SYMBOL INDEX (336 symbols across 50 files)

FILE: build/lib/wgdi/align_dotplot.py
  class align_dotplot (line 7) | class align_dotplot:
    method __init__ (line 8) | def __init__(self, options):
    method pair_position (line 26) | def pair_position(self, alignment, loc1, loc2, colors):
    method run (line 35) | def run(self):
    method process_ancestor (line 93) | def process_ancestor(self, ancestor_file, lens_index):
    method process_blockinfo (line 101) | def process_blockinfo(self, lens1, lens2):
    method alignment (line 111) | def alignment(self, gff1, gff2, bkinfo):
    method create_block_dataframe (line 140) | def create_block_dataframe(self, row):
    method ancestor_position (line 150) | def ancestor_position(self, ax, gff, lens, mark):

FILE: build/lib/wgdi/ancestral_karyotype.py
  class ancestral_karyotype (line 6) | class ancestral_karyotype:
    method __init__ (line 7) | def __init__(self, options):
    method run (line 15) | def run(self):

FILE: build/lib/wgdi/ancestral_karyotype_repertoire.py
  class ancestral_karyotype_repertoire (line 8) | class ancestral_karyotype_repertoire():
    method __init__ (line 9) | def __init__(self, options):
    method run (line 19) | def run(self):

FILE: build/lib/wgdi/base.py
  function gen_md5_id (line 15) | def gen_md5_id(item):
  function config (line 20) | def config():
  function load_conf (line 27) | def load_conf(file, section):
  function rewrite (line 34) | def rewrite(file, section):
  function read_colinearscan (line 48) | def read_colinearscan(file):
  function read_mcscanx (line 74) | def read_mcscanx(fn):
  function read_jcvi (line 100) | def read_jcvi(fn):
  function read_collinearity (line 120) | def read_collinearity(fn):
  function read_ks (line 144) | def read_ks(file, col):
  function get_median (line 154) | def get_median(data):
  function cds_to_pep (line 163) | def cds_to_pep(cds_file, pep_file, fmt='fasta'):
  function newblast (line 172) | def newblast(file, score, evalue, gene_loc1, gene_loc2, reverse):
  function newgff (line 186) | def newgff(file):
  function newlens (line 198) | def newlens(file, position):
  function read_classification (line 209) | def read_classification(file):
  function gene_location (line 220) | def gene_location(gff, lens, step, position):
  function dotplot_frame (line 233) | def dotplot_frame(fig, ax, lens1, lens2, step1, step2, genome1_name, gen...
  function Bezier3 (line 259) | def Bezier3(plist, t):
  function Bezier4 (line 265) | def Bezier4(plist, t):
  function Rectangle (line 271) | def Rectangle(ax, loc, height, width, color, alpha):
  function str_to_bool (line 276) | def str_to_bool(s):

FILE: build/lib/wgdi/block_correspondence.py
  class block_correspondence (line 6) | class block_correspondence():
    method __init__ (line 7) | def __init__(self, options):
    method run (line 28) | def run(self):
    method preprocess_blockinfo (line 50) | def preprocess_blockinfo(self, bkinfo, lens1, lens2):
    method initialize_correspondence (line 66) | def initialize_correspondence(self, lens1, lens2):
    method remove_tandem (line 79) | def remove_tandem(self, bkinfo):
    method remove_ks_hit (line 88) | def remove_ks_hit(self, bkinfo):
    method get_ks_value (line 97) | def get_ks_value(self, ks_str):
    method collinearity_region (line 103) | def collinearity_region(self, cor, bkinfo, lens):
    method is_valid_homo (line 124) | def is_valid_homo(self, row):

FILE: build/lib/wgdi/block_info.py
  class block_info (line 6) | class block_info:
    method __init__ (line 7) | def __init__(self, options):
    method block_position (line 18) | def block_position(self, collinearity, blast, gff1, gff2, ks):
    method get_ks_value (line 77) | def get_ks_value(self, ks, k):
    method calculate_ks_statistics (line 87) | def calculate_ks_statistics(self, blk_ks):
    method calculate_homo_statistics (line 96) | def calculate_homo_statistics(self, blk_homo):
    method blast_homo (line 102) | def blast_homo(self, blast, gff1, gff2, repeat_number):
    method tandem_ratio (line 122) | def tandem_ratio(self, blast, gff2, block):
    method run (line 136) | def run(self):
    method auto_file (line 167) | def auto_file(self, gff1, gff2):
    method process_mcscanx (line 182) | def process_mcscanx(self, gff1, gff2):
    method process_jcvi (line 194) | def process_jcvi(self, gff1, gff2):

FILE: build/lib/wgdi/block_ks.py
  class block_ks (line 8) | class block_ks:
    method __init__ (line 9) | def __init__(self, options):
    method block_position (line 34) | def block_position(self, bkinfo, lens1, lens2, step1, step2):
    method remove_tandem (line 62) | def remove_tandem(self, bkinfo):
    method run (line 75) | def run(self):

FILE: build/lib/wgdi/circos.py
  class circos (line 13) | class circos():
    method __init__ (line 14) | def __init__(self, options):
    method plot_circle (line 31) | def plot_circle(self, loc_chr, radius, color='black', lw=1, alpha=1, l...
    method plot_labels (line 39) | def plot_labels(self, root, labels, loc_chr, radius, horizontalalignme...
    method Wedge (line 51) | def Wedge(self, ax, loc, radius, start, end, width, color, alpha):
    method plot_bar (line 56) | def plot_bar(self, df, radius, length, lw, color, alpha):
    method chr_location (line 75) | def chr_location(self, lens, angle_gap, angle):
    method deal_alignment (line 83) | def deal_alignment(self, alignment, gff, lens, loc_chr, angle):
    method deal_ancestor (line 105) | def deal_ancestor(self, alignment, gff, lens, loc_chr, angle, al):
    method plot_collinearity (line 133) | def plot_collinearity(self, data, radius, lw=0.02, alpha=1):
    method plot_legend (line 153) | def plot_legend(self, ax, chr_color, width, height):
    method run (line 169) | def run(self):

FILE: build/lib/wgdi/collinearity.py
  class collinearity (line 5) | class collinearity:
    method __init__ (line 6) | def __init__(self, options, points):
    method get_matrix (line 30) | def get_matrix(self):
    method run (line 42) | def run(self):
    method score_matrix (line 72) | def score_matrix(self):
    method max_path (line 117) | def max_path(self, points):
    method p_value_estimated (line 146) | def p_value_estimated(self, gap, L1, L2):

FILE: build/lib/wgdi/dotplot.py
  class dotplot (line 10) | class dotplot():
    method __init__ (line 11) | def __init__(self, options):
    method pair_positon (line 31) | def pair_positon(self, blast, gff1, gff2, rednum, repeat_number):
    method run (line 58) | def run(self):
    method ancestor_posion (line 122) | def ancestor_posion(self, ax, gff, lens, mark):

FILE: build/lib/wgdi/fusion_positions_database.py
  class fusion_positions_database (line 5) | class fusion_positions_database:
    method __init__ (line 6) | def __init__(self, options):
    method run (line 11) | def run(self):

FILE: build/lib/wgdi/fusions_detection.py
  class fusions_detection (line 4) | class fusions_detection:
    method __init__ (line 5) | def __init__(self, options):
    method run (line 14) | def run(self):
    method count_non_overlapping (line 45) | def count_non_overlapping(self, group):

FILE: build/lib/wgdi/karyotype.py
  class karyotype (line 7) | class karyotype():
    method __init__ (line 8) | def __init__(self, options):
    method run (line 22) | def run(self):

FILE: build/lib/wgdi/karyotype_mapping.py
  class karyotype_mapping (line 7) | class karyotype_mapping:
    method __init__ (line 8) | def __init__(self, options):
    method karyotype_left (line 28) | def karyotype_left(self, pairs, ancestor, gff1, gff2):
    method karyotype_top (line 44) | def karyotype_top(self, pairs, ancestor, gff1, gff2):
    method karyotype_map (line 60) | def karyotype_map(self, gff, lens):
    method colinear_gene_pairs (line 91) | def colinear_gene_pairs(self, bkinfo, gff1, gff2):
    method new_ancestor (line 109) | def new_ancestor(self, ancestor, gff1, gff2, blast):
    method run (line 169) | def run(self):

FILE: build/lib/wgdi/ks.py
  class ks (line 11) | class ks:
    method __init__ (line 12) | def __init__(self, options):
    method auto_file (line 26) | def auto_file(self):
    method run (line 57) | def run(self):
    method pair_kaks (line 127) | def pair_kaks(self, k):
    method align (line 143) | def align(self):
    method pal2nal (line 158) | def pal2nal(self):
    method run_yn00 (line 167) | def run_yn00(self):

FILE: build/lib/wgdi/ks_peaks.py
  class kspeaks (line 8) | class kspeaks:
    method __init__ (line 9) | def __init__(self, options):
    method remove_tandem (line 32) | def remove_tandem(self, bkinfo):
    method ks_kde (line 46) | def ks_kde(self, df):
    method run (line 77) | def run(self):

FILE: build/lib/wgdi/ksfigure.py
  class ksfigure (line 11) | class ksfigure():
    method __init__ (line 12) | def __init__(self, options):
    method Gaussian_distribution (line 32) | def Gaussian_distribution(self, t, k):
    method run (line 45) | def run(self):

FILE: build/lib/wgdi/peaksfit.py
  class peaksfit (line 13) | class peaksfit():
    method __init__ (line 14) | def __init__(self, options):
    method ks_values (line 29) | def ks_values(self, df):
    method gaussian_fuc (line 40) | def gaussian_fuc(self, x, *params):
    method kde_fit (line 49) | def kde_fit(self, data, x):
    method run (line 67) | def run(self):

FILE: build/lib/wgdi/pindex.py
  class pindex (line 9) | class pindex():
    method __init__ (line 10) | def __init__(self, options):
    method Pindex (line 23) | def Pindex(self, sub1, sub2):
    method retain (line 42) | def retain(self, arr):
    method run (line 56) | def run(self):
    method cal_pindex (line 70) | def cal_pindex(self, alignment):
    method turn_percentage (line 100) | def turn_percentage(self, x):
    method infomation (line 103) | def infomation(self, df):

FILE: build/lib/wgdi/polyploidy_classification.py
  class polyploidy_classification (line 5) | class polyploidy_classification:
    method __init__ (line 6) | def __init__(self, options):
    method run (line 19) | def run(self):

FILE: build/lib/wgdi/retain.py
  class retain (line 5) | class retain:
    method __init__ (line 6) | def __init__(self, options):
    method run (line 21) | def run(self):
    method align_chr (line 91) | def align_chr(self, alignment):
    method moving_average (line 108) | def moving_average(self, arr):

FILE: build/lib/wgdi/run.py
  function run_subprogram (line 73) | def run_subprogram(program, conf, name):
  function run_configure (line 79) | def run_configure():
  function module_to_run (line 83) | def module_to_run(argument, conf):
  function main (line 119) | def main():

FILE: build/lib/wgdi/run_colliearity.py
  class mycollinearity (line 13) | class mycollinearity():
    method __init__ (line 14) | def __init__(self, options):
    method deal_blast_for_chromosomes (line 42) | def deal_blast_for_chromosomes(self, blast, rednum, repeat_number):
    method deal_blast_for_genomes (line 59) | def deal_blast_for_genomes(self, blast, rednum, repeat_number):
    method run (line 88) | def run(self):
    method single_pool (line 158) | def single_pool(self, group, gff1, gff2, lens1, lens2):

FILE: build/lib/wgdi/shared_fusion.py
  class shared_fusion (line 4) | class shared_fusion:
    method __init__ (line 5) | def __init__(self, options):
    method run (line 18) | def run(self):
    method block_fusions (line 62) | def block_fusions(self, bkinfo, ancestor_left, ancestor_top):

FILE: build/lib/wgdi/trees.py
  class trees (line 13) | class trees():
    method __init__ (line 14) | def __init__(self, options):
    method grouping (line 36) | def grouping(self, alignment):
    method codon (line 85) | def codon(self):
    method pal2nal (line 105) | def pal2nal(self):
    method align (line 115) | def align(self):
    method trimal (line 130) | def trimal(self):
    method divvier (line 140) | def divvier(self):
    method buildtrees (line 150) | def buildtrees(self):
    method run (line 174) | def run(self):

FILE: wgdi/align_dotplot.py
  class align_dotplot (line 7) | class align_dotplot:
    method __init__ (line 8) | def __init__(self, options):
    method pair_position (line 26) | def pair_position(self, alignment, loc1, loc2, colors):
    method run (line 35) | def run(self):
    method process_ancestor (line 93) | def process_ancestor(self, ancestor_file, lens_index):
    method process_blockinfo (line 101) | def process_blockinfo(self, lens1, lens2):
    method alignment (line 111) | def alignment(self, gff1, gff2, bkinfo):
    method create_block_dataframe (line 140) | def create_block_dataframe(self, row):
    method ancestor_position (line 150) | def ancestor_position(self, ax, gff, lens, mark):

FILE: wgdi/ancestral_karyotype.py
  class ancestral_karyotype (line 6) | class ancestral_karyotype:
    method __init__ (line 7) | def __init__(self, options):
    method run (line 15) | def run(self):

FILE: wgdi/ancestral_karyotype_repertoire.py
  class ancestral_karyotype_repertoire (line 8) | class ancestral_karyotype_repertoire():
    method __init__ (line 9) | def __init__(self, options):
    method run (line 19) | def run(self):

FILE: wgdi/base.py
  function gen_md5_id (line 15) | def gen_md5_id(item):
  function config (line 20) | def config():
  function load_conf (line 27) | def load_conf(file, section):
  function rewrite (line 34) | def rewrite(file, section):
  function read_colinearscan (line 48) | def read_colinearscan(file):
  function read_mcscanx (line 74) | def read_mcscanx(fn):
  function read_jcvi (line 100) | def read_jcvi(fn):
  function read_collinearity (line 120) | def read_collinearity(fn):
  function read_ks (line 144) | def read_ks(file, col):
  function get_median (line 154) | def get_median(data):
  function cds_to_pep (line 163) | def cds_to_pep(cds_file, pep_file, fmt='fasta'):
  function newblast (line 172) | def newblast(file, score, evalue, gene_loc1, gene_loc2, reverse):
  function newgff (line 186) | def newgff(file):
  function newlens (line 198) | def newlens(file, position):
  function read_classification (line 209) | def read_classification(file):
  function gene_location (line 220) | def gene_location(gff, lens, step, position):
  function dotplot_frame (line 233) | def dotplot_frame(fig, ax, lens1, lens2, step1, step2, genome1_name, gen...
  function Bezier3 (line 259) | def Bezier3(plist, t):
  function Bezier4 (line 265) | def Bezier4(plist, t):
  function Rectangle (line 271) | def Rectangle(ax, loc, height, width, color, alpha):
  function str_to_bool (line 276) | def str_to_bool(s):

FILE: wgdi/block_correspondence.py
  class block_correspondence (line 6) | class block_correspondence():
    method __init__ (line 7) | def __init__(self, options):
    method run (line 28) | def run(self):
    method preprocess_blockinfo (line 50) | def preprocess_blockinfo(self, bkinfo, lens1, lens2):
    method initialize_correspondence (line 66) | def initialize_correspondence(self, lens1, lens2):
    method remove_tandem (line 79) | def remove_tandem(self, bkinfo):
    method remove_ks_hit (line 88) | def remove_ks_hit(self, bkinfo):
    method get_ks_value (line 97) | def get_ks_value(self, ks_str):
    method collinearity_region (line 103) | def collinearity_region(self, cor, bkinfo, lens):
    method is_valid_homo (line 124) | def is_valid_homo(self, row):

FILE: wgdi/block_info.py
  class block_info (line 6) | class block_info:
    method __init__ (line 7) | def __init__(self, options):
    method block_position (line 18) | def block_position(self, collinearity, blast, gff1, gff2, ks):
    method get_ks_value (line 77) | def get_ks_value(self, ks, k):
    method calculate_ks_statistics (line 87) | def calculate_ks_statistics(self, blk_ks):
    method calculate_homo_statistics (line 96) | def calculate_homo_statistics(self, blk_homo):
    method blast_homo (line 102) | def blast_homo(self, blast, gff1, gff2, repeat_number):
    method tandem_ratio (line 122) | def tandem_ratio(self, blast, gff2, block):
    method run (line 136) | def run(self):
    method auto_file (line 167) | def auto_file(self, gff1, gff2):
    method process_mcscanx (line 182) | def process_mcscanx(self, gff1, gff2):
    method process_jcvi (line 194) | def process_jcvi(self, gff1, gff2):

FILE: wgdi/block_ks.py
  class block_ks (line 8) | class block_ks:
    method __init__ (line 9) | def __init__(self, options):
    method block_position (line 34) | def block_position(self, bkinfo, lens1, lens2, step1, step2):
    method remove_tandem (line 62) | def remove_tandem(self, bkinfo):
    method run (line 75) | def run(self):

FILE: wgdi/circos.py
  class circos (line 13) | class circos():
    method __init__ (line 14) | def __init__(self, options):
    method plot_circle (line 31) | def plot_circle(self, loc_chr, radius, color='black', lw=1, alpha=1, l...
    method plot_labels (line 39) | def plot_labels(self, root, labels, loc_chr, radius, horizontalalignme...
    method Wedge (line 51) | def Wedge(self, ax, loc, radius, start, end, width, color, alpha):
    method plot_bar (line 56) | def plot_bar(self, df, radius, length, lw, color, alpha):
    method chr_location (line 75) | def chr_location(self, lens, angle_gap, angle):
    method deal_alignment (line 83) | def deal_alignment(self, alignment, gff, lens, loc_chr, angle):
    method deal_ancestor (line 105) | def deal_ancestor(self, alignment, gff, lens, loc_chr, angle, al):
    method plot_collinearity (line 133) | def plot_collinearity(self, data, radius, lw=0.02, alpha=1):
    method plot_legend (line 153) | def plot_legend(self, ax, chr_color, width, height):
    method run (line 169) | def run(self):

FILE: wgdi/collinearity.py
  class collinearity (line 5) | class collinearity:
    method __init__ (line 6) | def __init__(self, options, points):
    method get_matrix (line 30) | def get_matrix(self):
    method run (line 42) | def run(self):
    method score_matrix (line 72) | def score_matrix(self):
    method max_path (line 117) | def max_path(self, points):
    method p_value_estimated (line 146) | def p_value_estimated(self, gap, L1, L2):

FILE: wgdi/dotplot.py
  class dotplot (line 10) | class dotplot():
    method __init__ (line 11) | def __init__(self, options):
    method pair_positon (line 31) | def pair_positon(self, blast, gff1, gff2, rednum, repeat_number):
    method run (line 58) | def run(self):
    method ancestor_posion (line 122) | def ancestor_posion(self, ax, gff, lens, mark):

FILE: wgdi/fusion_positions_database.py
  class fusion_positions_database (line 5) | class fusion_positions_database:
    method __init__ (line 6) | def __init__(self, options):
    method run (line 11) | def run(self):

FILE: wgdi/fusions_detection.py
  class fusions_detection (line 4) | class fusions_detection:
    method __init__ (line 5) | def __init__(self, options):
    method run (line 14) | def run(self):
    method count_non_overlapping (line 45) | def count_non_overlapping(self, group):

FILE: wgdi/karyotype.py
  class karyotype (line 7) | class karyotype():
    method __init__ (line 8) | def __init__(self, options):
    method run (line 22) | def run(self):

FILE: wgdi/karyotype_mapping.py
  class karyotype_mapping (line 7) | class karyotype_mapping:
    method __init__ (line 8) | def __init__(self, options):
    method karyotype_left (line 28) | def karyotype_left(self, pairs, ancestor, gff1, gff2):
    method karyotype_top (line 44) | def karyotype_top(self, pairs, ancestor, gff1, gff2):
    method karyotype_map (line 60) | def karyotype_map(self, gff, lens):
    method colinear_gene_pairs (line 91) | def colinear_gene_pairs(self, bkinfo, gff1, gff2):
    method new_ancestor (line 109) | def new_ancestor(self, ancestor, gff1, gff2, blast):
    method run (line 169) | def run(self):

FILE: wgdi/ks.py
  class ks (line 11) | class ks:
    method __init__ (line 12) | def __init__(self, options):
    method auto_file (line 26) | def auto_file(self):
    method run (line 57) | def run(self):
    method pair_kaks (line 127) | def pair_kaks(self, k):
    method align (line 143) | def align(self):
    method pal2nal (line 158) | def pal2nal(self):
    method run_yn00 (line 167) | def run_yn00(self):

FILE: wgdi/ks_peaks.py
  class kspeaks (line 8) | class kspeaks:
    method __init__ (line 9) | def __init__(self, options):
    method remove_tandem (line 32) | def remove_tandem(self, bkinfo):
    method ks_kde (line 46) | def ks_kde(self, df):
    method run (line 77) | def run(self):

FILE: wgdi/ksfigure.py
  class ksfigure (line 11) | class ksfigure():
    method __init__ (line 12) | def __init__(self, options):
    method Gaussian_distribution (line 32) | def Gaussian_distribution(self, t, k):
    method run (line 45) | def run(self):

FILE: wgdi/peaksfit.py
  class peaksfit (line 13) | class peaksfit():
    method __init__ (line 14) | def __init__(self, options):
    method ks_values (line 29) | def ks_values(self, df):
    method gaussian_fuc (line 40) | def gaussian_fuc(self, x, *params):
    method kde_fit (line 49) | def kde_fit(self, data, x):
    method run (line 67) | def run(self):

FILE: wgdi/pindex.py
  class pindex (line 9) | class pindex():
    method __init__ (line 10) | def __init__(self, options):
    method Pindex (line 23) | def Pindex(self, sub1, sub2):
    method retain (line 42) | def retain(self, arr):
    method run (line 56) | def run(self):
    method cal_pindex (line 70) | def cal_pindex(self, alignment):
    method turn_percentage (line 100) | def turn_percentage(self, x):
    method infomation (line 103) | def infomation(self, df):

FILE: wgdi/polyploidy_classification.py
  class polyploidy_classification (line 5) | class polyploidy_classification:
    method __init__ (line 6) | def __init__(self, options):
    method run (line 19) | def run(self):

FILE: wgdi/retain.py
  class retain (line 5) | class retain:
    method __init__ (line 6) | def __init__(self, options):
    method run (line 21) | def run(self):
    method align_chr (line 91) | def align_chr(self, alignment):
    method moving_average (line 108) | def moving_average(self, arr):

FILE: wgdi/run.py
  function run_subprogram (line 73) | def run_subprogram(program, conf, name):
  function run_configure (line 79) | def run_configure():
  function module_to_run (line 83) | def module_to_run(argument, conf):
  function main (line 119) | def main():

FILE: wgdi/run_colliearity.py
  class mycollinearity (line 13) | class mycollinearity():
    method __init__ (line 14) | def __init__(self, options):
    method deal_blast_for_chromosomes (line 42) | def deal_blast_for_chromosomes(self, blast, rednum, repeat_number):
    method deal_blast_for_genomes (line 59) | def deal_blast_for_genomes(self, blast, rednum, repeat_number):
    method run (line 88) | def run(self):
    method single_pool (line 158) | def single_pool(self, group, gff1, gff2, lens1, lens2):

FILE: wgdi/shared_fusion.py
  class shared_fusion (line 4) | class shared_fusion:
    method __init__ (line 5) | def __init__(self, options):
    method run (line 18) | def run(self):
    method block_fusions (line 62) | def block_fusions(self, bkinfo, ancestor_left, ancestor_top):

FILE: wgdi/trees.py
  class trees (line 13) | class trees():
    method __init__ (line 14) | def __init__(self, options):
    method grouping (line 36) | def grouping(self, alignment):
    method codon (line 85) | def codon(self):
    method pal2nal (line 105) | def pal2nal(self):
    method align (line 115) | def align(self):
    method trimal (line 130) | def trimal(self):
    method divvier (line 140) | def divvier(self):
    method buildtrees (line 150) | def buildtrees(self):
    method run (line 174) | def run(self):