SB Find repeats - mendessoares/BuddySuite GitHub Wiki

--find_repeats, -frp

Description

Search through all sequences and return lists of sequences with duplicate IDs and/or identical sequences.

Argument

Columns ( int )

Optional. Specify the number of columns that IDs should be organized into.

Examples

Input file: Mle-Panx-C_terms.nex

#NEXUS
begin data;
	dimensions ntax=16 nchar=50;
	format datatype=protein missing=? gap=-;
matrix
'Mle-Panxα12'  -m--vidilsgf------------kgitpfkgitlddgwdqinrsfmfvl
'Mle-Panxα9'   ----mldilskf------------kgvtpfkgitiddgwdqlnrsfmfvl
'Mle-Panxα10B' -m--rlsekstshdckacitrshnedcarrwgitiddgwdqlnrsfmfgl
'Mle-Panxα7A'  -m--gveilfpi----------inratapiksvniddlssqlnrtfmfyl
'Mle-Panxα8'   -m--vlevlalf------------prlapfkvitlddvwdqwnrsfmfim
'Mle-Panxα1'   -mywifeicqei------------kraqscrkfaidgpfdwtnriimptl
'Mle-Panxα9'   ----mldilskf------------kgvtpfkgitiddgwdqlnrsfmfvl
'Mle-Panxα2'   -m--vldlisgs----------l-ngflkiksvsiddqwdqinrtylvmf
'Mle-Panxα5'   -m--iywvwavf------------krmapfkvvtlddrwdqmnrsfmmpl
'Mle-Panxα4'   -m--viellagy------------kglspfkdatvddswdqinrcyvfia
'Mle-Panxα3'   ml--llgslgti------------knlsifkdlslddwldqmnrtfmfll
'Mle-Panxα6'   -m--lleilanf------------kgatpfkeivlddkwdqinrcymfll
'Mle-Panxα8'   ----mldilskf------------kgvtpfkgitiddgwdqlnrsfmfvl
'Mle-Panxα11'  -m--lisslvqf------------srlspfkeitiddgwdqlnrsfmfvl
'Mle-Panxα10A' -m--rlsekstshdckacitrshnedcarrwgitiddgwdqlnrsfmfgl
'Mle-Panxα6'   ----mldilskf------------kgvtpfkgitiddgwdqlnrsfmfvl
;
end;

Usage example 1

$: sb Mle-Panx-C_terms.nex -drp

Output

#### Records with duplicate IDs: ####
Mle-Panxα9
Mle-Panxα8
Mle-Panxα6

#### Records with duplicate sequences: ####
[Mle-Panxα10A, Mle-Panxα10B]
[Mle-Panxα9, Mle-Panxα9, Mle-Panxα8, Mle-Panxα6]

Usage example 2

$: sb Mle-Panx-C_terms.nex -drp 2

Output

#### Records with duplicate IDs: ####
Mle-Panxα9	Mle-Panxα8
Mle-Panxα6

#### Records with duplicate sequences: ####
[Mle-Panxα10A, Mle-Panxα10B], [Mle-Panxα9, Mle-Panxα9, Mle-Panxα8, Mle-Panxα6]