBounds[label]))
outofbounds_sim += counter.mSimulatedCounts[
sample].mOutOfBounds[label]
totals_sim += counter.mSimulatedCounts[sample].mTotals[label]
outofbounds_obs += counter.mObservedCounts.mOutOfBounds[label]
totals_obs += counter.mObservedCounts.mTotals[label]
E.info(
"out of bounds observations: observed=%i/%i (%5.2f%%), simulations=%i/%i (%5.2f%%)"
% (
outofbounds_obs,
totals_obs,
100.0 * outofbounds_obs / totals_obs,
outofbounds_sim,
totals_sim,
100.0 * outofbounds_sim / totals_sim,
))
for label in labels:
if outfile_auc:
mmin, mmax, mmean = counter.getEnvelope(
label, transform=normalize_transform)
obs = normalize_transform(
counter.mObservedCounts[label],
counter.mObservedCounts.mOutOfBounds[label])
def block_iterator(a1, a2, a3, num_bins):
x = 0
while x < num_bins:
while x < num_bins and a1[x] <= a2[x]:
x += 1
start = x
while x < options.num_bins and a1[x] > a2[x]:
x += 1
end = x
total_a1 = a1[start:end].sum()
total_a3 = a3[start:end].sum()
if total_a1 > total_a3:
yield (total_a1 - total_a3, start, end, total_a1,
total_a3)
blocks = list(
block_iterator(obs, mmax, mmean, options.num_bins))
if options.output_all:
for delta, start, end, total_obs, total_mean in blocks:
if end - start <= 1:
continue
outfile_auc.write(
"%s\t%i\t%i\t%i\t%f\t%f\t%f\t%f\t%f\n" %
(label, start * options.resolution,
end * options.resolution,
(end - start) * options.resolution, total_obs,
total_mean, delta, total_obs / total_mean, 100.0 *
(total_obs / total_mean - 1.0)))
# output best block
blocks.sort()
delta, start, end, total_obs, total_mean = blocks[-1]
outfile_auc.write(
"%s\t%i\t%i\t%i\t%f\t%f\t%f\t%f\t%f\n" %
(label, start * options.resolution,
end * options.resolution,
(end - start) * options.resolution, total_obs, total_mean,
delta, total_obs / total_mean, 100.0 *
(total_obs / total_mean - 1.0)))
if outfile_proximity:
# find error bars at median
st = counter.mStats[label]
outfile_proximity.write(
"%s\t%i\t%f\t%i\t%i\t%i\t%s\t%i\t%i\n" % (
label,
st.observed * options.resolution,
st.pvalue,
st.expected * options.resolution,
st.ci95lower * options.resolution,
st.ci95upper * options.resolution,
IOTools.val2str(st.qvalue),
segments_per_label[label],
workspaces_per_label[label],
))
if options.plot:
for counter in counters:
plotCounts(counter, options, transform)
# plot summary stats
plt.figure()
plt.title("distribution of workspace length")
data = []
for contig, segs in workspace.iteritems():
if len(segs) == 0:
continue
data.extend([x[1] - x[0] for x in segs])
vals, bins = numpy.histogram(data,
bins=numpy.arange(0, max(data), 100),
new=True)
t = float(sum(vals))
plt.plot(bins[:-1], numpy.cumsum(vals) / t)
plt.gca().set_xscale('log')
plt.legend()
t = float(sum(vals))
plt.xlabel("size of workspace")
plt.ylabel("cumulative relative frequency")
if options.hardcopy:
plt.savefig(os.path.expanduser(options.hardcopy %
"workspace_size"))
plt.figure()
plt.title("segments per block")
vals, bins = numpy.histogram(segments_per_workspace,
bins=numpy.arange(
0, max(segments_per_workspace), 1),
new=True)
plt.plot(bins[:-1], vals)
plt.xlabel("segments per block")
plt.ylabel("absolute frequency")
if options.hardcopy:
plt.savefig(
os.path.expanduser(options.hardcopy % "segments_per_block"))
plt.figure()
plt.title("workspaces per label")
plt.barh(range(0, len(labels)),
[workspaces_per_label[x] for x in labels],
height=0.5)
plt.yticks(range(0, len(labels)), labels)
plt.ylabel("workspaces per label")
plt.xlabel("absolute frequency")
plt.gca().set_xscale('log')
if options.hardcopy:
plt.savefig(
os.path.expanduser(options.hardcopy % "workspaces_per_label"))
plt.figure()
plt.title("segments per label")
plt.barh(range(0, len(labels)),
[segments_per_label[x] for x in labels],
height=0.5)
plt.yticks(range(0, len(labels)), labels)
plt.ylabel("segments per label")
plt.xlabel("absolute frequency")
plt.xticks(range(0, len(labels)), labels)
if options.hardcopy:
plt.savefig(
os.path.expanduser(options.hardcopy % "segments_per_label"))
if not options.hardcopy:
plt.show()
E.Stop()
def main( argv = None ):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
parser = E.OptionParser( version = "%prog version: $Id: gff2annotator2tsv.py 2861 2010-02-23 17:36:32Z andreas $", usage = globals()["__doc__"])
parser.add_option( "-g", "--genome-file", dest="genome_file", type="string",
help="filename with genome." )
parser.add_option( "-f", "--features", dest="features", type="string",
help="feature to collect [default=None]." )
parser.add_option( "-i", "--files", dest="files", action="append",
help="use multiple annotations [default=None]." )
parser.add_option( "-a", "--annotations", dest="annotations", type="string",
help="aggregate name for annotations if only single file is provided from STDIN [default=None]." )
parser.add_option( "--input-filename-map", dest="input_filename_map", type="string",
help="filename with a map of gene_ids to categories [default=None]." )
parser.add_option( "--output-filename-synonyms", dest="output_filename_synonyms", type="string",
help="output filename for synonyms. For workspace building, the gff source will be used as the id (instead of the contig) [default=None]." )
parser.add_option( "-m", "--max-length", dest="max_length", type="string",
help="maximum segment length [default=None]." )
parser.add_option( "-s", "--section", dest="section", type="choice",
choices=("segments", "annotations", "annotations-genes", "annotations-go", "workspace", "annotations-gff" ),
help="annotator section [default=None]." )
parser.add_option( "--subset", dest="subsets", type="string", action="append",
help="add filenames to delimit subsets within the gff files. The syntax is filename.gff,label,filename.ids [default=None]." )
parser.add_option( "--remove-regex", dest="remove_regex", type="string",
help="regular expression of contigs to remove [default=None]." )
parser.set_defaults(
genome_file = None,
feature = None,
section = "segments",
annotations = "annotations",
max_length = 100000,
files = [],
subsets = [],
input_filename_map = None,
output_filename_synonyms = None,
input_format = "gff",
remove_regex = None,
)
(options, args) = E.Start( parser )
options.files += args
if len(options.files) == 0: options.files.append("-")
options.files = list( itertools.chain( *[ re.split( "[,; ]+", x) for x in options.files ] ) )
if options.subsets:
subsets = collections.defaultdict( list )
for s in options.subsets:
filename_gff,label,filename_ids = s.split( "," )
subsets[filename_gff].append( (label,filename_ids) )
options.subsets = subsets
if options.genome_file:
fasta = IndexedFasta.IndexedFasta( options.genome_file )
else:
fasta = None
if options.section == "segments":
prefix = "##Segs"
elif options.section.startswith( "annotations" ):
prefix = "##Id"
elif options.section == "workspace":
prefix = "##Work"
else:
raise ValueError("unknown section %s" % options.section)
ninput, ncontigs, nsegments, ndiscarded = 0, 0, 0, 0
if options.remove_regex:
options.remove_regex = re.compile( options.remove_regex )
if options.section in ("segments", "workspace"):
iterator = GTF.iterator_filtered( GFF.iterator( options.stdin ),
feature=options.feature )
if options.output_filename_synonyms:
outfile_synonyms = open(options.output_filename_synonyms, "w")
with_records = True
else:
outfile_synonyms = None
with_records = False
intervals =GTF.readAsIntervals( iterator, with_records = with_records )
ninput, nsegments, ndiscarded, ncontigs = \
PipelineEnrichment.outputSegments( options.stdout,
intervals,
options.section,
outfile_synonyms = outfile_synonyms,
max_length = options.max_length,
remove_regex = options.remove_regex )
if outfile_synonyms:
outfile_synonyms.close()
elif options.section == "annotations-go":
assert options.input_filename_map, "please supply option --input-filename-map"
iterator = GTF.iterator_filtered( GTF.iterator( options.stdin ),
feature=options.feature )
geneid2categories = IOTools.readMultiMap( open( options.input_filename_map, "r") )
category2segments = collections.defaultdict( list )
for contig, gffs in GTF.readAsIntervals( iterator, with_gene_id = True ).items():
if options.remove_regex and options.remove_regex.search( contig ): continue
for start, end, geneid in gffs:
if geneid not in geneid2categories: continue
for category in geneid2categories[geneid]:
category2segments[category].append(nsegments)
options.stdout.write( "%s\t%i\t%s\t(%i,%i)\n" % (prefix, nsegments, contig, start, end ) )
nsegments += 1
for category, segments in category2segments.iteritems():
options.stdout.write("##Ann\t%s\t%s\n" % (category, "\t".join( ["%i" % x for x in segments ] ) ) )
E.info( "set %s annotated with %i segments" % (category, len(segments)) )
elif options.section == "annotations":
for filename in options.files:
E.info( "adding filename %s" % filename )
start = nsegments
is_gtf = False
if filename == "-":
iterator = GTF.iterator_filtered( GFF.iterator( sys.stdin ),
feature=options.feature )
filename = options.annotations
elif filename.endswith(".gtf"):
is_gtf = True
with open( filename, "r") as infile:
iterator = GTF.iterator_filtered( GTF.iterator( infile ),
feature=options.feature )
else:
with open( filename, "r") as infile:
iterator = GTF.iterator_filtered( GFF.iterator( infile ),
feature=options.feature )
E.debug("processing %s" % (filename))
if not options.subsets or filename not in options.subsets:
for contig, gffs in GTF.readAsIntervals( iterator ).items():
if options.remove_regex and options.remove_regex.search( contig ): continue
for x in gffs:
options.stdout.write( "%s\t%i\t%s\t(%i,%i)\n" % (prefix, nsegments, contig, x[0], x[1] ) )
nsegments += 1
options.stdout.write("##Ann\t%s\t%s\n" % (filename, "\t".join( ["%i" % x for x in range(start, nsegments) ] ) ) )
E.info( "set %s annotated with %i segments" % (filename, nsegments - start) )
else:
raise ValueError("don't know how to filter %s" % filename )
elif options.section == "annotations-gff":
for filename in options.files:
if filename == "-":
iterator = GTF.iterator( sys.stdin )
else:
iterator = GTF.iterator_filtered( GFF.iterator( open( filename, "r") ) )
segments = collections.defaultdict( list )
for gff in iterator:
segments[":".join((gff.source,gff.feature))].append( (gff.contig,gff.start, gff.end) )
feature2segments = {}
for feature, s in segments.iteritems():
s.sort()
s1 = nsegments
for contig, start, end in s:
if options.remove_regex and options.remove_regex.search( contig ): continue
options.stdout.write( "%s\t%i\t%s\t(%i,%i)\n" % (prefix, nsegments, contig, start, end ) )
nsegments += 1
feature2segments[feature] = (s1, nsegments)
for feature, id_range in feature2segments.iteritems():
start, end = id_range
options.stdout.write("##Ann\t%s\t%s\n" % (feature, "\t".join( ["%i" % x for x in xrange( start,end) ] ) ) )
E.info( "set %s annotated with %i segments" % (feature, end-start) )
elif options.section == "annotations-genes":
for filename in options.files:
E.info( "adding filename %s" % filename )
start = nsegments
assert filename.endswith(".gtf") or filename.endswith(".gtf.gz"), \
"requiring .gtf files for gene list filtering, received %s" % filename
infile = IOTools.openFile( filename )
iterator = GTF.iterator_filtered( GTF.iterator( infile ),
feature=options.feature )
E.debug("processing %s" % (filename))
if not options.subsets or filename not in options.subsets:
## output all
for contig, gffs in GTF.readAsIntervals( iterator ).items():
if options.remove_regex and options.remove_regex.search( contig ): continue
for x in gffs:
options.stdout.write( "%s\t%i\t%s\t(%i,%i)\n" % (prefix, nsegments, contig, x[0],x[1] ) )
nsegments += 1
options.stdout.write("##Ann\t%s\t%s\n" % (filename, "\t".join( ["%i" % x for x in range(start, nsegments) ] ) ) )
E.info( "set %s annotated with %i segments" % (filename, nsegments - start) )
else:
## create subsets
E.debug("applying subsets for %s" % filename )
geneid2label, label2segments = collections.defaultdict(list) , {}
for label, filename_ids in options.subsets[filename]:
gene_ids = IOTools.readList( open(filename_ids, "r") )
for gene_id in gene_ids: geneid2label[gene_id].append( label )
label2segments[label] = []
for contig, gffs in GTF.readAsIntervals( iterator, with_gene_id = True ).items():
if options.remove_regex and options.remove_regex.search( contig ): continue
for start, end, gene_id in gffs:
if gene_id not in geneid2label: continue
for label in geneid2label[gene_id]:
label2segments[label].append(nsegments)
options.stdout.write( "%s\t%i\t%s\t(%i,%i)\n" % (prefix, nsegments, contig, start, end ) )
nsegments += 1
for label, segments in label2segments.iteritems():
options.stdout.write("##Ann\t%s\t%s\n" % (label, "\t".join( ["%i" % x for x in segments ] ) ) )
E.info( "set %s (%s) annotated with %i segments" % (label, filename, len(segments)) )
E.info( "ninput=%i, ncontigs=%i, nsegments=%i, ndiscarded=%i" % (ninput, ncontigs, nsegments, ndiscarded))
E.Stop()
