Index

A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z

A

add_argument() (biolite.pipeline.BasePipeline method)
add_openmp() (biolite.wrappers.BaseWrapper method)
add_stage() (biolite.pipeline.BasePipeline method)
(biolite.pipeline.Pipeline method)
add_threading() (biolite.wrappers.BaseWrapper method)
attr (biolite.diagnostics.OutputPattern attribute)
AttributeDict (class in biolite.utils)

B

barplot() (biolite.report.BaseReport method)
BasePipeline (class in biolite.pipeline)
BaseReport (class in biolite.report)
BaseWrapper (class in biolite.wrappers)
biolite.catalog (module)
biolite.config (module)
biolite.database (module)
biolite.diagnostics (module)
biolite.pipeline (module)
biolite.report (module)
biolite.utils (module)
biolite.workflows (module)
biolite.wrappers (module)
bitscore (biolite.workflows.BlastHit attribute)
blast_annotate_seqs() (in module biolite.workflows)
blast_hits() (in module biolite.workflows)
blast_top_hits() (in module biolite.workflows)
BlastHit (class in biolite.workflows)
Blastn (class in biolite.wrappers)
Blastp (class in biolite.wrappers)
Blastx (class in biolite.wrappers)
Bowtie2 (class in biolite.wrappers)
Bowtie2Build (class in biolite.wrappers)
bytes_to_gb() (in module biolite.utils)

C

calculate_rpkms() (in module biolite.workflows)
cat_to_file() (in module biolite.utils)
CatalogRecord (class in biolite.catalog)
check() (biolite.report.BaseReport method)
check_arg() (biolite.wrappers.BaseWrapper method)
check_init() (in module biolite.diagnostics)
checkpoint() (biolite.pipeline.BasePipeline method)
clean_rrna() (in module biolite.workflows)
clean_swissprot() (in module biolite.workflows)
clean_univec() (in module biolite.workflows)
confidence (biolite.workflows.ContigHeader attribute)
(biolite.workflows.rRNAhit attribute)
connect() (in module biolite.database)
contig_stats() (in module biolite.workflows)
ContigHeader (class in biolite.workflows)
CountLines (class in biolite.wrappers)
Coverage (class in biolite.wrappers)

D

definition (biolite.workflows.BlastHit attribute)
die() (in module biolite.utils)
disconnect() (in module biolite.database)
dump() (in module biolite.diagnostics)
dump_all() (in module biolite.diagnostics)
dump_by_id() (in module biolite.diagnostics)
Dustmasker (class in biolite.wrappers)
dustmasker() (in module biolite.workflows)

E

entity (biolite.diagnostics.OutputPattern attribute)
estimate_insert_size() (in module biolite.wrappers)
evalue (biolite.workflows.BlastHit attribute)
Exclude (class in biolite.wrappers)
execute() (in module biolite.database)
exit_profiler() (in module biolite.diagnostics)
extract_arg() (biolite.report.BaseReport method)
extract_oases_exemplars() (in module biolite.workflows)
extraction_id (biolite.catalog.CatalogRecord attribute)

F

failed_executable() (in module biolite.utils)
Fasta2Fastq (class in biolite.wrappers)
Fastq2Fasta (class in biolite.wrappers)
FastQC (class in biolite.wrappers)
Field (class in biolite.report)
filter_coverage_table() (in module biolite.workflows)
FilterIllumina (class in biolite.wrappers)
finish() (biolite.pipeline.Pipeline method)
format (biolite.report.Field attribute)

G

Gblocks (class in biolite.wrappers)
gene (biolite.workflows.rRNAhit attribute)
generator() (biolite.report.BaseReport method)
get() (biolite.pipeline.BasePipeline method)
get_all_files() (biolite.pipeline.Pipeline method)
get_caller_info() (in module biolite.utils)
get_caller_locals() (in module biolite.utils)
get_command() (in module biolite.config)
get_entity() (in module biolite.diagnostics)
get_file() (biolite.pipeline.Pipeline method)
get_resource() (in module biolite.config)
get_run_id() (in module biolite.diagnostics)

H

head() (in module biolite.utils)
head_to_file() (in module biolite.utils)
header() (biolite.report.BaseReport method)
hide_run() (in module biolite.diagnostics)
histogram() (biolite.report.BaseReport method)
histogram_categorical() (biolite.report.BaseReport method)
histogram_overlay() (biolite.report.BaseReport method)

I

id (biolite.catalog.CatalogRecord attribute)
(biolite.workflows.BlastHit attribute)
IlluminaPipeline (class in biolite.pipeline)
import_arguments() (biolite.pipeline.BasePipeline method)
import_module() (biolite.pipeline.BasePipeline method)
import_pipeline() (biolite.pipeline.BasePipeline method)
import_stages() (biolite.pipeline.BasePipeline method)
(biolite.pipeline.IlluminaPipeline method)
info() (in module biolite.utils)
ingest() (biolite.pipeline.BasePipeline method)
init() (biolite.report.BaseReport method)
(biolite.wrappers.BaseWrapper method)
(in module biolite.config)
(in module biolite.diagnostics)
insert() (in module biolite.catalog)
InsertStats (class in biolite.wrappers)
Interleave (class in biolite.wrappers)
itis_id (biolite.catalog.CatalogRecord attribute)

K

key (biolite.report.Field attribute)

L

length (biolite.workflows.BlastHit attribute)
(biolite.workflows.ContigHeader attribute)
library_id (biolite.catalog.CatalogRecord attribute)
library_type (biolite.catalog.CatalogRecord attribute)
lineplot() (biolite.report.BaseReport method)
list_programs() (in module biolite.diagnostics)
list_runs() (in module biolite.diagnostics)
list_stages() (biolite.pipeline.BasePipeline method)
load_cache() (in module biolite.diagnostics)
local_lookup() (in module biolite.diagnostics)
locus (biolite.workflows.ContigHeader attribute)
(biolite.workflows.rRNAhit attribute)
log() (in module biolite.diagnostics)
log_dict() (in module biolite.diagnostics)
log_path() (in module biolite.diagnostics)
log_program_output() (in module biolite.diagnostics)
log_program_version() (in module biolite.diagnostics)
lookup() (biolite.report.BaseReport method)
(in module biolite.diagnostics)
lookup_by_id() (in module biolite.diagnostics)
lookup_entities() (in module biolite.diagnostics)
lookup_like() (in module biolite.diagnostics)
lookup_prev_run() (in module biolite.diagnostics)
lookup_run() (in module biolite.diagnostics)
lookup_runs() (in module biolite.diagnostics)

M

Macse (class in biolite.wrappers)
make_record() (in module biolite.catalog)
make_state() (biolite.pipeline.BasePipeline method)
MakeBlastDB (class in biolite.wrappers)
mask (biolite.workflows.BlastHit attribute)
Mcl (class in biolite.wrappers)
mem_to_mb() (in module biolite.utils)
memusage() (in module biolite.utils)
merge() (in module biolite.diagnostics)
MultiBlast (class in biolite.wrappers)
multiblast() (in module biolite.workflows)
multilineplot() (biolite.report.BaseReport method)
multiscatterplot() (biolite.report.BaseReport method)

N

ncbi_id (biolite.catalog.CatalogRecord attribute)
note (biolite.catalog.CatalogRecord attribute)
number_range() (in module biolite.utils)

O

Oases (class in biolite.wrappers)
oases_assemblies() (in module biolite.workflows)
oases_clean() (in module biolite.workflows)
oases_concat_assembly() (in module biolite.workflows)
oases_merge_assembly() (in module biolite.workflows)
orient (biolite.workflows.BlastHit attribute)
(biolite.workflows.rRNAhit attribute)
OutputPattern (class in biolite.diagnostics)

P

ParallelButterfly (class in biolite.wrappers)
ParallelMacse (class in biolite.wrappers)
parse_args() (biolite.pipeline.BasePipeline method)
paths (biolite.catalog.CatalogRecord attribute)
percent (biolite.workflows.BlastHit attribute)
percent() (biolite.report.BaseReport method)
Phyutility (class in biolite.wrappers)
PileupStats (class in biolite.wrappers)
Pipeline (class in biolite.pipeline)
profile_aggregate() (in module biolite.report)
profile_table() (biolite.report.BaseReport method)

Q

query (biolite.workflows.BlastHit attribute)
(biolite.workflows.rRNAhit attribute)
query() (biolite.report.BaseReport method)

R

Randomize (class in biolite.wrappers)
rank (biolite.workflows.BlastHit attribute)
Raxml (class in biolite.wrappers)
re (biolite.diagnostics.OutputPattern attribute)
readlines_reverse() (in module biolite.utils)
register_exit_profiler() (in module biolite.diagnostics)
rerun() (biolite.pipeline.BasePipeline method)
restart() (biolite.pipeline.BasePipeline method)
Rpsblast (class in biolite.wrappers)
rrna_blast_hits() (in module biolite.workflows)
rRNAhit (class in biolite.workflows)
run() (biolite.pipeline.BasePipeline method)
(biolite.pipeline.Pipeline method)
(biolite.wrappers.BaseWrapper method)
run_jar() (biolite.wrappers.BaseWrapper method)
run_stage() (biolite.pipeline.BasePipeline method)
rusage_diff() (in module biolite.utils)

S

safe_call() (in module biolite.utils)
safe_mkdir() (in module biolite.utils)
safe_print() (in module biolite.utils)
safe_remove() (in module biolite.utils)
safe_str() (in module biolite.utils)
SamIndex (class in biolite.wrappers)
SamPileup (class in biolite.wrappers)
sample_prep (biolite.catalog.CatalogRecord attribute)
SamSort (class in biolite.wrappers)
SamToBam (class in biolite.wrappers)
SamView (class in biolite.wrappers)
scatterplot() (biolite.report.BaseReport method)
score (biolite.workflows.BlastHit attribute)
search() (in module biolite.catalog)
Segmasker (class in biolite.wrappers)
select() (in module biolite.catalog)
select_all() (in module biolite.catalog)
seq_center (biolite.catalog.CatalogRecord attribute)
sequencer (biolite.catalog.CatalogRecord attribute)
set_outdir() (biolite.pipeline.Pipeline method)
size() (biolite.pipeline.BasePipeline method)
sort_and_index_sam() (in module biolite.workflows)
sorted_alphanum() (in module biolite.utils)
species (biolite.catalog.CatalogRecord attribute)
split_paths() (in module biolite.catalog)
stage() (biolite.pipeline.BasePipeline method)
str2list() (biolite.report.BaseReport method)
(in module biolite.diagnostics)
summarize() (biolite.report.BaseReport method)

T

table() (biolite.report.BaseReport method)
tail() (in module biolite.utils)
tail_to_file() (in module biolite.utils)
timestamp (biolite.catalog.CatalogRecord attribute)
timestamp() (in module biolite.diagnostics)
(in module biolite.utils)
tissue (biolite.catalog.CatalogRecord attribute)
title (biolite.report.Field attribute)
(biolite.workflows.BlastHit attribute)
transcript (biolite.workflows.ContigHeader attribute)
TreePruning (class in biolite.wrappers)
Trinity (class in biolite.wrappers)
trinity_assembly() (in module biolite.workflows)
truncate_file() (in module biolite.utils)
type (biolite.report.Field attribute)

U

unhide_run() (in module biolite.diagnostics)
unpack_oases_header() (in module biolite.workflows)

V

VelvetG (class in biolite.wrappers)
VelvetH (class in biolite.wrappers)
version() (biolite.wrappers.BaseWrapper method)
version_jar() (biolite.wrappers.BaseWrapper method)

W

which() (in module biolite.utils)

Z

zip() (biolite.report.BaseReport method)
zipdir() (in module biolite.utils)