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A
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B
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C
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D
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E
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F
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G
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I
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L
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M
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N
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P
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Q
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R
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S
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T
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U
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W
A
add_errors() (in module wub.simulate.seq)
aligned_pairs_to_matches() (in module wub.bam.compare)
alignment_stats() (in module wub.util.seq)
args_string_to_dict() (in module wub.util.parse)
B
bam_compare() (in module wub.bam.compare)
base_complement() (in module wub.util.seq)
base_composition() (in module wub.util.seq)
C
calc_consistency_score() (in module wub.bam.compare)
check_lastdb_files() (in module wub.mappers.lastal)
chrom (wub.simulate.genome.Fragment attribute)
cigar (wub.simulate.seq.MutatedSeq attribute)
cigar_list_to_string() (in module wub.simulate.seq)
clean_lastdb_files() (in module wub.mappers.lastal)
cleanup_dnadiff_report() (in module wub.wrappers.dnadiff)
close() (wub.bam.sam_writer.SamWriter method)
(wub.vis.report.Report method)
compare_alignments() (in module wub.bam.compare)
compare_genomes_lastal() (in module wub.mappers.lastal)
compress_raw_cigar_list() (in module wub.simulate.seq)
count_clipped() (in module wub.bam.compare)
count_reads() (in module wub.bam.read_counter)
count_reads_realtime() (in module wub.bam.read_counter)
count_records() (in module wub.util.seq)
D
dna_record_to_rna() (in module wub.util.seq)
dnadiff() (in module wub.wrappers.dnadiff)
E
end (wub.simulate.genome.Fragment attribute)
ensure_executable() (in module wub.util.cmd)
error_and_read_stats() (in module wub.bam.stats)
ExampleTest (class in wub.tests.test_example)
F
filter_query_coverage() (in module wub.bam.filter)
filter_ref_coverage() (in module wub.bam.filter)
filter_top_per_query() (in module wub.bam.filter)
(in module wub.mappers.lastal)
find_executable() (in module wub.util.cmd)
frag_coverage() (in module wub.bam.stats)
Fragment (class in wub.simulate.genome)
G
gc_content() (in module wub.util.seq)
GC_per_read() (in module wub.read_stats.contig_stats)
get_alignment_score() (in module wub.bam.filter)
get_extension() (in module wub.util.misc)
get_fname() (in module wub.util.misc)
get_hard_clip_offset() (in module wub.bam.compare)
get_stats() (in module wub.read_stats.contig_stats)
I
interval_string_to_tuples() (in module wub.util.parse)
is_coarse_match() (in module wub.bam.compare)
L
L50() (in module wub.read_stats.contig_stats)
lastal_align() (in module wub.mappers.lastal)
lastdb() (in module wub.mappers.lastal)
LastRecord (class in wub.mappers.lastal)
M
mean_qscore() (in module wub.util.seq)
mkdir() (in module wub.util.misc)
mock_qualities() (in module wub.util.seq)
MutatedSeq (class in wub.simulate.seq)
N
N50() (in module wub.read_stats.contig_stats)
new_dna_record() (in module wub.util.seq)
new_sam_record() (wub.bam.sam_writer.SamWriter method)
normalise_array() (in module wub.util.parse)
P
parse_coords() (in module wub.parsers.blastn)
(in module wub.parsers.mummer)
parse_dnadiff_report() (in module wub.wrappers.dnadiff)
parse_lastal() (in module wub.mappers.lastal)
phred_to_prob() (in module wub.util.seq)
pickle_dump() (in module wub.util.misc)
pickle_load() (in module wub.util.misc)
pileup_stats() (in module wub.bam.stats)
plot_arrays() (wub.vis.report.Report method)
plot_bars_simple() (wub.vis.report.Report method)
plot_boxplots() (wub.vis.report.Report method)
plot_dicts() (wub.vis.report.Report method)
plot_heatmap() (wub.vis.report.Report method)
plot_histograms() (wub.vis.report.Report method)
plot_line() (wub.vis.report.Report method)
plot_pcolor() (wub.vis.report.Report method)
plot_scatter() (wub.vis.report.Report method)
prob_to_phred() (in module wub.util.seq)
Property (class in wub.wrappers.dnadiff)
PropertyWithPerc (class in wub.wrappers.dnadiff)
pysam_open() (in module wub.bam.common)
Q
q_aln (wub.mappers.lastal.LastRecord attribute)
q_aln_len (wub.mappers.lastal.LastRecord attribute)
q_len (wub.mappers.lastal.LastRecord attribute)
q_name (wub.mappers.lastal.LastRecord attribute)
q_start (wub.mappers.lastal.LastRecord attribute)
q_strand (wub.mappers.lastal.LastRecord attribute)
quality_array_to_string() (in module wub.util.seq)
quality_string_to_array() (in module wub.util.seq)
query (wub.wrappers.dnadiff.Property attribute)
(wub.wrappers.dnadiff.PropertyWithPerc attribute)
query_perc (wub.wrappers.dnadiff.PropertyWithPerc attribute)
R
r_aln (wub.mappers.lastal.LastRecord attribute)
r_aln_len (wub.mappers.lastal.LastRecord attribute)
r_len (wub.mappers.lastal.LastRecord attribute)
r_name (wub.mappers.lastal.LastRecord attribute)
r_start (wub.mappers.lastal.LastRecord attribute)
r_strand (wub.mappers.lastal.LastRecord attribute)
random_base() (in module wub.simulate.seq)
random_base_except() (in module wub.simulate.seq)
read_alignment() (in module wub.util.seq)
read_seq_records() (in module wub.util.seq)
read_seq_records_dict() (in module wub.util.seq)
read_stats() (in module wub.bam.stats)
readfast() (in module wub.read_stats.contig_stats)
real_del (wub.simulate.seq.MutatedSeq attribute)
real_ins (wub.simulate.seq.MutatedSeq attribute)
real_qual (wub.simulate.seq.MutatedSeq attribute)
real_subst (wub.simulate.seq.MutatedSeq attribute)
record_lengths() (in module wub.util.seq)
ref (wub.wrappers.dnadiff.Property attribute)
(wub.wrappers.dnadiff.PropertyWithPerc attribute)
ref_perc (wub.wrappers.dnadiff.PropertyWithPerc attribute)
Report (class in wub.vis.report)
reverse_complement() (in module wub.util.seq)
rna_record_to_dna() (in module wub.util.seq)
S
sample_chromosome() (in module wub.simulate.genome)
sample_direction() (in module wub.simulate.seq)
sample_error_type() (in module wub.simulate.seq)
sample_truncated_gamma() (in module wub.simulate.dist)
SamWriter (class in wub.bam.sam_writer)
score (wub.mappers.lastal.LastRecord attribute)
separated_list_to_floats() (in module wub.util.parse)
seq (wub.simulate.genome.Fragment attribute)
(wub.simulate.seq.MutatedSeq attribute)
setUp() (wub.tests.test_example.ExampleTest method)
(wub.tests.test_mappers_lastal.TestMappersLastal method)
simulate_fragment() (in module wub.simulate.genome)
simulate_fragments() (in module wub.simulate.genome)
simulate_genome() (in module wub.simulate.genome)
simulate_sequence() (in module wub.simulate.seq)
simulate_sequencing_errors() (in module wub.simulate.seq)
start (wub.simulate.genome.Fragment attribute)
stats_from_aligned_read() (in module wub.bam.stats)
T
tearDown() (wub.tests.test_example.ExampleTest method)
(wub.tests.test_mappers_lastal.TestMappersLastal method)
test_add_errors() (wub.tests.test_simulate_seq.TestSimulateSeq method)
test_alignment_stats() (wub.tests.test_util_seq.TestUtilSeq method)
test_args_string_to_dict() (wub.tests.test_util_parse.TestUtilParse method)
test_args_string_to_dict_empty() (wub.tests.test_util_parse.TestUtilParse method)
test_bam_read_counter() (wub.tests.test_bam_compare.TestBamCompare method)
(wub.tests.test_bam_read_counter.TestBamReadCounter method)
test_cigar_list_to_string() (wub.tests.test_simulate_seq.TestSimulateSeq method)
test_compress_raw_cigar_list() (wub.tests.test_simulate_seq.TestSimulateSeq method)
test_dnadiff() (wub.tests.test_wrappers_dnadiff.TestWrappersDnadiff method)
test_error_and_read_stats() (wub.tests.test_bam_stats.TestBamStats method)
test_fragment_stats() (wub.tests.test_bam_stats.TestBamStats method)
test_lastal_compare_genomes() (wub.tests.test_mappers_lastal.TestMappersLastal method)
test_mean_qscore() (wub.tests.test_util_seq.TestUtilSeq method)
test_mean_qscore_large() (wub.tests.test_util_seq.TestUtilSeq method)
test_mock_qualities() (wub.tests.test_util_seq.TestUtilSeq method)
test_N50() (wub.tests.test_contig_stats.TestContigStats method)
test_new_dna_record() (wub.tests.test_util_seq.TestUtilSeq method)
test_normalise_array() (wub.tests.test_util_parse.TestUtilParse method)
test_nucmer_coord_parse() (wub.tests.test_blastn_coord_parse.TestBlastnCoordParse method)
(wub.tests.test_nucmer_coord_parse.TestNucmerCoordParse method)
test_parse_lastal_difference() (wub.tests.test_mappers_lastal.TestMappersLastal method)
test_parse_lastal_identical() (wub.tests.test_mappers_lastal.TestMappersLastal method)
test_parse_lastal_zero() (wub.tests.test_mappers_lastal.TestMappersLastal method)
test_phred_to_prob() (wub.tests.test_util_seq.TestUtilSeq method)
test_pileup_stats() (wub.tests.test_bam_stats.TestBamStats method)
test_prob_to_phred() (wub.tests.test_util_seq.TestUtilSeq method)
test_prob_to_phred_max() (wub.tests.test_util_seq.TestUtilSeq method)
test_read_stats() (wub.tests.test_bam_stats.TestBamStats method)
test_reverse_complement() (wub.tests.test_util_seq.TestUtilSeq method)
test_separated_list_to_floats() (wub.tests.test_util_parse.TestUtilParse method)
test_simulate_fragment() (wub.tests.test_simulate_genome.TestSimulateGenome method)
test_simulate_fragment_edge() (wub.tests.test_simulate_genome.TestSimulateGenome method)
test_simulate_genome() (wub.tests.test_simulate_genome.TestSimulateGenome method)
test_simulate_sequencing_errors() (wub.tests.test_simulate_seq.TestSimulateSeq method)
test_success() (wub.tests.test_example.ExampleTest method)
TestBamCompare (class in wub.tests.test_bam_compare)
TestBamReadCounter (class in wub.tests.test_bam_read_counter)
TestBamStats (class in wub.tests.test_bam_stats)
TestBlastnCoordParse (class in wub.tests.test_blastn_coord_parse)
TestContigStats (class in wub.tests.test_contig_stats)
TestMappersLastal (class in wub.tests.test_mappers_lastal)
TestNucmerCoordParse (class in wub.tests.test_nucmer_coord_parse)
TestSimulateGenome (class in wub.tests.test_simulate_genome)
TestSimulateSeq (class in wub.tests.test_simulate_seq)
TestUtilParse (class in wub.tests.test_util_parse)
TestUtilSeq (class in wub.tests.test_util_seq)
TestWrappersDnadiff (class in wub.tests.test_wrappers_dnadiff)
U
uid (wub.simulate.genome.Fragment attribute)
W
word_composition() (in module wub.util.seq)
write() (wub.bam.sam_writer.SamWriter method)
write_seq_records() (in module wub.util.seq)
wub (module)
wub.bam (module)
wub.bam.common (module)
wub.bam.compare (module)
wub.bam.filter (module)
wub.bam.read_counter (module)
wub.bam.sam_writer (module)
wub.bam.stats (module)
wub.mappers (module)
wub.mappers.lastal (module)
wub.parsers (module)
wub.parsers.blastn (module)
wub.parsers.mummer (module)
wub.read_stats (module)
wub.read_stats.contig_stats (module)
wub.simulate (module)
wub.simulate.dist (module)
wub.simulate.genome (module)
wub.simulate.seq (module)
wub.tests (module)
wub.tests.test_bam_compare (module)
wub.tests.test_bam_read_counter (module)
wub.tests.test_bam_stats (module)
wub.tests.test_blastn_coord_parse (module)
wub.tests.test_contig_stats (module)
wub.tests.test_example (module)
wub.tests.test_mappers_lastal (module)
wub.tests.test_nucmer_coord_parse (module)
wub.tests.test_simulate_genome (module)
wub.tests.test_simulate_seq (module)
wub.tests.test_util_parse (module)
wub.tests.test_util_seq (module)
wub.tests.test_wrappers_dnadiff (module)
wub.util (module)
wub.util.cmd (module)
wub.util.misc (module)
wub.util.parse (module)
wub.util.seq (module)
wub.vis (module)
wub.vis.report (module)
wub.wrappers (module)
wub.wrappers.dnadiff (module)
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