Mercurial > repos > greg > genetrack
changeset 0:0368815ae4d5 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 17 Nov 2015 14:19:45 -0500 |
| parents | |
| children | 31cc73d7c234 |
| files | genetrack.py genetrack.xml genetrack_macros.xml genetrack_util.py test-data/genetrack_input1.gff test-data/genetrack_input2.gff test-data/genetrack_input3.ssccidx test-data/genetrack_input_unsorted4.gff test-data/genetrack_output2.gff test-data/genetrack_output3.gff test-data/genetrack_output4.gff tool_dependencies.xml |
| diffstat | 12 files changed, 1229 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genetrack.py Tue Nov 17 14:19:45 2015 -0500 @@ -0,0 +1,70 @@ +""" +genetrack.py + +Input: either ssccidx or gff format of reads +.ssccidx format: tab-separated chromosome (chr##), index, + reads, - reads +.gff format: standard gff, score interpreted as number of reads + +Output: Called peaks in either gff or txt format +.txt format: tab-separated chromosome, strand, start, end, read count +.gff format: standard gff, score is read count +""" +import argparse +import csv +import os +import genetrack_util + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('--input_format', dest='input_format', help='Input format.') + parser.add_argument('--input', dest='inputs', action='append', nargs=2, help="Input datasets") + parser.add_argument('--sigma', dest='sigma', type=int, default=5, help='Sigma.') + parser.add_argument('--exclusion', dest='exclusion', type=int, default=20, help='Exclusion zone.') + parser.add_argument('--up_width', dest='up_width', type=int, default=10, help='Upstream width of called peaks.') + parser.add_argument('--down_width', dest='down_width', type=int, default=10, help='Downstream width of called peaks.') + parser.add_argument('--filter', dest='filter', type=int, default=3, help='Absolute read filter.') + parser.add_argument('--chunk_size', dest='chunk_size', type=int, default=10, help='Size, in millions of base pairs.') + args = parser.parse_args() + + os.mkdir('output') + for (dataset_path, hid) in args.inputs: + if args.input_format == 'gff': + # Make sure the reads for each chromosome are sorted by index. + input_path = genetrack_util.sort_chromosome_reads_by_index(dataset_path) + else: + # We're processing ssccidx data. + input_path = dataset_path + output_name = 's%se%su%sd%sF%s_on_data_%s' % (str(args.sigma), + str(args.exclusion), + str(args.up_width), + str(args.down_width), + str(args.filter), + str(hid)) + output_path = os.path.join('output', output_name) + reader = csv.reader(open(input_path, 'rU'), delimiter='\t') + writer = csv.writer(open(output_path, 'wt'), delimiter='\t') + chunk_size = args.chunk_size * 10 ** 6 + width = args.sigma * 5 + manager = genetrack_util.ChromosomeManager(reader) + while not manager.done: + cname = manager.chromosome_name() + # Should we process this chromosome? + data = manager.load_chromosome() + if not data: + continue + keys = genetrack_util.make_keys(data) + lo, hi = genetrack_util.get_range(data) + for chunk in genetrack_util.get_chunks(lo, hi, size=chunk_size, overlap=width): + (slice_start, slice_end), process_bounds = chunk + window = genetrack_util.get_window(data, slice_start, slice_end, keys) + genetrack_util.process_chromosome(cname, + window, + writer, + process_bounds, + args.width, + args.sigma, + args.up_width, + args.down_width, + args.exclusion, + args.filter)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genetrack.xml Tue Nov 17 14:19:45 2015 -0500 @@ -0,0 +1,111 @@ +<?xml version="1.0"?> +<tool id="genetrack" name="Genetrack" version="@WRAPPER_VERSION@.0"> + <description>peak predictor</description> + <macros> + <import>genetrack_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> + python $__tool_directory__/genetrack.py + --input_format $input_format_cond.input_format + #if str($input_format_cond.input_format) == "ssccidx": + #for $i in $input_format_cond.input_ssccidx: + --input "${i}" "${i.hid}" + #end for + #elif str($input_format_cond.input_format) == "gff": + #for $i in $input_format_cond.input_gff: + --input "${i}" "${i.hid}" + #end for + #end if + --sigma $sigma + --exclusion $exclusion + --up_width $up_width + --down_width $down_width + --filter $filter + --chunk_size $chunk_size + </command> + <inputs> + <conditional name="input_format_cond"> + <param name="input_format" type="select" label="Format of files for conversion"> + <option value="ssccidx">Genetracktool</option> + <option value="gff" selected="True">Gff</option> + </param> + <when value="ssccidx"> + <param name="input_ssccidx" type="data" format="ssccidx" multiple="True" label="Predict peaks on" /> + </when> + <when value="gff"> + <param name="input_gff" type="data" format="gff" multiple="True" label="Predict peaks on" /> + </when> + </conditional> + <param name="sigma" type="integer" value="5" min="1" label="Sigma to use when smoothing reads" help="Higher values increase computation but produce more smoothing." /> + <param name="exclusion" type="integer" value="20" min="1" label="Peak exclusion zone" help="Exclusion zone around each peak that prevents others from being called." /> + <param name="up_width" type="integer" value="10" min="0" label="Upstream width of called peaks" /> + <param name="down_width" type="integer" value="10" min="0" label="Downstream width of called peaks" /> + <param name="filter" type="integer" value="3" min="0" label="Absolute read filter" help="Removes peaks with lower peak height." /> + <param name="chunk_size" type="integer" value="10" min="1" label="Chunk each chromosome into" help="Value is millions of base pairs where each size increment uses about 20MB of memory." /> + </inputs> + <outputs> + <collection name="genetrack_output" type="list" label="Genetrack results on ${on_string}"> + <discover_datasets pattern="(?P<designation>.*)" directory="output" ext="gff" visible="false" /> + </collection> + </outputs> + <tests> + <test> + <param name="input_gff" value="genetrack_input2.gff" ftype="gff" /> + <param name="input_format" value="gff" /> + <param name="sigma" value="5" /> + <param name="exclusion" value="20" /> + <param name="up_width" value="10" /> + <param name="down_width" value="10" /> + <param name="filter" value="3" /> + <param name="chunk_size" value="10" /> + <output_collection name="genetrack_output" type="list"> + <element name="s5e20u10d10F3_on_data_1" file="genetrack_output2.gff" ftype="gff" /> + </output_collection> + </test> + <test> + <param name="input_ssccidx" value="genetrack_input3.ssccidx" ftype="ssccidx" /> + <param name="input_format" value="ssccidx" /> + <param name="sigma" value="5" /> + <param name="exclusion" value="20" /> + <param name="up_width" value="10" /> + <param name="down_width" value="10" /> + <param name="filter" value="3" /> + <param name="chunk_size" value="10" /> + <output_collection name="genetrack_output" type="list"> + <element name="s5e20u10d10F3_on_data_1" file="genetrack_output3.gff" ftype="gff" /> + </output_collection> + </test> + <test> + <param name="input_gff" value="genetrack_input_unsorted4.gff" ftype="gff" /> + <param name="input_format" value="gff" /> + <param name="sigma" value="5" /> + <param name="exclusion" value="20" /> + <param name="up_width" value="10" /> + <param name="down_width" value="10" /> + <param name="filter" value="3" /> + <param name="chunk_size" value="10" /> + <output_collection name="genetrack_output" type="list"> + <element name="s5e20u10d10F3_on_data_1" file="genetrack_output4.gff" ftype="gff" /> + </output_collection> + </test> + </tests> + <help> +**What it does** + +Genetrack takes a standard set of data on both the sense and antisense strands and smooths their relative reads. +It then calls the peaks present in the smoothed dataset and uses those peak locations to calculate the final +reads from surrounding reads. Finally, it ensures each peak is above a threshold and that two peaks are not +too close to each other. + +**Options** + +* **Sigma to use when smoothing reads** - Sigma to use when smoothing reads to call peaks. +* **Peak exclusion zone** - Exclusion zone around each peak that prevents others from being called. +* **Upstream width of called peaks** - Upstream width of called peaks. +* **Downstream width of called peaks** - Downstream width of called peaks. +* **Filter** - Absolute read filter. Restricts output to only peaks with larger peak height. +* **Chunk each chromosome into** - Size, in millions of base pairs, to chunk each chromosome when processing. Each 1 million size uses approximately 20MB of memory. + </help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genetrack_macros.xml Tue Nov 17 14:19:45 2015 -0500 @@ -0,0 +1,22 @@ +<?xml version='1.0' encoding='UTF-8'?> +<macros> + <token name="@WRAPPER_VERSION@">1.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.9">numpy</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + <regex match="Error:"/> + <regex match="Exception:"/> + </stdio> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btn119</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genetrack_util.py Tue Nov 17 14:19:45 2015 -0500 @@ -0,0 +1,434 @@ +import bisect +import math +import numpy +import re +import subprocess +import sys +import tempfile + +ROMAN = ['0', 'I', 'II', 'III', 'IV', 'V', 'VI', 'VII', 'VIII', 'IX', 'X', + 'XI', 'XII', 'XIII', 'XIV', 'XV', 'XVI', 'XVII', 'XVIII', 'XIX', 'XX', + 'XXI', 'XXII', 'XXIII', 'XXIV', 'XXV', 'XXVI', 'XXVII', 'XXVIII', 'XXIX', + 'XXX'] + + +def noop(data): + return data + + +def zeropad_to_numeric(data): + return re.sub(r'chr0(\d)', r'chr\1', data) + + +def numeric_to_zeropad(data): + return re.sub(r'chr(\d([^\d]|$))', r'chr0\1', data) + + +def roman_to_numeric(data): + def convert(match): + """ + Converts a single roman numeral to a number + """ + numeral = match.group(1) + numeral = numeral.upper() + if numeral not in ROMAN: + # Unable to convert detected Roman numeral + return match.group(0) + return 'chr'+str(ROMAN.index(numeral))+(match.group(2) or '') + r = re.compile('chr([IVX]+)([^IVX]|$)', flags=re.IGNORECASE) + data = r.sub(convert, data) + return data + + +def numeric_to_roman(data): + def convert(match): + """ + Converts a number to a roman numeral + """ + number = int(match.group(1)) + if number >= len(ROMAN): + # Number is out of range to convert to a Roman numeral + return match.group(0) + return 'chr'+ROMAN[number]+(match.group(2) or '') + r = re.compile('chr(\d+)([^\d]|$)') + data = r.sub(convert, data) + return data + +FORMATS = ['zeropad', 'numeric', 'roman'] +IN_CONVERT = {'zeropad': zeropad_to_numeric, 'roman': roman_to_numeric, 'numeric': noop} +OUT_CONVERT = {'zeropad': numeric_to_zeropad, 'roman': numeric_to_roman, 'numeric': noop} + + +def conversion_functions(in_fmt, out_fmt): + """ + Returns the proper list of functions to apply to perform a conversion + """ + return [IN_CONVERT[in_fmt], OUT_CONVERT[out_fmt]] + + +def autodetect_format(data): + if re.search('chr0\d', data): + fmt = 'zeropad' + elif re.search('chr[IVXivx]', data): + fmt = 'roman' + else: + fmt = 'numeric' + return fmt + + +def convert_data(data, in_fmt, out_fmt): + if in_fmt == 'autodetect': + in_fmt = autodetect_format(data) + for fn in conversion_functions(in_fmt, out_fmt): + data = fn(data) + return data + + +class ChromosomeManager(object): + """ + Manages a CSV reader of an index file to only load one chrom at a time + """ + + def __init__(self, reader): + self.done = False + self.reader = reader + self.processed_chromosomes = [] + self.current_index = 0 + self.next_valid() + + def next(self): + self.line = self.reader.next() + + def is_valid(self, line): + if len(line) not in [4, 5, 9]: + return False + try: + [int(i) for i in line[1:]] + self.format = 'ssccidx' + return True + except ValueError: + try: + if len(line) < 6: + return False + [int(line[4]), int(line[5])] + self.format = 'gff' + return True + except ValueError: + return False + + def next_valid(self): + """ + Advance to the next valid line in the reader + """ + self.line = self.reader.next() + s = 0 + while not self.is_valid(self.line): + self.line = self.reader.next() + s += 1 + if s > 0: + # Skip initial line(s) of file + pass + + def parse_line(self, line): + if self.format == 'ssccidx': + return [int(line[1]), int(line[2]), int(line[3])] + else: + return [int(line[3]), line[6], line[5]] + + def chromosome_name(self): + """ + Return the name of the chromosome about to be loaded + """ + return self.line[0] + + def load_chromosome(self, collect_data=True): + """ + Load the current chromosome into an array and return it + """ + cname = self.chromosome_name() + if cname in self.processed_chromosomes: + stop_err('File is not grouped by chromosome') + self.data = [] + while self.line[0] == cname: + if collect_data: + read = self.parse_line(self.line) + if read[0] < self.current_index: + msg = 'Reads in chromosome %s are not sorted by index. (At index %d)' % (cname, self.current_index) + stop_err(msg) + self.current_index = read[0] + self.add_read(read) + try: + self.next() + except StopIteration: + self.done = True + break + self.processed_chromosomes.append(cname) + self.current_index = 0 + data = self.data + # Don't retain reference anymore to save memory + del self.data + return data + + def add_read(self, read): + if self.format == 'ssccidx': + self.data.append(read) + else: + index, strand, value = read + if value == '' or value == '.': + value = 1 + else: + value = int(value) + if not self.data: + self.data.append([index, 0, 0]) + current_read = self.data[-1] + if self.data[-1][0] == index: + current_read = self.data[-1] + elif self.data[-1][0] < index: + self.data.append([index, 0, 0]) + current_read = self.data[-1] + else: + msg = 'Reads in chromosome %s are not sorted by index. (At index %d)' % (self.chromosome_name(), index) + stop_err(msg) + if strand == '+': + current_read[1] += value + elif strand == '-': + current_read[2] += value + else: + msg = 'Strand "%s" at chromosome "%s" index %d is not valid.' % (strand, self.chromosome_name(), index) + stop_err(msg) + + def skip_chromosome(self): + """ + Skip the current chromosome, discarding data + """ + self.load_chromosome(collect_data=False) + + +class Peak(object): + def __init__(self, index, pos_width, neg_width): + self.index = index + self.start = index - neg_width + self.end = index + pos_width + self.value = 0 + self.deleted = False + self.safe = False + + def __repr__(self): + return '[%d] %d' % (self.index, self.value) + + +def gff_row(cname, start, end, score, source, type='.', strand='.', phase='.', attrs={}): + return (cname, source, type, start, end, score, strand, phase, gff_attrs(attrs)) + + +def gff_attrs(d): + if not d: + return '.' + return ';'.join('%s=%s' % item for item in d.items()) + + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit(1) + + +def is_int(i): + try: + int(i) + return True + except ValueError: + return False + + +def make_keys(data): + return [read[0] for read in data] + + +def make_peak_keys(peaks): + return [peak.index for peak in peaks] + + +def get_window(data, start, end, keys): + """ + Returns all reads from the data set with index between the two indexes + """ + start_index = bisect.bisect_left(keys, start) + end_index = bisect.bisect_right(keys, end) + return data[start_index:end_index] + + +def get_index(value, keys): + """ + Returns the index of the value in the keys using bisect + """ + return bisect.bisect_left(keys, value) + + +def get_range(data): + lo = min([item[0] for item in data]) + hi = max([item[0] for item in data]) + return lo, hi + + +def get_chunks(lo, hi, size, overlap=500): + """ + Divides a range into chunks of maximum size size. Returns a list of + 2-tuples (slice_range, process_range), each a 2-tuple (start, end). + process_range has zero overlap and should be given to process_chromosome + as-is, and slice_range is overlapped and should be used to slice the + data (using get_window) to be given to process_chromosome. + """ + chunks = [] + for start_index in range(lo, hi, size): + process_start = start_index + # Don't go over upper bound + process_end = min(start_index + size, hi) + # Don't go under lower bound + slice_start = max(process_start - overlap, lo) + # Don't go over upper bound + slice_end = min(process_end + overlap, hi) + chunks.append(((slice_start, slice_end), (process_start, process_end))) + return chunks + + +def allocate_array(data, width): + """ + Allocates a new array with the dimensions required to fit all reads in + the argument. The new array is totally empty. Returns the array and the + shift (number to add to a read index to get the position in the array it + should be at). + """ + lo, hi = get_range(data) + rng = hi - lo + shift = width - lo + return numpy.zeros(rng+width*2, numpy.float), shift + + +def normal_array(width, sigma, normalize=True): + """ + Returns an array of the normal distribution of the specified width + """ + sigma2 = float(sigma)**2 + + def normal_func(x): + return math.exp(-x * x / (2 * sigma2)) + + # width is the half of the distribution + values = map(normal_func, range(-width, width)) + values = numpy.array(values, numpy.float) + # normalization + if normalize: + values = 1.0/math.sqrt(2 * numpy.pi * sigma2) * values + return values + + +def call_peaks(array, shift, data, keys, direction, down_width, up_width, exclusion): + peaks = [] + + def find_peaks(): + # Go through the array and call each peak + results = (array > numpy.roll(array, 1)) & (array > numpy.roll(array, -1)) + indexes = numpy.where(results) + for index in indexes[0]: + pos = down_width or exclusion // 2 + neg = up_width or exclusion // 2 + # Reverse strand + if direction == 2: + # Swap positive and negative widths + pos, neg = neg, pos + peaks.append(Peak(int(index)-shift, pos, neg)) + find_peaks() + + def calculate_reads(): + # Calculate the number of reads in each peak + for peak in peaks: + reads = get_window(data, peak.start, peak.end, keys) + peak.value = sum([read[direction] for read in reads]) + # Flat list of indexes with frequency + indexes = [r for read in reads for r in [read[0]] * read[direction]] + peak.stddev = numpy.std(indexes) + calculate_reads() + + def perform_exclusion(): + # Process the exclusion zone + peak_keys = make_peak_keys(peaks) + peaks_by_value = peaks[:] + peaks_by_value.sort(key=lambda peak: -peak.value) + for peak in peaks_by_value: + peak.safe = True + window = get_window(peaks, + peak.index-exclusion//2, + peak.index+exclusion//2, + peak_keys) + for excluded in window: + if excluded.safe: + continue + i = get_index(excluded.index, peak_keys) + del peak_keys[i] + del peaks[i] + perform_exclusion() + return peaks + + +def process_chromosome(cname, data, writer, process_bounds, width, sigma, down_width, up_width, exclusion, filter): + """ + Process a chromosome. Takes the chromosome name, list of reads, a CSV + writer to write processes results to, the bounds (2-tuple) to write + results in, and options. + """ + if not data: + return + keys = make_keys(data) + # Create the arrays that hold the sum of the normals + forward_array, forward_shift = allocate_array(data, width) + reverse_array, reverse_shift = allocate_array(data, width) + normal = normal_array(width, sigma) + + def populate_array(): + # Add each read's normal to the array + for read in data: + index, forward, reverse = read + # Add the normals to the appropriate regions + if forward: + forward_array[index+forward_shift-width:index+forward_shift+width] += normal * forward + if reverse: + reverse_array[index+reverse_shift-width:index+reverse_shift+width] += normal * reverse + populate_array() + forward_peaks = call_peaks(forward_array, forward_shift, data, keys, 1, down_width, up_width, exclusion) + reverse_peaks = call_peaks(reverse_array, reverse_shift, data, keys, 2, down_width, up_width, exclusion) + # Convert chromosome name in preparation for writing output + cname = convert_data(cname, 'zeropad', 'numeric') + + def write(cname, strand, peak): + start = max(peak.start, 1) + end = peak.end + value = peak.value + stddev = peak.stddev + if value > filter: + # This version of genetrack outputs only gff files. + writer.writerow(gff_row(cname=cname, + source='genetrack', + start=start, + end=end, + score=value, + strand=strand, + attrs={'stddev': stddev})) + + for peak in forward_peaks: + if process_bounds[0] < peak.index < process_bounds[1]: + write(cname, '+', peak) + for peak in reverse_peaks: + if process_bounds[0] < peak.index < process_bounds[1]: + write(cname, '-', peak) + + +def sort_chromosome_reads_by_index( input_path ): + """ + Return a gff file with chromosome reads sorted by index. + """ + # Will this sort produce different results across platforms? + output_path = tempfile.NamedTemporaryFile( delete=False ).name + command = 'sort -k 1,1 -k 4,4n "%s" > "%s"' % (input_path, output_path) + p = subprocess.Popen(command, shell=True) + p.wait() + return output_path
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genetrack_input1.gff Tue Nov 17 14:19:45 2015 -0500 @@ -0,0 +1,100 @@ +chr1 genetrack . 1 19 450 + . stddev=4.77582440689 +chr1 genetrack . 31 51 583 + . stddev=5.04887975977 +chr1 genetrack . 34 54 88 - . stddev=2.896077962 +chr1 genetrack . 55 75 689 - . stddev=4.30660216862 +chr1 genetrack . 65 85 688 + . stddev=5.42600427981 +chr1 genetrack . 85 105 676 - . stddev=4.49818285888 +chr1 genetrack . 111 131 5134 + . stddev=6.21477198515 +chr1 genetrack . 135 155 4059 - . stddev=4.75030601387 +chr1 genetrack . 142 162 818 + . stddev=4.61530674023 +chr1 genetrack . 162 182 509 + . stddev=5.54002911575 +chr1 genetrack . 173 193 1844 - . stddev=4.57155440482 +chr1 genetrack . 197 217 513 + . stddev=6.03335915224 +chr1 genetrack . 201 221 889 - . stddev=4.25878183562 +chr1 genetrack . 218 238 1213 - . stddev=4.50854580513 +chr1 genetrack . 237 257 585 + . stddev=4.99399478661 +chr1 genetrack . 245 265 1605 - . stddev=5.11855734302 +chr1 genetrack . 263 283 1914 - . stddev=5.30293908946 +chr1 genetrack . 281 301 144 + . stddev=5.80110142799 +chr1 genetrack . 292 312 919 - . stddev=4.83235586146 +chr1 genetrack . 317 337 227 + . stddev=5.39529430562 +chr1 genetrack . 341 361 399 - . stddev=4.78763133608 +chr1 genetrack . 363 383 494 + . stddev=5.06265712248 +chr1 genetrack . 369 389 643 - . stddev=5.18741859391 +chr1 genetrack . 394 414 548 - . stddev=5.35724250762 +chr1 genetrack . 395 415 286 + . stddev=6.40676329916 +chr1 genetrack . 423 443 462 - . stddev=4.14819371578 +chr1 genetrack . 424 444 225 + . stddev=5.43077649451 +chr1 genetrack . 442 462 325 + . stddev=4.88036859603 +chr1 genetrack . 452 472 446 - . stddev=5.2172377816 +chr1 genetrack . 464 484 288 + . stddev=5.3671065623 +chr1 genetrack . 467 487 899 - . stddev=3.96802149366 +chr1 genetrack . 486 506 216 - . stddev=4.58116999076 +chr1 genetrack . 489 509 14 + . stddev=2.56845065662 +chr1 genetrack . 521 541 212 - . stddev=1.41926272859 +chr1 genetrack . 531 551 22 + . stddev=4.29226673437 +chr1 genetrack . 561 581 15 + . stddev=2.31516738056 +chr1 genetrack . 563 583 9 - . stddev=3.97523196 +chr1 genetrack . 579 599 18 + . stddev=4.21819983838 +chr1 genetrack . 602 622 35 - . stddev=3.0751140679 +chr1 genetrack . 603 623 38 + . stddev=0.0 +chr1 genetrack . 634 654 5 - . stddev=0.4 +chr1 genetrack . 638 658 26 + . stddev=3.92251127144 +chr1 genetrack . 650 670 63 - . stddev=1.3232803175 +chr1 genetrack . 669 689 4 + . stddev=1.73205080757 +chr1 genetrack . 689 709 29 - . stddev=2.02716392506 +chr1 genetrack . 761 781 10 + . stddev=1.6 +chr1 genetrack . 813 833 6 + . stddev=0.0 +chr1 genetrack . 856 876 3 - . stddev=0.0 +chr1 genetrack . 881 901 9 + . stddev=0.0 +chr1 genetrack . 908 928 10 + . stddev=3.4292856399 +chr1 genetrack . 923 943 13 + . stddev=2.30769230769 +chr1 genetrack . 928 948 6 - . stddev=4.71404520791 +chr1 genetrack . 948 968 14 + . stddev=0.0 +chr1 genetrack . 956 976 2 - . stddev=0.0 +chr1 genetrack . 986 1006 2 + . stddev=3.0 +chr1 genetrack . 986 1006 5 - . stddev=0.0 +chr1 genetrack . 1009 1029 11 + . stddev=0.0 +chr1 genetrack . 1050 1070 2 - . stddev=0.0 +chr1 genetrack . 1051 1071 6 + . stddev=0.0 +chr1 genetrack . 1065 1085 5 - . stddev=0.0 +chr1 genetrack . 1092 1112 7 - . stddev=0.0 +chr1 genetrack . 1115 1135 9 - . stddev=0.99380799 +chr1 genetrack . 1118 1138 3 + . stddev=0.0 +chr1 genetrack . 1128 1148 10 - . stddev=0.0 +chr1 genetrack . 1149 1169 5 + . stddev=0.0 +chr1 genetrack . 1224 1244 4 - . stddev=0.0 +chr1 genetrack . 1231 1251 2 + . stddev=0.0 +chr1 genetrack . 1256 1276 7 + . stddev=0.0 +chr1 genetrack . 1297 1317 8 + . stddev=0.0 +chr1 genetrack . 1298 1318 4 - . stddev=0.866025403784 +chr1 genetrack . 1323 1343 55 - . stddev=1.36980423286 +chr1 genetrack . 1382 1402 5 - . stddev=0.0 +chr1 genetrack . 1442 1462 4 - . stddev=0.433012701892 +chr1 genetrack . 1460 1480 2 + . stddev=0.0 +chr1 genetrack . 1522 1542 6 - . stddev=0.0 +chr1 genetrack . 1547 1567 8 - . stddev=3.30718913883 +chr1 genetrack . 1557 1577 7 + . stddev=0.451753951453 +chr1 genetrack . 1604 1624 11 - . stddev=0.0 +chr1 genetrack . 1690 1710 2 + . stddev=0.0 +chr1 genetrack . 1714 1734 3 - . stddev=0.0 +chr1 genetrack . 1747 1767 2 - . stddev=0.0 +chr1 genetrack . 1765 1785 5 - . stddev=0.0 +chr1 genetrack . 1834 1854 5 - . stddev=0.0 +chr1 genetrack . 1859 1879 8 - . stddev=0.0 +chr1 genetrack . 1870 1890 2 + . stddev=0.0 +chr1 genetrack . 1915 1935 5 - . stddev=0.4 +chr1 genetrack . 1935 1955 4 - . stddev=0.0 +chr1 genetrack . 2005 2025 6 + . stddev=0.0 +chr1 genetrack . 2056 2076 5 - . stddev=0.0 +chr1 genetrack . 2079 2099 5 + . stddev=4.0 +chr1 genetrack . 2088 2108 2 - . stddev=0.0 +chr1 genetrack . 2120 2140 31 - . stddev=0.706738783878 +chr1 genetrack . 2131 2151 16 + . stddev=0.7806247498 +chr1 genetrack . 2191 2211 4 + . stddev=0.0 +chr1 genetrack . 2227 2247 6 + . stddev=0.0 +chr1 genetrack . 2235 2255 5 - . stddev=1.46969384567 +chr1 genetrack . 2260 2280 6 + . stddev=0.0 +chr1 genetrack . 2278 2298 2 - . stddev=0.0 +chr1 genetrack . 2421 2441 23 - . stddev=3.58583645226 +chr1 genetrack . 2446 2466 6 - . stddev=0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genetrack_input2.gff Tue Nov 17 14:19:45 2015 -0500 @@ -0,0 +1,100 @@ +chr1 genetrack . 17 37 918 + . stddev=5.96715849116 +chr1 genetrack . 31 51 245 - . stddev=2.66582799529 +chr1 genetrack . 40 60 2060 + . stddev=2.7859667372 +chr1 genetrack . 62 82 1300 - . stddev=4.13061337623 +chr1 genetrack . 73 93 397 + . stddev=0.0 +chr1 genetrack . 89 109 521 + . stddev=0.747112137937 +chr1 genetrack . 123 143 5129 + . stddev=3.01025384354 +chr1 genetrack . 125 145 4659 - . stddev=3.8642622228 +chr1 genetrack . 155 175 897 - . stddev=3.22709952671 +chr1 genetrack . 171 191 956 - . stddev=4.95899971687 +chr1 genetrack . 180 200 1527 + . stddev=4.62574275346 +chr1 genetrack . 185 205 494 - . stddev=1.4255957 +chr1 genetrack . 192 212 2538 + . stddev=5.04731591122 +chr1 genetrack . 206 226 2087 - . stddev=3.6160253713 +chr1 genetrack . 238 258 2496 + . stddev=2.11105291581 +chr1 genetrack . 242 262 5047 - . stddev=3.62629343395 +chr1 genetrack . 254 274 1525 + . stddev=4.46082441647 +chr1 genetrack . 281 301 15 + . stddev=1.74610678049 +chr1 genetrack . 302 322 626 - . stddev=0.0 +chr1 genetrack . 308 328 1544 + . stddev=4.43066151722 +chr1 genetrack . 334 354 533 + . stddev=1.34355443899 +chr1 genetrack . 344 364 726 - . stddev=1.36767079956 +chr1 genetrack . 347 367 286 + . stddev=0.0 +chr1 genetrack . 358 378 792 - . stddev=1.47737416556 +chr1 genetrack . 374 394 608 + . stddev=1.44652711793 +chr1 genetrack . 389 409 126 - . stddev=0.471404520791 +chr1 genetrack . 439 459 618 - . stddev=5.47536569145 +chr1 genetrack . 441 461 1393 + . stddev=4.75587332865 +chr1 genetrack . 461 481 754 - . stddev=3.28891288785 +chr1 genetrack . 483 503 58 + . stddev=0.0 +chr1 genetrack . 538 558 1015 - . stddev=0.0 +chr1 genetrack . 728 748 39 - . stddev=0.0 +chr1 genetrack . 757 777 23 + . stddev=0.0 +chr1 genetrack . 799 819 607 + . stddev=0.0 +chr1 genetrack . 844 864 665 + . stddev=0.0 +chr1 genetrack . 877 897 468 + . stddev=0.0 +chr1 genetrack . 903 923 107 - . stddev=0.0 +chr1 genetrack . 944 964 2 - . stddev=0.0 +chr1 genetrack . 1092 1112 740 + . stddev=0.0 +chr1 genetrack . 1127 1147 940 - . stddev=3.96036497305 +chr1 genetrack . 1183 1203 25 + . stddev=0.0 +chr1 genetrack . 1291 1311 454 - . stddev=0.0 +chr1 genetrack . 1329 1349 207 - . stddev=0.0 +chr1 genetrack . 1484 1504 584 + . stddev=0.0 +chr1 genetrack . 2075 2095 1181 + . stddev=0.0 +chr1 genetrack . 2102 2122 481 + . stddev=0.0455486534308 +chr1 genetrack . 2125 2145 199 - . stddev=0.0 +chr1 genetrack . 2452 2472 1246 + . stddev=0.0 +chr1 genetrack . 2602 2622 34 + . stddev=0.0 +chr1 genetrack . 2833 2853 1062 + . stddev=1.01561431542 +chr1 genetrack . 2838 2858 1144 - . stddev=1.09438744148 +chr1 genetrack . 3011 3031 1212 - . stddev=0.0 +chr1 genetrack . 3116 3136 555 - . stddev=0.0 +chr1 genetrack . 3130 3150 17 + . stddev=0.0 +chr1 genetrack . 3378 3398 525 - . stddev=0.0 +chr1 genetrack . 3669 3689 845 + . stddev=0.0 +chr1 genetrack . 3785 3805 23 - . stddev=0.0 +chr1 genetrack . 3847 3867 316 - . stddev=0.0 +chr1 genetrack . 3868 3888 491 + . stddev=0.0 +chr1 genetrack . 4097 4117 536 - . stddev=0.0 +chr1 genetrack . 4326 4346 482 + . stddev=0.0 +chr1 genetrack . 4395 4415 3 + . stddev=0.0 +chr1 genetrack . 4461 4481 1110 + . stddev=0.0 +chr1 genetrack . 4500 4520 125 - . stddev=0.0 +chr1 genetrack . 4620 4640 147 + . stddev=0.0 +chr1 genetrack . 4826 4846 1761 + . stddev=4.82408982772 +chr1 genetrack . 4902 4922 710 + . stddev=0.0 +chr1 genetrack . 5110 5130 828 + . stddev=0.0 +chr1 genetrack . 5402 5422 282 - . stddev=0.0 +chr1 genetrack . 5501 5521 75 + . stddev=0.0 +chr1 genetrack . 5707 5727 2 + . stddev=0.0 +chr1 genetrack . 5717 5737 737 - . stddev=0.36608362591 +chr1 genetrack . 6086 6106 646 + . stddev=0.039314009595 +chr1 genetrack . 6098 6118 230 - . stddev=0.0657945476105 +chr1 genetrack . 6187 6207 329 - . stddev=0.0 +chr1 genetrack . 6290 6310 5 + . stddev=0.0 +chr1 genetrack . 6356 6376 285 + . stddev=0.0 +chr1 genetrack . 6380 6400 34 - . stddev=0.0 +chr1 genetrack . 6401 6421 1587 + . stddev=5.61831543503 +chr1 genetrack . 6415 6435 953 - . stddev=3.52372902021 +chr1 genetrack . 6432 6452 742 + . stddev=0.0 +chr1 genetrack . 6496 6516 691 + . stddev=0.0 +chr1 genetrack . 6506 6526 61 - . stddev=1.5137105198 +chr1 genetrack . 6843 6863 28 + . stddev=0.0 +chr1 genetrack . 7058 7078 518 - . stddev=0.0 +chr1 genetrack . 7124 7144 654 + . stddev=0.0 +chr1 genetrack . 7765 7785 714 + . stddev=0.0 +chr1 genetrack . 7847 7867 3 + . stddev=0.0 +chr1 genetrack . 8209 8229 17 + . stddev=0.0 +chr1 genetrack . 8272 8292 2 - . stddev=0.0 +chr1 genetrack . 8459 8479 10 + . stddev=0.0 +chr1 genetrack . 8471 8491 5 - . stddev=0.0 +chr1 genetrack . 8715 8735 5 + . stddev=0.0 +chr1 genetrack . 8834 8854 332 + . stddev=0.0 +chr1 genetrack . 8839 8859 593 - . stddev=0.0 +chr1 genetrack . 9034 9054 24 + . stddev=0.0 +chr1 genetrack . 9058 9078 4 + . stddev=0.0 +chr1 genetrack . 9485 9505 36 + . stddev=0.0 +chr1 genetrack . 9710 9730 480 + . stddev=0.0 +chr1 genetrack . 9923 9943 606 - . stddev=0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genetrack_input3.ssccidx Tue Nov 17 14:19:45 2015 -0500 @@ -0,0 +1,100 @@ +chrom index forward reverse value +chr01 7 2 0 2 +chr01 8 3 0 3 +chr01 10 2 0 2 +chr01 14 1 0 1 +chr01 15 1 0 1 +chr01 16 1 0 1 +chr01 31 1 0 1 +chr01 32 1 0 1 +chr01 35 1 0 1 +chr01 37 2 0 2 +chr01 38 65 0 65 +chr01 39 8 4 12 +chr01 40 3 0 3 +chr01 41 3 2 5 +chr01 42 3 1 4 +chr01 43 2 2 4 +chr01 44 0 1 1 +chr01 46 3 0 3 +chr01 52 0 1 1 +chr01 54 7 0 7 +chr01 55 2 0 2 +chr01 56 1 0 1 +chr01 58 0 1 1 +chr01 61 0 1 1 +chr01 62 1 3 4 +chr01 63 0 1 1 +chr01 64 2 4 6 +chr01 66 0 13 13 +chr01 67 0 4 4 +chr01 72 0 5 5 +chr01 75 4 0 4 +chr01 77 0 6 6 +chr01 81 13 0 13 +chr01 83 1 0 1 +chr01 85 0 4 4 +chr01 86 0 1 1 +chr01 89 4 0 4 +chr01 90 1 0 1 +chr01 91 2 0 2 +chr01 92 4 1 5 +chr01 93 4 0 4 +chr01 96 1 0 1 +chr01 97 1 0 1 +chr01 98 4 0 4 +chr01 99 8 0 8 +chr01 102 1 1 2 +chr01 105 0 1 1 +chr01 107 0 3 3 +chr01 109 0 4 4 +chr01 110 2 1 3 +chr01 111 6 0 6 +chr01 112 0 3 3 +chr01 113 24 0 24 +chr01 114 0 32 32 +chr01 115 5 4 9 +chr01 116 36 5 41 +chr01 117 194 5 199 +chr01 118 100 2 102 +chr01 119 98 19 117 +chr01 120 92 7 99 +chr01 121 112 11 123 +chr01 122 36 3 39 +chr01 123 18 16 34 +chr01 124 9 14 23 +chr01 125 14 12 26 +chr01 126 20 1 21 +chr01 127 4 2 6 +chr01 128 66 6 72 +chr01 129 3 6 9 +chr01 130 2 10 12 +chr01 131 62 0 62 +chr01 132 20 1 21 +chr01 133 64 1 65 +chr01 134 58 0 58 +chr01 135 83 4 87 +chr01 136 92 1 93 +chr01 137 12 0 12 +chr01 138 0 3 3 +chr01 139 0 2 2 +chr01 142 0 48 48 +chr01 143 0 15 15 +chr01 144 0 74 74 +chr01 145 23 11 34 +chr01 146 1 120 121 +chr01 147 0 574 574 +chr01 148 0 11 11 +chr01 150 1 0 1 +chr01 151 3 4 7 +chr01 152 0 2 2 +chr01 153 1 3 4 +chr01 155 8 11 19 +chr01 156 0 14 14 +chr01 158 0 3 3 +chr01 159 0 1 1 +chr01 160 0 1 1 +chr01 161 0 5 5 +chr01 163 0 2 2 +chr01 164 0 29 29 +chr01 165 0 1 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genetrack_input_unsorted4.gff Tue Nov 17 14:19:45 2015 -0500 @@ -0,0 +1,100 @@ +chr1 genetrack . 1 19 450 + . stddev=4.77582440689 +chr1 genetrack . 31 51 583 + . stddev=5.04887975977 +chr1 genetrack . 34 54 88 - . stddev=2.896077962 +chr1 genetrack . 55 75 689 - . stddev=4.30660216862 +chr1 genetrack . 65 85 688 + . stddev=5.42600427981 +chr1 genetrack . 85 105 676 - . stddev=4.49818285888 +chr1 genetrack . 111 131 5134 + . stddev=6.21477198515 +chr1 genetrack . 135 155 4059 - . stddev=4.75030601387 +chr1 genetrack . 142 162 818 + . stddev=4.61530674023 +chr1 genetrack . 162 182 509 + . stddev=5.54002911575 +chr1 genetrack . 173 193 1844 - . stddev=4.57155440482 +chr1 genetrack . 197 217 513 + . stddev=6.03335915224 +chr1 genetrack . 201 221 889 - . stddev=4.25878183562 +chr1 genetrack . 218 238 1213 - . stddev=4.50854580513 +chr1 genetrack . 237 257 585 + . stddev=4.99399478661 +chr1 genetrack . 245 265 1605 - . stddev=5.11855734302 +chr1 genetrack . 263 283 1914 - . stddev=5.30293908946 +chr1 genetrack . 281 301 144 + . stddev=5.80110142799 +chr1 genetrack . 292 312 919 - . stddev=4.83235586146 +chr1 genetrack . 317 337 227 + . stddev=5.39529430562 +chr1 genetrack . 341 361 399 - . stddev=4.78763133608 +chr1 genetrack . 363 383 494 + . stddev=5.06265712248 +chr1 genetrack . 369 389 643 - . stddev=5.18741859391 +chr1 genetrack . 394 414 548 - . stddev=5.35724250762 +chr1 genetrack . 395 415 286 + . stddev=6.40676329916 +chr1 genetrack . 423 443 462 - . stddev=4.14819371578 +chr1 genetrack . 424 444 225 + . stddev=5.43077649451 +chr1 genetrack . 442 462 325 + . stddev=4.88036859603 +chr1 genetrack . 452 472 446 - . stddev=5.2172377816 +chr1 genetrack . 464 484 288 + . stddev=5.3671065623 +chr1 genetrack . 467 487 899 - . stddev=3.96802149366 +chr1 genetrack . 486 506 216 - . stddev=4.58116999076 +chr1 genetrack . 489 509 14 + . stddev=2.56845065662 +chr1 genetrack . 521 541 212 - . stddev=1.41926272859 +chr1 genetrack . 531 551 22 + . stddev=4.29226673437 +chr1 genetrack . 561 581 15 + . stddev=2.31516738056 +chr1 genetrack . 563 583 9 - . stddev=3.97523196 +chr1 genetrack . 579 599 18 + . stddev=4.21819983838 +chr1 genetrack . 602 622 35 - . stddev=3.0751140679 +chr1 genetrack . 603 623 38 + . stddev=0.0 +chr1 genetrack . 634 654 5 - . stddev=0.4 +chr1 genetrack . 638 658 26 + . stddev=3.92251127144 +chr1 genetrack . 650 670 63 - . stddev=1.3232803175 +chr1 genetrack . 669 689 4 + . stddev=1.73205080757 +chr1 genetrack . 689 709 29 - . stddev=2.02716392506 +chr1 genetrack . 761 781 10 + . stddev=1.6 +chr1 genetrack . 813 833 6 + . stddev=0.0 +chr1 genetrack . 856 876 3 - . stddev=0.0 +chr1 genetrack . 881 901 9 + . stddev=0.0 +chr1 genetrack . 908 928 10 + . stddev=3.4292856399 +chr1 genetrack . 923 943 13 + . stddev=2.30769230769 +chr1 genetrack . 928 948 6 - . stddev=4.71404520791 +chr1 genetrack . 948 968 14 + . stddev=0.0 +chr1 genetrack . 956 976 2 - . stddev=0.0 +chr1 genetrack . 986 1006 2 + . stddev=3.0 +chr1 genetrack . 986 1006 5 - . stddev=0.0 +chr1 genetrack . 1009 1029 11 + . stddev=0.0 +chr1 genetrack . 1050 1070 2 - . stddev=0.0 +chr1 genetrack . 1051 1071 6 + . stddev=0.0 +chr1 genetrack . 1065 1085 5 - . stddev=0.0 +chr1 genetrack . 1092 1112 7 - . stddev=0.0 +chr1 genetrack . 1115 1135 9 - . stddev=0.99380799 +chr1 genetrack . 1118 1138 3 + . stddev=0.0 +chr1 genetrack . 1128 1148 10 - . stddev=0.0 +chr1 genetrack . 1149 1169 5 + . stddev=0.0 +chr1 genetrack . 1224 1244 4 - . stddev=0.0 +chr1 genetrack . 1231 1251 2 + . stddev=0.0 +chr1 genetrack . 1256 1276 7 + . stddev=0.0 +chr1 genetrack . 1297 1317 8 + . stddev=0.0 +chr1 genetrack . 1298 1318 4 - . stddev=0.866025403784 +chr1 genetrack . 1323 1343 55 - . stddev=1.36980423286 +chr1 genetrack . 1382 1402 5 - . stddev=0.0 +chr1 genetrack . 1442 1462 4 - . stddev=0.433012701892 +chr1 genetrack . 1460 1480 2 + . stddev=0.0 +chr1 genetrack . 1522 1542 6 - . stddev=0.0 +chr1 genetrack . 1547 1567 8 - . stddev=3.30718913883 +chr1 genetrack . 1557 1577 7 + . stddev=0.451753951453 +chr1 genetrack . 1604 1624 11 - . stddev=0.0 +chr1 genetrack . 1690 1710 2 + . stddev=0.0 +chr1 genetrack . 1714 1734 3 - . stddev=0.0 +chr1 genetrack . 1747 1767 2 - . stddev=0.0 +chr1 genetrack . 1765 1785 5 - . stddev=0.0 +chr1 genetrack . 1834 1854 5 - . stddev=0.0 +chr1 genetrack . 1859 1879 8 - . stddev=0.0 +chr1 genetrack . 1870 1890 2 + . stddev=0.0 +chr1 genetrack . 1915 1935 5 - . stddev=0.4 +chr1 genetrack . 1935 1955 4 - . stddev=0.0 +chr1 genetrack . 2005 2025 6 + . stddev=0.0 +chr1 genetrack . 2056 2076 5 - . stddev=0.0 +chr1 genetrack . 2079 2099 5 + . stddev=4.0 +chr1 genetrack . 2088 2108 2 - . stddev=0.0 +chr1 genetrack . 2120 2140 31 - . stddev=0.706738783878 +chr1 genetrack . 2131 2151 16 + . stddev=0.7806247498 +chr1 genetrack . 2191 2211 4 + . stddev=0.0 +chr1 genetrack . 2227 2247 6 + . stddev=0.0 +chr1 genetrack . 2235 2255 5 - . stddev=1.46969384567 +chr1 genetrack . 2260 2280 6 + . stddev=0.0 +chr1 genetrack . 2278 2298 2 - . stddev=0.0 +chr1 genetrack . 2421 2441 23 - . stddev=3.58583645226 +chr1 genetrack . 2446 2466 6 - . stddev=0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genetrack_output2.gff Tue Nov 17 14:19:45 2015 -0500 @@ -0,0 +1,92 @@ +chr1 genetrack . 30 50 2060 + . stddev=0.0 +chr1 genetrack . 63 83 397 + . stddev=0.0 +chr1 genetrack . 79 99 521 + . stddev=0.0 +chr1 genetrack . 113 133 5129 + . stddev=0.0 +chr1 genetrack . 182 202 2538 + . stddev=0.0 +chr1 genetrack . 228 248 2496 + . stddev=0.0 +chr1 genetrack . 244 264 1525 + . stddev=0.0 +chr1 genetrack . 271 291 15 + . stddev=0.0 +chr1 genetrack . 298 318 1544 + . stddev=0.0 +chr1 genetrack . 324 344 533 + . stddev=0.0 +chr1 genetrack . 335 355 286 + . stddev=0.0 +chr1 genetrack . 364 384 608 + . stddev=0.0 +chr1 genetrack . 431 451 1393 + . stddev=0.0 +chr1 genetrack . 473 493 58 + . stddev=0.0 +chr1 genetrack . 747 767 23 + . stddev=0.0 +chr1 genetrack . 789 809 607 + . stddev=0.0 +chr1 genetrack . 834 854 665 + . stddev=0.0 +chr1 genetrack . 867 887 468 + . stddev=0.0 +chr1 genetrack . 1082 1102 740 + . stddev=0.0 +chr1 genetrack . 1173 1193 25 + . stddev=0.0 +chr1 genetrack . 1474 1494 584 + . stddev=0.0 +chr1 genetrack . 2065 2085 1181 + . stddev=0.0 +chr1 genetrack . 2092 2112 481 + . stddev=0.0 +chr1 genetrack . 2442 2462 1246 + . stddev=0.0 +chr1 genetrack . 2592 2612 34 + . stddev=0.0 +chr1 genetrack . 2823 2843 1062 + . stddev=0.0 +chr1 genetrack . 3120 3140 17 + . stddev=0.0 +chr1 genetrack . 3659 3679 845 + . stddev=0.0 +chr1 genetrack . 3858 3878 491 + . stddev=0.0 +chr1 genetrack . 4316 4336 482 + . stddev=0.0 +chr1 genetrack . 4451 4471 1110 + . stddev=0.0 +chr1 genetrack . 4610 4630 147 + . stddev=0.0 +chr1 genetrack . 4816 4836 1761 + . stddev=0.0 +chr1 genetrack . 4892 4912 710 + . stddev=0.0 +chr1 genetrack . 5100 5120 828 + . stddev=0.0 +chr1 genetrack . 5491 5511 75 + . stddev=0.0 +chr1 genetrack . 6076 6096 646 + . stddev=0.0 +chr1 genetrack . 6280 6300 5 + . stddev=0.0 +chr1 genetrack . 6346 6366 285 + . stddev=0.0 +chr1 genetrack . 6391 6411 1587 + . stddev=0.0 +chr1 genetrack . 6422 6442 742 + . stddev=0.0 +chr1 genetrack . 6486 6506 691 + . stddev=0.0 +chr1 genetrack . 6833 6853 28 + . stddev=0.0 +chr1 genetrack . 7114 7134 654 + . stddev=0.0 +chr1 genetrack . 7755 7775 714 + . stddev=0.0 +chr1 genetrack . 8199 8219 17 + . stddev=0.0 +chr1 genetrack . 8449 8469 10 + . stddev=0.0 +chr1 genetrack . 8705 8725 5 + . stddev=0.0 +chr1 genetrack . 8824 8844 332 + . stddev=0.0 +chr1 genetrack . 9024 9044 24 + . stddev=0.0 +chr1 genetrack . 9048 9068 4 + . stddev=0.0 +chr1 genetrack . 9475 9495 36 + . stddev=0.0 +chr1 genetrack . 9700 9720 480 + . stddev=0.0 +chr1 genetrack . 21 41 245 - . stddev=0.0 +chr1 genetrack . 52 72 1300 - . stddev=0.0 +chr1 genetrack . 115 135 4659 - . stddev=0.0 +chr1 genetrack . 145 165 897 - . stddev=0.0 +chr1 genetrack . 161 181 956 - . stddev=0.0 +chr1 genetrack . 174 194 494 - . stddev=0.0 +chr1 genetrack . 196 216 2087 - . stddev=0.0 +chr1 genetrack . 232 252 5047 - . stddev=0.0 +chr1 genetrack . 292 312 626 - . stddev=0.0 +chr1 genetrack . 334 354 726 - . stddev=0.0 +chr1 genetrack . 348 368 792 - . stddev=0.0 +chr1 genetrack . 379 399 126 - . stddev=0.0 +chr1 genetrack . 429 449 618 - . stddev=0.0 +chr1 genetrack . 451 471 754 - . stddev=0.0 +chr1 genetrack . 528 548 1015 - . stddev=0.0 +chr1 genetrack . 718 738 39 - . stddev=0.0 +chr1 genetrack . 893 913 107 - . stddev=0.0 +chr1 genetrack . 1117 1137 940 - . stddev=0.0 +chr1 genetrack . 1281 1301 454 - . stddev=0.0 +chr1 genetrack . 1319 1339 207 - . stddev=0.0 +chr1 genetrack . 2115 2135 199 - . stddev=0.0 +chr1 genetrack . 2828 2848 1144 - . stddev=0.0 +chr1 genetrack . 3001 3021 1212 - . stddev=0.0 +chr1 genetrack . 3106 3126 555 - . stddev=0.0 +chr1 genetrack . 3368 3388 525 - . stddev=0.0 +chr1 genetrack . 3775 3795 23 - . stddev=0.0 +chr1 genetrack . 3837 3857 316 - . stddev=0.0 +chr1 genetrack . 4087 4107 536 - . stddev=0.0 +chr1 genetrack . 4490 4510 125 - . stddev=0.0 +chr1 genetrack . 5392 5412 282 - . stddev=0.0 +chr1 genetrack . 5707 5727 737 - . stddev=0.0 +chr1 genetrack . 6088 6108 230 - . stddev=0.0 +chr1 genetrack . 6177 6197 329 - . stddev=0.0 +chr1 genetrack . 6370 6390 34 - . stddev=0.0 +chr1 genetrack . 6405 6425 953 - . stddev=0.0 +chr1 genetrack . 6496 6516 61 - . stddev=0.0 +chr1 genetrack . 7048 7068 518 - . stddev=0.0 +chr1 genetrack . 8461 8481 5 - . stddev=0.0 +chr1 genetrack . 8829 8849 593 - . stddev=0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genetrack_output3.gff Tue Nov 17 14:19:45 2015 -0500 @@ -0,0 +1,10 @@ +chr1 genetrack . 1 20 10 + . stddev=3.25729949498 +chr1 genetrack . 28 48 92 + . stddev=2.09743181697 +chr1 genetrack . 73 93 33 + . stddev=6.09264259969 +chr1 genetrack . 85 105 30 + . stddev=3.96106046407 +chr1 genetrack . 109 129 839 + . stddev=3.6259952943 +chr1 genetrack . 121 141 675 + . stddev=5.59352633853 +chr1 genetrack . 31 51 10 - . stddev=1.84390889146 +chr1 genetrack . 56 76 32 - . stddev=3.28764258246 +chr1 genetrack . 110 130 159 - . stddev=5.21810978727 +chr1 genetrack . 136 156 893 - . stddev=2.27140632107
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genetrack_output4.gff Tue Nov 17 14:19:45 2015 -0500 @@ -0,0 +1,84 @@ +chr1 genetrack . 21 41 583 + . stddev=0.0 +chr1 genetrack . 55 75 688 + . stddev=0.0 +chr1 genetrack . 101 121 5134 + . stddev=0.0 +chr1 genetrack . 132 152 818 + . stddev=0.0 +chr1 genetrack . 152 172 509 + . stddev=0.0 +chr1 genetrack . 187 207 513 + . stddev=0.0 +chr1 genetrack . 227 247 585 + . stddev=0.0 +chr1 genetrack . 271 291 144 + . stddev=0.0 +chr1 genetrack . 307 327 227 + . stddev=0.0 +chr1 genetrack . 353 373 494 + . stddev=0.0 +chr1 genetrack . 385 405 286 + . stddev=0.0 +chr1 genetrack . 414 434 225 + . stddev=0.0 +chr1 genetrack . 432 452 325 + . stddev=0.0 +chr1 genetrack . 454 474 288 + . stddev=0.0 +chr1 genetrack . 479 499 14 + . stddev=0.0 +chr1 genetrack . 521 541 22 + . stddev=0.0 +chr1 genetrack . 551 571 15 + . stddev=0.0 +chr1 genetrack . 569 589 18 + . stddev=0.0 +chr1 genetrack . 593 613 38 + . stddev=0.0 +chr1 genetrack . 628 648 26 + . stddev=0.0 +chr1 genetrack . 659 679 4 + . stddev=0.0 +chr1 genetrack . 751 771 10 + . stddev=0.0 +chr1 genetrack . 803 823 6 + . stddev=0.0 +chr1 genetrack . 871 891 9 + . stddev=0.0 +chr1 genetrack . 898 918 10 + . stddev=0.0 +chr1 genetrack . 913 933 13 + . stddev=0.0 +chr1 genetrack . 938 958 14 + . stddev=0.0 +chr1 genetrack . 999 1019 11 + . stddev=0.0 +chr1 genetrack . 1041 1061 6 + . stddev=0.0 +chr1 genetrack . 1139 1159 5 + . stddev=0.0 +chr1 genetrack . 1246 1266 7 + . stddev=0.0 +chr1 genetrack . 1287 1307 8 + . stddev=0.0 +chr1 genetrack . 1547 1567 7 + . stddev=0.0 +chr1 genetrack . 1995 2015 6 + . stddev=0.0 +chr1 genetrack . 2069 2089 5 + . stddev=0.0 +chr1 genetrack . 2121 2141 16 + . stddev=0.0 +chr1 genetrack . 2181 2201 4 + . stddev=0.0 +chr1 genetrack . 2217 2237 6 + . stddev=0.0 +chr1 genetrack . 2250 2270 6 + . stddev=0.0 +chr1 genetrack . 24 44 88 - . stddev=0.0 +chr1 genetrack . 45 65 689 - . stddev=0.0 +chr1 genetrack . 75 95 676 - . stddev=0.0 +chr1 genetrack . 125 145 4059 - . stddev=0.0 +chr1 genetrack . 163 183 1844 - . stddev=0.0 +chr1 genetrack . 191 211 889 - . stddev=0.0 +chr1 genetrack . 208 228 1213 - . stddev=0.0 +chr1 genetrack . 235 255 1605 - . stddev=0.0 +chr1 genetrack . 253 273 1914 - . stddev=0.0 +chr1 genetrack . 282 302 919 - . stddev=0.0 +chr1 genetrack . 331 351 399 - . stddev=0.0 +chr1 genetrack . 359 379 643 - . stddev=0.0 +chr1 genetrack . 384 404 548 - . stddev=0.0 +chr1 genetrack . 413 433 462 - . stddev=0.0 +chr1 genetrack . 442 462 446 - . stddev=0.0 +chr1 genetrack . 457 477 899 - . stddev=0.0 +chr1 genetrack . 476 496 216 - . stddev=0.0 +chr1 genetrack . 511 531 212 - . stddev=0.0 +chr1 genetrack . 553 573 9 - . stddev=0.0 +chr1 genetrack . 592 612 35 - . stddev=0.0 +chr1 genetrack . 640 660 63 - . stddev=0.0 +chr1 genetrack . 679 699 29 - . stddev=0.0 +chr1 genetrack . 918 938 6 - . stddev=0.0 +chr1 genetrack . 976 996 5 - . stddev=0.0 +chr1 genetrack . 1055 1075 5 - . stddev=0.0 +chr1 genetrack . 1082 1102 7 - . stddev=0.0 +chr1 genetrack . 1106 1126 9 - . stddev=0.0 +chr1 genetrack . 1117 1137 10 - . stddev=0.0 +chr1 genetrack . 1214 1234 4 - . stddev=0.0 +chr1 genetrack . 1288 1308 4 - . stddev=0.0 +chr1 genetrack . 1313 1333 55 - . stddev=0.0 +chr1 genetrack . 1372 1392 5 - . stddev=0.0 +chr1 genetrack . 1432 1452 4 - . stddev=0.0 +chr1 genetrack . 1512 1532 6 - . stddev=0.0 +chr1 genetrack . 1537 1557 8 - . stddev=0.0 +chr1 genetrack . 1594 1614 11 - . stddev=0.0 +chr1 genetrack . 1755 1775 5 - . stddev=0.0 +chr1 genetrack . 1824 1844 5 - . stddev=0.0 +chr1 genetrack . 1849 1869 8 - . stddev=0.0 +chr1 genetrack . 1905 1925 5 - . stddev=0.0 +chr1 genetrack . 1925 1945 4 - . stddev=0.0 +chr1 genetrack . 2046 2066 5 - . stddev=0.0 +chr1 genetrack . 2110 2130 31 - . stddev=0.0 +chr1 genetrack . 2225 2245 5 - . stddev=0.0 +chr1 genetrack . 2411 2431 23 - . stddev=0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Nov 17 14:19:45 2015 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="numpy" version="1.9"> + <repository changeset_revision="816d3480b0b1" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>