AB Extract regions - mendessoares/BuddySuite GitHub Wiki

--extract_regions, -er

Description

Extract columns from your alignments.

Arguments

Start ( int )

The initial residue to include in the new alignment

End ( int )

The final residue to include in the new alignment

Examples

Input file: Mnemiopsis.phyr

 3 158
Mle-Panxα9  -MLDILSKFKGVTPFKGITIDDGWDQLNRSFMFVLLVVMGTTVTVRQYTGSVISCDGFKKFGSTFAEDYCWTQGLYTVLEGYDQPSQNIPYPGLLPDEAPPCTPVRLKDGTRLKCPDPDQLLSPTRISHLWYQWVPFYFWLAAAAFFMPYLLYKNFGM
Mle-Panxα8  MVLEVLALFPRLAPFKVITLDDVWDQWNRSFMFIMTVLFGSIVTIRSYTGSVIECDGFLKVPVEFAKDYCWTQGIYTLREGYDYHSSLLPYPGVFPEDAPGCLDKVLDNGGRVICPMDKKYRKYQRVYHSWYQFTAFYFWTASCAFFLPYMMFKFFGM
Mle-Panxα6  MLLEILANFKGATPFKEIVLDDKWDQINRCYMFLLCVIFGTVVTFRQYTGGIIACDGLTKFSAAFAEDYCWTQGLYTIKEAYDIVDNSLPYPGLLPEDAPPCLSRRLVSGGRIECPPADLYLEPTRVHHTWYQWIPFYFWVISIAFIGPYIVYKQLGV

 5 165
Ael_PanxβA  -MVVIRELKDILSMKIKTRHDGFCDQFNRMIMTKILIIMSVIVGFNYFYDEVSCMVFKKSDLQKEFISSSCWISGFYIFEEMKTRL-DKSSYYGIPYTINHDGIRKD-GTLCATRDR-LGLVEGCAPMTKVYYLQYQWMPFYIGSLSTFYYMPYIVFKMVNRDLM
Ael_PanxβB  -MVVIRGLKDILSIKMKTRHDSICDQFNRLFMTRVLLIMSVIMGFDYYSDKVSCMVLGESHLGKDFIHAACWISGFYIYEEMKTRL-DKSSYYGIPYTIDNDGIEYD-GSLCPTRDK-NGKIPGCNPMTKVYYLQYQWMPFYVGSLAIFYYIPYIIFRMVNTDLV
Ael_PanxβD  ----MEVLKDILSVQLKSRDDSYSDQFNRIFMCKLFLMSSIIMSVDYFSDNVNCMIPDNAQHSSSFFHSACWINGFYIFDEMRSRL-EKSGYYGIPQRVDFDGINRVTGELCITKNL-FGEAADCEPMTRIYYLHYQWMPVYMVSLGMFFYLPYIVFRFVNTDMI
Ael_PanxβE  --MIGDAISNIISIKIKHRDDGVTDQYNRILMVKMIIMLSAIVGYNYYSDKVSCIVANEDDGIDGFVADTCWIQGFYVFKEMKKRL-GESAYLGLPRNMDYDGLDSN-GVLCSTTDRGSDSIQTCQKMKKVYYLQYQYFPFLLAGLAMLFYFPYIVFKVTNTDLV
Ael_PanxβF  MGPFEDSIGKIFSFNIKRRADGITDQYNRILMVKICIIFTFVLGIDYFTNKTTCITPDMMRID---PTRTCWNEGFYIYPELENLPAKESSYYGIPKQIDNDGIDEN-GSPCTTKNI-FIKFLSCKPLKKQYYRQYQFMPFLIAVYGIIFYIPHIMFMVINTDII

Usage example 1

$: alb Mnemiopsis.phyr -er 1 50

Output

 3 50
Mle-Panxα9  -MLDILSKFKGVTPFKGITIDDGWDQLNRSFMFVLLVVMGTTVTVRQYTG
Mle-Panxα8  MVLEVLALFPRLAPFKVITLDDVWDQWNRSFMFIMTVLFGSIVTIRSYTG
Mle-Panxα6  MLLEILANFKGATPFKEIVLDDKWDQINRCYMFLLCVIFGTVVTFRQYTG

 5 50
Ael_PanxβA  -MVVIRELKDILSMKIKTRHDGFCDQFNRMIMTKILIIMSVIVGFNYFYD
Ael_PanxβB  -MVVIRGLKDILSIKMKTRHDSICDQFNRLFMTRVLLIMSVIMGFDYYSD
Ael_PanxβD  ----MEVLKDILSVQLKSRDDSYSDQFNRIFMCKLFLMSSIIMSVDYFSD
Ael_PanxβE  --MIGDAISNIISIKIKHRDDGVTDQYNRILMVKMIIMLSAIVGYNYYSD
Ael_PanxβF  MGPFEDSIGKIFSFNIKRRADGITDQYNRILMVKICIIFTFVLGIDYFTN

Usage example 2

$: alb Mnemiopsis.phyr -er 10 110

Output

 3 101
Mle-Panxα9  KGVTPFKGITIDDGWDQLNRSFMFVLLVVMGTTVTVRQYTGSVISCDGFKKFGSTFAEDYCWTQGLYTVLEGYDQPSQNIPYPGLLPDEAPPCTPVRLKDG
Mle-Panxα8  PRLAPFKVITLDDVWDQWNRSFMFIMTVLFGSIVTIRSYTGSVIECDGFLKVPVEFAKDYCWTQGIYTLREGYDYHSSLLPYPGVFPEDAPGCLDKVLDNG
Mle-Panxα6  KGATPFKEIVLDDKWDQINRCYMFLLCVIFGTVVTFRQYTGGIIACDGLTKFSAAFAEDYCWTQGLYTIKEAYDIVDNSLPYPGLLPEDAPPCLSRRLVSG

 5 101
Ael_PanxβA  DILSMKIKTRHDGFCDQFNRMIMTKILIIMSVIVGFNYFYDEVSCMVFKKSDLQKEFISSSCWISGFYIFEEMKTRL-DKSSYYGIPYTINHDGIRKD-GT
Ael_PanxβB  DILSIKMKTRHDSICDQFNRLFMTRVLLIMSVIMGFDYYSDKVSCMVLGESHLGKDFIHAACWISGFYIYEEMKTRL-DKSSYYGIPYTIDNDGIEYD-GS
Ael_PanxβD  DILSVQLKSRDDSYSDQFNRIFMCKLFLMSSIIMSVDYFSDNVNCMIPDNAQHSSSFFHSACWINGFYIFDEMRSRL-EKSGYYGIPQRVDFDGINRVTGE
Ael_PanxβE  NIISIKIKHRDDGVTDQYNRILMVKMIIMLSAIVGYNYYSDKVSCIVANEDDGIDGFVADTCWIQGFYVFKEMKKRL-GESAYLGLPRNMDYDGLDSN-GV
Ael_PanxβF  KIFSFNIKRRADGITDQYNRILMVKICIIFTFVLGIDYFTNKTTCITPDMMRID---PTRTCWNEGFYIYPELENLPAKESSYYGIPKQIDNDGIDEN-GS