NAME

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

VERSION

version 0.210570

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=.nsq --ref_bank_suffix=.psq \
    --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=.nsq --ref_bank_suffix=.psq --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 Taxonomy
    ./yaml-generator-42.pl --bank_dir ./banks/ --ref_bank_dir ./ref_banks/ --tax_dir  \
    ~/taxdump/ --bank_suffix=.nsq --ref_bank_suffix=.psq --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 Taxonomy
    ./yaml-generator-42.pl --bank_dir ./banks/ --ref_bank_dir ./ref_banks/ --tax_dir  \
    ~/taxdump/ --bank_suffix=.nsq --ref_bank_suffix=.psq --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=<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.

--trim_homologues=<str>
--trim_max_shift=<n>
--trim_extra_margin=<n>
--merge_orthologues=<str>
--merge_min_ident=<n>
--merge_min_len=<n>
--aligner_mode=<str>

off, blast, exonerate, exoblast.

--ali_skip_self=<str>

on or off

--ali_cover_mul=<n>
--ali_keep_old_new_tags=<str>

'on' or 'off'

--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>
--ali_keep_lengthened_seqs=<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.