Index

A

absolute_path (seqenv.common.autopaths.DirectoryPath attribute) (seqenv.common.autopaths.FilePath attribute) add() (seqenv.common.database.Database method) add_by_steps() (seqenv.common.database.Database method) add_column() (seqenv.common.database.Database method) add_legend() (seqenv.ontology.Ontology method) add_seq() (seqenv.fasta.FASTA method)

add_str() (seqenv.fasta.FASTA method) add_style() (seqenv.ontology.Ontology method) add_table() (seqenv.common.database.Database method) add_weights() (seqenv.ontology.Ontology method) Analysis (class in seqenv.analysis)

B

b_blk (seqenv.common.color.Color attribute) b_blu (seqenv.common.color.Color attribute) b_cyn (seqenv.common.color.Color attribute) b_grn (seqenv.common.color.Color attribute) b_pur (seqenv.common.color.Color attribute) b_red (seqenv.common.color.Color attribute) b_wht (seqenv.common.color.Color attribute) b_ylw (seqenv.common.color.Color attribute) biom_output() (seqenv.outputs.OutputGenerator method)

blast_params (seqenv.seqsearch.SeqSearch attribute) blast_queries (seqenv.seqsearch.parallel.ParallelSeqSearch attribute) blast_query (seqenv.seqsearch.SeqSearch attribute) BLASTquery (class in seqenv.seqsearch.blast) blk (seqenv.common.color.Color attribute) blu (seqenv.common.color.Color attribute) bold (seqenv.common.color.Color attribute) branch (seqenv.common.git.GitRepo attribute) buffer_size (seqenv.fasta.FASTA attribute)

C

cached() (in module seqenv.common.cache) check_format() (seqenv.common.database.Database method) child_to_parents (seqenv.analysis.Analysis attribute) chunk (seqenv.common.autopaths.Filesize attribute) class_property (class in seqenv.common.cache) clean_path() (seqenv.common.autopaths.DirectoryPath class method) (seqenv.common.autopaths.FilePath class method) close() (seqenv.common.database.Database method) (seqenv.fasta.FASTA method) Color (class in seqenv.common.color) color (seqenv.common.timer.Timer attribute) columns (seqenv.common.database.Database attribute) command (seqenv.seqsearch.blast.BLASTquery attribute) (seqenv.seqsearch.vsearch.VSEARCHquery attribute)

concept_to_name (seqenv.analysis.Analysis attribute) connection (seqenv.common.database.Database attribute) count (seqenv.fasta.FASTA attribute) count_bytes (seqenv.common.autopaths.FilePath attribute) count_entries() (seqenv.common.database.Database method) count_lines (seqenv.common.autopaths.FilePath attribute) create() (seqenv.common.autopaths.DirectoryPath method) (seqenv.common.database.Database method) (seqenv.fasta.FASTA method) create_if_not_exists() (seqenv.common.autopaths.DirectoryPath method) cursor (seqenv.common.database.Database attribute) cyn (seqenv.common.color.Color attribute)

D

Database (class in seqenv.common.database) db (seqenv.analysis.Analysis attribute) detailed_error() (seqenv.common.database.Database method) df_abundances (seqenv.analysis.Analysis attribute) df_sample_names (seqenv.outputs.OutputGenerator attribute) df_seqs_concepts (seqenv.outputs.OutputGenerator attribute) directory (seqenv.common.autopaths.DirectoryPath attribute) (seqenv.common.autopaths.FilePath attribute)

DirectoryPath (class in seqenv.common.autopaths) dot_files() (seqenv.outputs.OutputGenerator method) download_from_url() (in module seqenv.common) draw_to_pdf() (seqenv.ontology.Ontology method) draw_with_networkx() (seqenv.ontology.Ontology method) draw_with_pygraphviz() (seqenv.ontology.Ontology method)

E

empty() (seqenv.common.tmpstuff.TmpFile class method) end (seqenv.common.color.Color attribute) execute() (seqenv.common.database.Database method)

exists (seqenv.common.autopaths.DirectoryPath attribute) (seqenv.common.autopaths.FilePath attribute) extension (seqenv.common.autopaths.FilePath attribute) (seqenv.fasta.FASTA attribute) extract_sequences() (seqenv.fasta.FASTA method)

F

f_blk (seqenv.common.color.Color attribute) f_blu (seqenv.common.color.Color attribute) f_cyn (seqenv.common.color.Color attribute) f_grn (seqenv.common.color.Color attribute) f_pur (seqenv.common.color.Color attribute) f_red (seqenv.common.color.Color attribute) f_wht (seqenv.common.color.Color attribute) f_ylw (seqenv.common.color.Color attribute) FASTA (class in seqenv.fasta) filename (seqenv.common.autopaths.FilePath attribute) FilePath (class in seqenv.common.autopaths) FilePermissions (class in seqenv.common.autopaths)

Filesize (class in seqenv.common.autopaths) filter() (seqenv.seqsearch.blast.BLASTquery method) (seqenv.seqsearch.SeqSearch method) filtering (seqenv.analysis.Analysis attribute) first (seqenv.common.database.Database attribute) flash (seqenv.common.color.Color attribute) flatter() (in module seqenv.common) float_format (seqenv.outputs.OutputGenerator attribute) flush() (seqenv.fasta.FASTA method) format (seqenv.fasta.FASTA attribute) format() (seqenv.common.autopaths.Filesize method) frame (seqenv.common.database.Database attribute) from_string() (seqenv.common.tmpstuff.TmpFile class method)

G

g_blk (seqenv.common.color.Color attribute) g_blu (seqenv.common.color.Color attribute) g_cyn (seqenv.common.color.Color attribute) g_grn (seqenv.common.color.Color attribute) g_pur (seqenv.common.color.Color attribute) g_red (seqenv.common.color.Color attribute) g_wht (seqenv.common.color.Color attribute) g_ylw (seqenv.common.color.Color attribute) GenWithLength (class in seqenv.common) get() (seqenv.common.database.Database method) get_and_order() (seqenv.common.database.Database method)

get_columns_of_table() (seqenv.common.database.Database method) get_entry() (seqenv.common.database.Database method) get_first() (seqenv.common.database.Database method) get_last() (seqenv.common.database.Database method) get_number() (seqenv.common.database.Database method) get_subgraph() (seqenv.ontology.Ontology method) gis_with_envo (seqenv.analysis.Analysis attribute) GitRepo (class in seqenv.common.git) goatools (seqenv.ontology.Ontology attribute) grn (seqenv.common.color.Color attribute) gzipped (seqenv.fasta.FASTA attribute)

H

hash (seqenv.common.git.GitRepo attribute)

I

i_blk (seqenv.common.color.Color attribute) i_blu (seqenv.common.color.Color attribute) i_cyn (seqenv.common.color.Color attribute) i_grn (seqenv.common.color.Color attribute) i_pur (seqenv.common.color.Color attribute) i_red (seqenv.common.color.Color attribute)

i_wht (seqenv.common.color.Color attribute) i_ylw (seqenv.common.color.Color attribute) ids (seqenv.fasta.FASTA attribute) index() (seqenv.common.database.Database method) is_symlink (seqenv.common.autopaths.DirectoryPath attribute) italic (seqenv.common.color.Color attribute)

J

join_outputs() (seqenv.seqsearch.parallel.ParallelSeqSearch method)

L

l_blk (seqenv.common.color.Color attribute) l_blu (seqenv.common.color.Color attribute) l_cyn (seqenv.common.color.Color attribute) l_grn (seqenv.common.color.Color attribute) l_pur (seqenv.common.color.Color attribute) l_red (seqenv.common.color.Color attribute) l_wht (seqenv.common.color.Color attribute)

l_ylw (seqenv.common.color.Color attribute) last (seqenv.common.database.Database attribute) light (seqenv.common.color.Color attribute) link_from() (seqenv.common.autopaths.FilePath method) link_to() (seqenv.common.autopaths.FilePath method) list_sequence_concept() (seqenv.outputs.OutputGenerator method)

M

main_table (seqenv.common.database.Database attribute) make_all() (seqenv.outputs.OutputGenerator method) make_executable() (seqenv.common.autopaths.FilePermissions method)

md5sum() (in module seqenv.common) must_exist() (seqenv.common.autopaths.FilePath method)

N

name (seqenv.common.autopaths.DirectoryPath attribute) networkx (seqenv.ontology.Ontology attribute) new_connection() (seqenv.common.database.Database method) new_temp_file() (in module seqenv.common.tmpstuff)

new_temp_path() (in module seqenv.common) (in module seqenv.common.tmpstuff) non_block_run() (seqenv.seqsearch.blast.BLASTquery method) number (seqenv.common.autopaths.FilePermissions attribute)

O

only_readable() (seqenv.common.autopaths.FilePermissions method) only_top_sequences (seqenv.analysis.Analysis attribute) Ontology (class in seqenv.ontology) ontology (seqenv.outputs.OutputGenerator attribute) open() (seqenv.common.database.Database method) (seqenv.fasta.FASTA method) orange_network (seqenv.ontology.Ontology attribute)

orange_obo (seqenv.ontology.Ontology attribute) orig_names_to_renamed (seqenv.analysis.Analysis attribute) output_3() (seqenv.outputs.OutputGenerator method) OutputGenerator (class in seqenv.outputs) own_connection (seqenv.common.database.Database attribute) own_cursor (seqenv.common.database.Database attribute)

P

ParallelSeqSearch (class in seqenv.seqsearch.parallel) parse() (seqenv.fasta.FASTA method) permissions (seqenv.common.autopaths.DirectoryPath attribute) precisions (seqenv.common.autopaths.Filesize attribute) prefix (seqenv.common.autopaths.FilePath attribute) (seqenv.common.timer.Timer attribute) prefix_path (seqenv.common.autopaths.FilePath attribute) prepare() (seqenv.common.database.Database method) pretty_now() (in module seqenv.common)

print_elapsed() (seqenv.common.timer.Timer method) print_end() (seqenv.common.timer.Timer method) print_start() (seqenv.common.timer.Timer method) print_test() (seqenv.ontology.Ontology method) print_total_elapsed() (seqenv.common.timer.Timer method) property_cached() (in module seqenv.common.cache) pur (seqenv.common.color.Color attribute) pygraphviz (seqenv.ontology.Ontology attribute)

Q

queries (seqenv.seqsearch.parallel.ParallelSeqSearch attribute)

query (seqenv.seqsearch.SeqSearch attribute)

R

red (seqenv.common.color.Color attribute) remote_branch (seqenv.common.git.GitRepo attribute) remove() (seqenv.common.autopaths.DirectoryPath method) (seqenv.common.autopaths.FilePath method) remove_when_symlink() (seqenv.common.autopaths.DirectoryPath method) rename_sequences() (seqenv.fasta.FASTA method)

renamed_fasta (seqenv.analysis.Analysis attribute) renamed_to_orig (seqenv.analysis.Analysis attribute) results (seqenv.seqsearch.blast.BLASTquery attribute) (seqenv.seqsearch.SeqSearch attribute) run() (seqenv.analysis.Analysis method) (seqenv.seqsearch.SeqSearch method) (seqenv.seqsearch.blast.BLASTquery method) (seqenv.seqsearch.parallel.ParallelSeqSearch method) (seqenv.seqsearch.vsearch.VSEARCHquery method)

S

search (seqenv.analysis.Analysis attribute) search_results (seqenv.analysis.Analysis attribute) sep (seqenv.outputs.OutputGenerator attribute) seq_to_counts (seqenv.analysis.Analysis attribute) seq_to_gis (seqenv.analysis.Analysis attribute) seqenv (module) seqenv.analysis (module) seqenv.common (module) seqenv.common.autopaths (module) seqenv.common.cache (module) seqenv.common.color (module) seqenv.common.database (module) seqenv.common.git (module) seqenv.common.timer (module) seqenv.common.tmpstuff (module) seqenv.fasta (module)

seqenv.fasta.splitable (module) seqenv.ontology (module) seqenv.outputs (module) seqenv.seqsearch (module) seqenv.seqsearch.blast (module) seqenv.seqsearch.parallel (module) seqenv.seqsearch.vsearch (module) SeqSearch (class in seqenv.seqsearch) serial_to_concept (seqenv.analysis.Analysis attribute) short_hash (seqenv.common.git.GitRepo attribute) size (seqenv.common.autopaths.FilePath attribute) split() (seqenv.fasta.splitable.SplitableFASTA method) splitable (seqenv.seqsearch.parallel.ParallelSeqSearch attribute) SplitableFASTA (class in seqenv.fasta.splitable) status (seqenv.fasta.splitable.SplitableFASTA attribute) suffix (seqenv.common.timer.Timer attribute)

T

tables (seqenv.common.database.Database attribute) tag (seqenv.common.git.GitRepo attribute) Timer (class in seqenv.common.timer) TmpFile (class in seqenv.common.tmpstuff)

tsv_samples_to_names() (seqenv.outputs.OutputGenerator method) tsv_seq_to_concepts() (seqenv.outputs.OutputGenerator method) tsv_seq_to_names() (seqenv.outputs.OutputGenerator method)

U

u_blk (seqenv.common.color.Color attribute) u_blu (seqenv.common.color.Color attribute) u_cyn (seqenv.common.color.Color attribute) u_grn (seqenv.common.color.Color attribute) u_pur (seqenv.common.color.Color attribute) u_red (seqenv.common.color.Color attribute) u_wht (seqenv.common.color.Color attribute)

u_ylw (seqenv.common.color.Color attribute) underline (seqenv.common.color.Color attribute) unique_gis (seqenv.analysis.Analysis attribute) uniquify() (seqenv.common.database.Database method) units (seqenv.common.autopaths.Filesize attribute) unzip() (in module seqenv.common) unzip_to() (seqenv.common.autopaths.FilePath method)

V

vacuum() (seqenv.common.database.Database method) vsearch_queries (seqenv.seqsearch.parallel.ParallelSeqSearch attribute)

vsearch_query (seqenv.seqsearch.SeqSearch attribute) VSEARCHquery (class in seqenv.seqsearch.vsearch)

W

wait() (seqenv.seqsearch.blast.BLASTquery method) wht (seqenv.common.color.Color attribute) write() (seqenv.common.autopaths.FilePath method) (seqenv.fasta.FASTA method)

write_to_dot() (seqenv.ontology.Ontology method) writelines() (seqenv.common.autopaths.FilePath method)

Y

ylw (seqenv.common.color.Color attribute)