code.pipeline package¶
Submodules¶
code.pipeline.clean_input module¶
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code.pipeline.clean_input.
clean_input
(config_input, config_pipline)¶
code.pipeline.make_aggregate module¶
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code.pipeline.make_aggregate.
aggregate_datasets
(config)¶
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code.pipeline.make_aggregate.
clean_duplicate
(config)¶
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code.pipeline.make_aggregate.
clean_redundant
(config)¶
code.pipeline.mixed2gaf module¶
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code.pipeline.mixed2gaf.
filter_mixed
(config)¶
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code.pipeline.mixed2gaf.
mixed2gaf
(config)¶
code.pipeline.run_argot2 module¶
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code.pipeline.run_argot2.
convert_blast
(config)¶
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code.pipeline.run_argot2.
download_argot2
(config)¶
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code.pipeline.run_argot2.
process_argot2
(config)¶
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code.pipeline.run_argot2.
run_hmmer
(config)¶
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code.pipeline.run_argot2.
submit_argot2
(config)¶
code.pipeline.run_iprs module¶
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code.pipeline.run_iprs.
iprs2gaf
(config)¶
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code.pipeline.run_iprs.
run_iprs
(config)¶
code.pipeline.run_mm_preproc module¶
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code.pipeline.run_mm_preproc.
compile_blast_out
(config)¶
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code.pipeline.run_mm_preproc.
make_tmp_fa
(config)¶
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code.pipeline.run_mm_preproc.
make_uniprotdb
(config)¶
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code.pipeline.run_mm_preproc.
process_fasta
(config)¶
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code.pipeline.run_mm_preproc.
run_uniprot_blast
(config)¶
code.pipeline.run_pannzer module¶
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code.pipeline.run_pannzer.
copy_blast
(config)¶
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code.pipeline.run_pannzer.
run_pannzer
(config)¶
code.pipeline.run_rbh_blast module¶
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code.pipeline.run_rbh_blast.
get_rbh_annotations
(config)¶
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code.pipeline.run_rbh_blast.
make_input_blastdb
(config)¶
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code.pipeline.run_rbh_blast.
outcols
= '6 qseqid sseqid qlen qstart qend slen sstart send evalue bitscore score length pident nident gaps'¶ Make the blast database for the input sequence first
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code.pipeline.run_rbh_blast.
run_tair_blast
(config)¶
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code.pipeline.run_rbh_blast.
run_uniprot_blast
(config)¶