AB Split to files - mendessoares/BuddySuite GitHub Wiki

--split_to_files, -stf

Description

Write a new file for each alignment in a multi-alignment AlignBuddy object. Not all alignment formats support multiple alignments in a single file, nor do all downstream software packages that you may want to feed your alignments into.

Arguments

Output directory ( path )

Specify where new files will be written to. If the path doesn't exist, it will be created for you.

Prefix ( str )

Optional. By default, each new alignment file will be prefixed with the word 'Alignment_', followed by a zero-padded number. If you prefer a different prefix, provide it as the second argument.

Examples

Input file: Pannexins.physr

 7 75
Mle-Panxα2   -MVLDLISGSLNGFL-KIKSVSIDDQWDQINRTYLVMFCILSGTIMTFKQNLGSI-IHCISDARGDDSSFAD--A
Mle-Panxα3   MLLLGSLGT-IKNLS-IFKDLSLDDWLDQMNRTFMFLLLCFMGTIVAVSQYTGKN-ISC--------DGFTK--F
Mle-Panxα4   -MVIELLAG-YKGLS-PFKDATVDDSWDQINRCYVFIAMVVMGAVTTMRQYSGTL-IAC--------DGFTK--F
Mle-Panxα5   -MIYWVWAV-FKRMA-PFKVVTLDDRWDQMNRSFMMPLTMSFAYLIDYGIIAGST-IKC--------TGFEDSFR
Mle-Panxα6   -MLLEILAN-FKGAT-PFKEIVLDDKWDQINRCYMFLLCVIFGTVVTFRQYTGGI-IAC--------DGLTK--F
Mle-Panxα7   -MGVEILFPIINRATAPIKSVNIDDLSSQLNRTFMFYLSLTFAITITIRQQLGGAYIAC--------DGFSRDEE
Mle-Panxα12  -MVIDILSG-FKGIT-PFKGITLDDGWDQINRSFMFVLCVLMGTVVTVRQYAGGI-ISC--------DGFTK--Y

 4 75
Dre-Panxγ1a  ----------MAIAHAATEYVFADFVLKDPASENR-------YKGIRLDLALDKIVTCVAVGLPLLLISLAFAQE
Dre-Panxγ1b  ----------MAIARVATEYVFSDFLLKE-QSDSK-------YKGVRLELATDKLVSFIAVGLPLLLISLAFAQE
Dre-Panxγ2   MQNILEQNLDMATALLAGEK-LKELIMPGSTQDEKGGVLAGLMVQLKLELPFDRVVTIGTVIIPILLVTLVFTRN
Dre-Panxγ3   ----------MSIANTAAQAILSDALLKESNGDNR-------IRHLELDLPLDKVIKFISVGLPLLLVSMAFARE

 4 75
Dme-Panxδ8  --MLDIFRGLKNLVKV----SHVKTDSIVFRLHYSITVMILMSFSLIITTRQYVGNPIDCVHTKDIPEDVLNTYC
Dme-Panxδ5  --MFSAVKPLSKYLQF----KSIRIYDSVFTIHSRCTVVILLTCSLLLSARQYFGDPIQCI-SEEKNIEYIQSYC
Dme-Panxδ7  --MLNTFSSVRQYLKF--DLTRVVIDNIVFKLHYRWTFVILLVATLLITSRQYIGEHIQCL-SDGVVSPVINTFC
Dme-Panxδ3  MAVFGMVSAVSGFIKIRYLLDKAVIDNMVFRCHYRITTAILFTCCIIVTANNLIGDPISCINDGAIPMHVINTFC

.... 15 more alignments ...

 7 75
Sra-Panxε10  --MVLTTVLSMI--RYVSEIDD--RDFVDRLHGFFTTNILIGLAVLVSFKQFGGKPIECLVPDIFTSSWEQYAEN
Sra-Panxε11  --MMIESLVGMI--KYLSPRED--DDWSDRMNYLYTPNILLAFSVLISFKQFGGRPIECMFPNKFPGSWEQYAEN
Sra-Panxε12  ----MNFVTSLL--SAISPLSD--GDFVDRLNYCYTTTILIVCSVFISGWSFVGQPIQCWFPAYYKGWWMEYALD
Sra-Panxε13  -------------------MRS--NDLLRQ--------------VLTSAKQYVGQPIQCWIPAQFTGAWEQYSEN
Sra-Panxε14  ----MLTLPDIV-KDYTALASDVIDDHFDRINCAYSVWILM-FAVIATTTAVYDKPIQCFHKLDHPENWVQGLNN
Sra-Panxε15  MNHQLGSQLGLLINKTKNSGHD--DDAVDRINYAKTAFILAGFALFVMAIQNIGDPITCWVPAEYPETWNRYIRQ
Sra-Panxε19  MFFHATLARAFI--QSLHLRGD--DDFTDRLNYYYTPIMLAVACLLISAKQYGGTPIECWINPHSKESMEQYIES

Usage example 1

$: alb Pannexins.physr -stf ~/Panx_alignments

Output

New file: /home/Panx_alignments/Alignment_01.physr
New file: /home/Panx_alignments/Alignment_02.physr
New file: /home/Panx_alignments/Alignment_03.physr

.... 15 more files ...

New file: /home/Panx_alignments/Alignment_19.physr

Usage example 2

Specify a custom prefix with a second argument

$: alb Pannexins.physr -stf ~/Panx_alignments 'Pannexin_'

Output

New file: /home/Panx_alignments/Pannexin_01.physr
New file: /home/Panx_alignments/Pannexin_02.physr
New file: /home/Panx_alignments/Pannexin_03.physr

.... 15 more files ...

New file: /home/Panx_alignments/Pannexin_19.physr