SYMBOL INDEX (124 symbols across 15 files)

FILE: lib/BtCore.py
  class BlobDb (line 18) | class BlobDb():
    method __init__ (line 22) | def __init__(self, title):
    method view (line 42) | def view(self, **kwargs):
    method getCovHeader (line 108) | def getCovHeader(self, cov_lib_names):
    method getCovLine (line 126) | def getCovLine(self, blob, cov_lib_names):
    method getConcoctCovHeader (line 134) | def getConcoctCovHeader(self, cov_lib_names):
    method getConcoctTaxLine (line 137) | def getConcoctTaxLine(self, blob, rank, taxrule):
    method getConcoctCovLine (line 141) | def getConcoctCovLine(self, blob, cov_lib_names):
    method getTableHeader (line 144) | def getTableHeader(self, taxrule, ranks, hits_flag, cov_lib_names):
    method getTableLine (line 185) | def getTableLine(self, blob, taxrule, ranks, hits_flag, cov_lib_names,...
    method dump (line 216) | def dump(self):
    method load (line 236) | def load(self, BlobDb_f):
    method getPlotData (line 242) | def getPlotData(self, rank, min_length, hide_nohits, taxrule, c_index,...
    method addCovLib (line 327) | def addCovLib(self, covLib):
    method parseFasta (line 332) | def parseFasta(self, fasta_f, fasta_type):
    method parseCoverage (line 359) | def parseCoverage(self, **kwargs):
    method parseHits (line 415) | def parseHits(self, hitLibs):
    method computeTaxonomy (line 427) | def computeTaxonomy(self, taxrules, nodesDB, min_score, min_bitscore_d...
    method getBlobs (line 446) | def getBlobs(self):
  class BlObj (line 450) | class BlObj():
    method __init__ (line 451) | def __init__(self, name, seq):
    method calculateGC (line 462) | def calculateGC(self, seq):
    method addCov (line 466) | def addCov(self, lib_name, cov):
    method addReadCov (line 469) | def addReadCov(self, lib_name, read_cov):
    method addHits (line 472) | def addHits(self, hitLibName, hitDict):
  class CovLibObj (line 477) | class CovLibObj():
    method __init__ (line 478) | def __init__(self, name, fmt, f):
  class HitLibObj (line 488) | class HitLibObj():
    method __init__ (line 489) | def __init__(self, name, fmt, f):
  class ViewObj (line 495) | class ViewObj():
    method __init__ (line 496) | def __init__(self, name='', out_f='', suffix='', header='', body=''):
    method output (line 503) | def output(self):
  class ExperimentalViewObj (line 725) | class ExperimentalViewObj():
    method __init__ (line 726) | def __init__(self, name='experimental', view_dir='',blobDb={},meta={}):
    method _format_float (line 741) | def _format_float(self,l,min_val=-float("inf")):
    method _remove_cov_suffix (line 746) | def _remove_cov_suffix(self,id,meta):
    method get_meta (line 754) | def get_meta(self):
    method _keyed_list (line 826) | def _keyed_list(self,l):
    method output (line 837) | def output(self):

FILE: lib/BtIO.py
  function create_dir (line 24) | def create_dir(directory="", overwrite=True):
  function parseList (line 36) | def parseList(infile):
  function parseReferenceCov (line 45) | def parseReferenceCov(infile):
  function parseCmdlist (line 60) | def parseCmdlist(temp):
  function parseCmdLabels (line 69) | def parseCmdLabels(labels):
  function parseCatColour (line 85) | def parseCatColour(infile):
  function parseDict (line 99) | def parseDict(infile, key, value):
  function parseColours (line 113) | def parseColours(infile):
  function parseSet (line 124) | def parseSet(infile):
  function parseFastaNameOrder (line 133) | def parseFastaNameOrder(infile):
  function readFasta (line 139) | def readFasta(infile):
  function runCmd (line 153) | def runCmd(**kwargs):
  function which (line 169) | def which(program):
  function checkAlnIndex (line 184) | def checkAlnIndex(aln):
  function getAlnHeaderIntersection (line 191) | def getAlnHeaderIntersection(aln, headers):
  function estimate_read_lengths (line 197) | def estimate_read_lengths(aln, set_of_blobs):
  function checkBam (line 205) | def checkBam(aln, set_of_blobs):
  function parseBam (line 218) | def parseBam(infile, set_of_blobs, estimate_cov):
  function estimate_coverage (line 229) | def estimate_coverage(aln, set_of_blobs):
  function check_mapped_read (line 241) | def check_mapped_read(read):
  function calculate_coverage (line 246) | def calculate_coverage(aln, reads_mapped, set_of_blobs):
  function write_read_pair_seqs (line 262) | def write_read_pair_seqs(pair_count_by_type, seqs_by_type, out_fs_by_type):
  function get_read_pair_fasta (line 284) | def get_read_pair_fasta(read, read_format):
  function init_read_pairs (line 298) | def init_read_pairs(outfile, include_unmapped, noninterleaved, include, ...
  function print_bam (line 321) | def print_bam(read_pair_out_fs, read_pair_type, read1, read2):
  function read_pair_generator (line 326) | def read_pair_generator(aln, region_string=None):
  function parseBamForFilter (line 348) | def parseBamForFilter(infile, include_unmapped, noninterleaved, outfile,...
  function get_table (line 393) | def get_table(table):
  function parseCovFromHeader (line 401) | def parseCovFromHeader(fasta_type, header):
  function parseCov (line 427) | def parseCov(infile, set_of_blobs):
  function checkCas (line 465) | def checkCas(infile):
  function parseCas (line 485) | def parseCas(infile, order_of_blobs):
  function readTax (line 512) | def readTax(infile, set_of_blobs):
  function getOutFile (line 549) | def getOutFile(base_file, prefix, suffix):
  function parseNodesDB (line 563) | def parseNodesDB(**kwargs):
  function readNamesNodes (line 623) | def readNamesNodes(names_f, nodes_f):
  function readNodesDB (line 643) | def readNodesDB(nodesDB_f):
  function writeNodesDB (line 658) | def writeNodesDB(nodesDB, nodesDB_f):
  function byteify (line 668) | def byteify(input):
  function writeJsonGzip (line 683) | def writeJsonGzip(obj, outfile):
  function writeJson (line 689) | def writeJson(obj, outfile, indent=0, separators=(',', ': ')):
  function parseJsonGzip (line 699) | def parseJsonGzip(infile):
  function parseJson (line 708) | def parseJson(infile):
  function readYaml (line 740) | def readYaml(infile):

FILE: lib/BtLog.py
  function error (line 12) | def error(message, *argv):

FILE: lib/BtPlot.py
  function n50 (line 34) | def n50(list_of_lengths):
  function getSortedGroups (line 49) | def getSortedGroups(data_dict, sort_order, sort_first=()):
  function generateColourDict (line 77) | def generateColourDict(colour_groups, groups):
  function set_canvas (line 97) | def set_canvas():
  function set_format_scatterplot (line 107) | def set_format_scatterplot(axScatter, **kwargs):
  function set_format_hist_x (line 136) | def set_format_hist_x(axHistx, axScatter):
  function set_format_hist_y (line 148) | def set_format_hist_y(axHisty, axScatter):
  function get_ref_label (line 158) | def get_ref_label(max_length, max_marker_size, fraction):
  function plot_ref_legend (line 164) | def plot_ref_legend(axScatter, max_length, max_marker_size, ignore_conti...
  function plot_legend (line 175) | def plot_legend(fig, axLegend, out_f, legend_flag, format, cumulative_fl...
  function check_input (line 184) | def check_input(args):
  class PlotObj (line 219) | class PlotObj():
    method __init__ (line 220) | def __init__(self, data_dict, cov_lib_dict, cov_lib_selection, plot_ty...
    method subselect_cov_libs (line 253) | def subselect_cov_libs(self, cov_lib_dict, cov_lib_selection):
    method get_cov_libs_total_reads_dict (line 279) | def get_cov_libs_total_reads_dict(self, cov_lib_dict):
    method get_cov_libs_mapped_reads_dict (line 282) | def get_cov_libs_mapped_reads_dict(self, cov_lib_dict):
    method get_stats_for_group (line 285) | def get_stats_for_group(self, group):
    method write_stats (line 304) | def write_stats(self, out_f):
    method compute_stats (line 342) | def compute_stats(self):
    method relabel_and_colour (line 392) | def relabel_and_colour(self, colour_dict, user_labels):
    method setupPlot (line 453) | def setupPlot(self, plot):
    method plotBar (line 543) | def plotBar(self, cov_lib, out_f):
    method plotScatter (line 594) | def plotScatter(self, cov_lib, info_flag, out_f):

FILE: lib/BtTax.py
  function noHit (line 12) | def noHit():
  function getTreeList (line 15) | def getTreeList(taxIds, nodesDB):
  function getLineages (line 32) | def getLineages(tree_lists, nodesDB):
  function taxRuleBestSum (line 50) | def taxRuleBestSum(taxDict, taxonomy, min_bitscore, min_bitscore_diff, t...
  function taxRuleBestSumOrder (line 75) | def taxRuleBestSumOrder(taxDict, taxonomy, min_bitscore, min_bitscore_di...
  function taxRule (line 100) | def taxRule(taxrule, hits, lineages, min_score, min_bitscore_diff, tax_c...
  function getTaxDict (line 111) | def getTaxDict(hits, lineages):

FILE: lib/bamfilter.py
  function main (line 32) | def main():

FILE: lib/blobplot.py
  function main (line 72) | def main():

FILE: lib/covplot.py
  function main (line 78) | def main():

FILE: lib/create.py
  function main (line 56) | def main():

FILE: lib/interface.py
  function main (line 49) | def main():

FILE: lib/map2cov.py
  function main (line 25) | def main():

FILE: lib/nodesdb.py
  function main (line 20) | def main():

FILE: lib/seqfilter.py
  function main (line 23) | def main():

FILE: lib/taxify.py
  function main (line 42) | def main():

FILE: lib/view.py
  function main (line 38) | def main():