NAME

yaml-generator-42.pl - Interactive or batch generator for 42 YAML config files

VERSION

version 0.190820

USAGE

# wizard: configuration assistant
./yaml-generator-42.pl --wizard

# basic: derive organisms name directly from filenames
./yaml-generator-42.pl --bank_dir ./banks/ --ref_bank_dir ./ref_banks/ \
--tax_dir ~/taxdump/ --bank_suffix=.faa --ref_bank_suffix=.faa \
--queries queries.idl [optional arguments]

# use idm files for banks, orgs and eventually tax_filters
./yaml-generator-42.pl --bank_dir ./banks/ --ref_bank_dir ./ref_banks/ --tax_dir  \
~/taxdump/ --bank_suffix=.faa --ref_bank_suffix=.faa --queries queries.idl  \
--bank_mapper banks/bank_mapper.idm  \
--ref_bank_mapper ref_banks/ref_bank_mapper.idm

# dynamic choice of tax_filter using NCBI's taxonomy
./yaml-generator-42.pl --bank_dir ./banks/ --ref_bank_dir ./ref_banks/ --tax_dir  \
~/taxdump/ --bank_suffix=.faa --ref_bank_suffix=.faa --queries queries.idl  \
--bank_mapper banks/bank_mapper.idm  \
--ref_bank_mapper ref_banks/ref_bank_mapper.idm \
--levels=family

# interactive choice of tax_filter using NCBI's taxonomy
./yaml-generator-42.pl --bank_dir ./banks/ --ref_bank_dir ./ref_banks/ --tax_dir  \
~/taxdump/ --bank_suffix=.faa --ref_bank_suffix=.faa --queries queries.idl  \
--bank_mapper banks/bank_mapper.idm  \
--ref_bank_mapper ref_banks/ref_bank_mapper.idm \
--levels=family --choose_tax_filter

REQUIRED ARGUMENTS

OPTIONAL ARGUMENTS

--wizard

Activate if you want an interactive step by step configuration.

--run_mode=<str>

'phylogenomic' or 'metagenomic'

--out_suffix=<str>

--queries <file>

--evalue=<n>

--SSUrRNA

--homologues_seg=<str>

--max_target_seqs=<str>

--templates_seg=<str>

--ref_brh_mode=<str>

on or off.

--ref_bank_dir <dir>

Path to reference bank files directory.

--ref_bank_suffix=<str>

--ref_bank_mapper <file>

Tab delimited file with bank and org in this order.

--ref_org_mul=<n>

--ref_score_mul=<n>

--tol_check=<str>

--tol_db <db>

Path to TreeOfLife database.

--trimming_mode=<str>

--trim_max_shift=<n>

--trim_extra_margin=<n>

--aligner_mode=<str>

off, blast, exonerate, exoblast.

--ali_patch_mode=<str>

on or off

--ali_cover_mul=<n>

--bank_dir <dir>

Path to bank files directory.

--bank_suffix=<str>

--bank_mapper <file>

Tab delimited file with bank, org and optionnaly tax_filter in this order.

--tax_dir <dir>

Path to taxdump directory.

--levels=<level>...

Taxonomic filter level(s). Several levels are allowed as input; in this case, the first defined level will be returned.

Available levels are: 'superkingdom' 'kingdom' 'phylum' 'subphylum' 'class' 'superorder' 'order' 'suborder' 'infraorder' 'parvorder' 'superfamily' 'family' 'subfamily' 'genus' 'species'

--choose_tax_filter=<n>

Interactively choose taxonomic filter. 0 => 'from org mapper file' 1 => "from NCBI's taxonomy - auto + prompt for missing" 2 => "from NCBI's taxonomy - auto + prompt for all"

--tax_reports=<str>

'on' or 'off'

--best_hit

Overides 'tax_' parameters and auto-sets 'tax_score_mul' to compute LCA in a MEGAN-like mode i.e. based on bitscore.

--megan_like

Overides 'tax_' parameters and auto-sets 'tax_score_mul' to compute LCA in a MEGAN-like mode i.e. based on bitscore.

--tax_max_hits=<n>

--tax_min_hits=<n>

--tax_min_ident=<n>

--tax_min_len=<n>

--tax_min_score=<n>

--tax_score_mul=<n>

--ls_action=<str>

keep or remove

--code=<n>

--version

--usage

--help

--man

Print the usual program information

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

CONTRIBUTOR

Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>

COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.