SB Delete large - mendessoares/BuddySuite GitHub Wiki

--delete_large, -dlg

Description

Delete all sequences that are larger than the given threshold

Argument

Threshold ( int )

The maximum sequence size that will be retained (the value is inclusive).

Example

Input file: Mnemiopsis.fa

>Mle-Panxα2 ML25998a.
MVLDLISGSLNGFLKIKSVSIDDQWDQINRTYLVMFCILSGTIMTFKQNLGSIIHCISDA
RGDDSSFADAHATFVQDYCAAQGLYTLKEVYDKSWPDEIPYPGILQMKTIGCFPGRQFKN
GTPIQCPDEKDLKPFTTVYHVWYMFVPFYFCAVGIAFYFPYTVFRHLSGIYDIKPMLNSL
ALDIGAYTEEDISRRIDNVSRWLYIKLDPYMNNMLPYTQIVHKHSIFYTVMLVKVMYLAT
SVSIFYATHRIFDQGNFALYGYDVLMSIPQETSYKVMDTIFPKMVGCEINMWGRTGEQSE
SLLCVLPQNIGNQYFFLIFWFLLILTILSNCISVIVTIFRFIFVSGSYKRFLATSLLNHE
ERYKLVFTHVGTTGRYILLLCADHSNPKIFEDLLEIVCSLLIANYHKRKRSRDKGHSRAE
GVGTKGRHGLSFVDSTV
>Mle-Panxα3 ML036514a.
MLLLGSLGTIKNLSIFKDLSLDDWLDQMNRTFMFLLLCFMGTIVAVSQYTGKNISCDGFT
KFGEDFSQDYCWTQGLYTIKEAYDLPESQIPYPGIIPENVPACREHALKNGGKIVCPPED
QVKPLTRARHLWYQWIPFYFWVIAPVFYLPYMFVKRMGLDRMKPLLKIMSDYYHCTTETP
SEEIIVKCADWVYNSIVDRLSEGSSWTSWRNRHGLGLAVLVSKFMYLGGSVLVMMMTTLM
FQVGDFKTYGIEWLRQFPNPENYSTSVKHKLFPKMVACEIKRWGTTGLEEENGMCVLAPN
VIYQYIFLIMWFALAITICTNFGNIFFYLFKLTATRYTYNKLVATGHFSHKHPGWKFMYY
RIGTSGRVLLNIVAQNTNPIIFGAIMEKLTPSVIKHLRIGHVPGEYLTDPA
>Mle-Panxα4 ML129317a.
MVIELLAGYKGLSPFKDATVDDSWDQINRCYVFIAMVVMGAVTTMRQYSGTLIACDGFTK
FHPQFAEDYCWSIGMYTVREAYDLPSSMVAYPGVIPWDMPACVPRLLKNGTRTKCGSEKD
VMPSEKIYHLWYQWASFYFWIVAILYYAPYIMFKQLGGGEYKPLIKLLCLASGSPEQQMQ
DIQERVVKWLFFRFKTYIFAKGYYAWLRKNSFSIAIGVTKLSYLLITILVFYLTGFMFEY
GSNTWYRYGADWYGTRFSSYHETNNSITLTKDIIFPKMVACEIKRWGPSGIEVETAQCVL
APNVLYQYLFLFTWYLLIAVFFTNLISCFLHISEMFFSNGTYNRMIDQGMLPDKPSYRYV
FMNIGAGGREIVQILTDNSNPLLFSKIFDDLTNLLITTSKNADVIENLSKLDSSVIELGS
KDSI
>Mle-Panxα5 ML223536a.
MIYWVWAVFKRMAPFKVVTLDDRWDQMNRSFMMPLTMSFAYLIDYGIIAGSTIKCTGFED
SFRSEAFVDEYCWTQGIYTLREAYDLENTKIPYPGIIPEGFPNCMPYERWDGMKVECPKE
EQYLKPTRVYHLYYQHIQLYFWLVCTLFYLPYMVGICLGFNYTKPLINLLHNPLTRDEEE
LEALLDKAARSLRLRLDIYSDQKSWFDLLYRRHTMLYLLFFIKLQYLGFSVAILGLTQAK
FKIGNFVTYGFEWVGSQVPNGSTYTLVQHKLFPKMAACEIKRWGASGLDVLRGMCVLPQN
VSNSYIFLVFWIFLLLTILGNVIGCILTVKQYLVKSEGYSKLVACTFWNDWNLRHLYWNV
GGSGRVILHHLADNLHPCTFEKLIRRYWWLKRNEYVQYNGHLKTS

Usage example

$: sb Mnemiopsis.fa -dlg 419

output

>Mle-Panxα3 ML036514a.
MLLLGSLGTIKNLSIFKDLSLDDWLDQMNRTFMFLLLCFMGTIVAVSQYTGKNISCDGFT
KFGEDFSQDYCWTQGLYTIKEAYDLPESQIPYPGIIPENVPACREHALKNGGKIVCPPED
QVKPLTRARHLWYQWIPFYFWVIAPVFYLPYMFVKRMGLDRMKPLLKIMSDYYHCTTETP
SEEIIVKCADWVYNSIVDRLSEGSSWTSWRNRHGLGLAVLVSKFMYLGGSVLVMMMTTLM
FQVGDFKTYGIEWLRQFPNPENYSTSVKHKLFPKMVACEIKRWGTTGLEEENGMCVLAPN
VIYQYIFLIMWFALAITICTNFGNIFFYLFKLTATRYTYNKLVATGHFSHKHPGWKFMYY
RIGTSGRVLLNIVAQNTNPIIFGAIMEKLTPSVIKHLRIGHVPGEYLTDPA
>Mle-Panxα5 ML223536a.
MIYWVWAVFKRMAPFKVVTLDDRWDQMNRSFMMPLTMSFAYLIDYGIIAGSTIKCTGFED
SFRSEAFVDEYCWTQGIYTLREAYDLENTKIPYPGIIPEGFPNCMPYERWDGMKVECPKE
EQYLKPTRVYHLYYQHIQLYFWLVCTLFYLPYMVGICLGFNYTKPLINLLHNPLTRDEEE
LEALLDKAARSLRLRLDIYSDQKSWFDLLYRRHTMLYLLFFIKLQYLGFSVAILGLTQAK
FKIGNFVTYGFEWVGSQVPNGSTYTLVQHKLFPKMAACEIKRWGASGLDVLRGMCVLPQN
VSNSYIFLVFWIFLLLTILGNVIGCILTVKQYLVKSEGYSKLVACTFWNDWNLRHLYWNV
GGSGRVILHHLADNLHPCTFEKLIRRYWWLKRNEYVQYNGHLKTS