SB Purge - mendessoares/BuddySuite GitHub Wiki

--purge, -prg

Description

Minimize a set of sequences by replacing groups of highly similar sequences with a single representative (inspired by the Purge tool from the MEME suite). The criteria used to determine similarity is BLAST bit-score, and a maximum threshold value is passed in as a parameter. For reference, recently duplicated paralogs will often have bit-scores around 400, while easily recognizable orthologs are often around 100-250.

The 'purged' sequence set is returned, as is a mapping of all sequences that have been removed (unless the -q flag is passed in). The mapping consists of each retained sequence ID, followed by the sequences that have been deleted because they match the retained sequence with a bit-score above the indicated threshold.

Argument

Max bit score ( int )

An integer specifying the maximum bit score threshold for inclusion in the purged sequence set (i.e., smaller values retain fewer sequences).

Examples

Input file: Drosophila.nex

#NEXUS
begin data;
    dimensions ntax=8 nchar=316;
    format datatype=protein missing=? gap=-;
matrix
'Dme-Panxδ1' YKLLGSLKSYLKWQIQTDNAVFRLHNSFTTVLLLTCSLIITATQYVGQPISCIVGVP-HVVNTFCWIHSTFTMPDRREVHPGVDF-KYYTYYQWVCFVLFFQAMACYTPKFLWNKFEGGLMRMIVGLNITRKRDALLDYLIKHVKRHKLY-AYWACEFLCCINIIVQMYLMNRFFDGEFLSYGTNIMKLSDVPQEQRVDPMVYVFPRVTKCTFHKYGPSGSLQKHDSLCILPLNIVNEKTYVFIWFWFWILLVLLGL--VFRCIIFPKFRPRLLNASNRIPMECRLDIGDWWLIYMLGRNLDPVIYKDVMSEFQVP
'Dme-Panxδ2' MDVFGSVKGLLKIDQV-DNNVFRMHYKATVIILIAFSLLVTSRQYIGDPIDCIVEIPLGVMDTYCWIYSTFTVPEGRDVQP--GSEKYHKYYQWVCFVLFFQAILFYVPRYLWKSWEGGRLKMLVDLSVNDKDRKIVDYFG-NLNRHNFYAFFFVCEALNFVNVIGQIYFVDFFLDGEFSTYGSDVLKFTELEPDERIDPMARVFPKVTKCTFHKYGPSGSVQTHDGLCVLPLNIVNEKIYVFLWFWFIILSIMSI-SLIYRIAVAPKLRHLLLRARSRAESEVEVAIGDWFLLYQLGKNIDPLIYKEVISDLEMG
'Dme-Panxδ3' -----GFI---K----IDNMVFRCHYRITAILFTC-CIIVTANNLIGDPISCI--IPMHVINTFCWITYTYTV---A--GPGLE-K--HSYYQWVPFVLFFQGLMFYVPHWVWKM-D-GKIRMITG--VDDRDRIL-KYFVNNT--HNGYSFYFFCELLNFINVIVNIFMVDKFLGGAFMSYGTDVLKFSNMDQ-DRFDPMIEIFPRLTKCTFHKFGPSGSVQKHDTLCVLALNILNEKIYIFLWFWFIILATISGVAVLYSVVI---TR-TIR----------K--EGDFLILHFLSQNLSTRSYSDML-Q----
'Dme-Panxδ4' MAAVKPLSKYLQFKVHIYDAIFTLHSKVTVALLLACTFLLSSKQYFGDPIQCF-G-D-KDMDAFCWIYGAYL-QCAVSK--VVEN--YITYYQWVVLVLLLESFVFYMPAFLWKIWEGGRLKHLCDFKRTHRV--LVNYFETHFR----YFVYVFCEILNLSISILNFLLLDVFFGGFWGRYRNALY-------NQWI-AV---FPKCAKCEYKG-GPSGSSNIYDYLCLLPLNILNEKIFAFLWIWFI-LAMLISLKFLYRLAVLYPMRLQLLRPKKHLQVALNCSFGDWFVLMRVGNNISPELFRKLLEEL---
'Dme-Panxδ5' MSAVKPLSKYLQFKIRIYDSVFTIHSRCTVVILLTCSLLLSARQYFGDPIQCI-S-EEKNIESYCWTMGTYYNEASIAE--GVEIRQYLRYYQWVIILLLFQSFVFYFPSCLWKVWEGRRLKQLCEVDNTRRM--LVKYFDMHFC----YMAYVFCEVLNFLISVVNIIVLEVFLNGFWSKYLRALW-------DRWV-SV---FPKIAKCELKF-GGSGTANVMDNLCILPLNILNEKIFVFLWAWFL-LALMSGLNLLCRLAICSRLREQMIRTKRHVKRALDLTIGDWFLMMKVSVNVNPMLFRDLMQEL---
'Dme-Panxδ6' MAAVKPLSNYLRLKVRIYDPIFTLHSKCTIVILLTCTFLLSAKQYFGEPILCL-S-SERQADSYCWTMGTYWNEQSIAE--GVETRMYLRYYQWVFMILLFQSLLFYFPSFLWKVWEGQRMEQLCEVDRTRQM--LTRYFPIHWC----YSIYAFCELLNVFISILNFWLMDVVFNGFWYKYIHALW-------NLWM-RV---FPKVAKCEFVY-GPSGTPNIMDILCVLPLNILNEKIFAVLYVWFL-FALLAIMNILYRLLICCPLRLQLLNPKSHVREVLSAGYGDWFVLMCVSINVNPTLFRELLEQL--D
'Dme-Panxδ7' --L--SV----R-Q-RIDNIVFKLHYRWTVILLVA-TLLITSRQYIGEHIQCL--VVSPVINTFCFFTPTF-VD--P---PGI--D-RHAYYQWVPFVLFFQALCFYIPHALWKW-EGGRIKALVK--LG-MERVKD---IRDM--RLNWG-HVFAEVLNLINLLLQITWTNRFLGGQFLTLG------HALKN-RSDEVV---FPKITKCKFHKFGDSGSIQMHDALCVMALNIMNEKIYIILWFWYAFLLIVTVLGLLWRLCF---VR-WSL----------P-LASNWMFLFFLRSNLS-----E-L----DN
'Dme-Panxδ8' LDIFRGLKNLVKVSVKTDSIVFRLHYSITVMILMSFSLIITTRQYVGNPIDCVTDIP-DVLNTYCWIQSTYTLKSLVSVYPGIGNKKHYKYYQWVCFCLFFQAILFYTPRWLWKSWEGGKIHALIDLDISEKKKLLLDYLWENLRYHNWW-AYYVCELLALINVIGQMFLMNRFFDGEFITFGLKVIDYMETDQEDRMDPMIYIFPRMTKCTFFKYGSSGEVEKHDAICILPLNVVNEKIYIFLWFWFILLTFLTLLTLIYRVIIFPRMRVYLFRMRFRVRRDIEIKMGDWFLLYLLGENIDTVIFRDVVQDLRL-
;
end;

Usage example 1

$: sb Drosophila.nex -prg 230

Output

### Deleted record mapping ###
Dme-Panxδ1
Dme-Panxδ2, Dme-Panxδ8

Dme-Panxδ3
Dme-Panxδ2, Dme-Panxδ8

Dme-Panxδ4
Dme-Panxδ5, Dme-Panxδ6

Dme-Panxδ7
##############################

#NEXUS
begin data;
	dimensions ntax=4 nchar=316;
	format datatype=protein missing=? gap=-;
matrix
'Dme-Panxδ1' YKLLGSLKSYLKWQIQTDNAVFRLHNSFTTVLLLTCSLIITATQYVGQPISCIVGVP-HVVNTFCWIHSTFTMPDRREVHPGVDF-KYYTYYQWVCFVLFFQAMACYTPKFLWNKFEGGLMRMIVGLNITRKRDALLDYLIKHVKRHKLY-AYWACEFLCCINIIVQMYLMNRFFDGEFLSYGTNIMKLSDVPQEQRVDPMVYVFPRVTKCTFHKYGPSGSLQKHDSLCILPLNIVNEKTYVFIWFWFWILLVLLGL--VFRCIIFPKFRPRLLNASNRIPMECRLDIGDWWLIYMLGRNLDPVIYKDVMSEFQVP
'Dme-Panxδ3' -----GFI---K----IDNMVFRCHYRITAILFTC-CIIVTANNLIGDPISCI--IPMHVINTFCWITYTYTV---A--GPGLE-K--HSYYQWVPFVLFFQGLMFYVPHWVWKM-D-GKIRMITG--VDDRDRIL-KYFVNNT--HNGYSFYFFCELLNFINVIVNIFMVDKFLGGAFMSYGTDVLKFSNMDQ-DRFDPMIEIFPRLTKCTFHKFGPSGSVQKHDTLCVLALNILNEKIYIFLWFWFIILATISGVAVLYSVVI---TR-TIR----------K--EGDFLILHFLSQNLSTRSYSDML-Q----
'Dme-Panxδ4' MAAVKPLSKYLQFKVHIYDAIFTLHSKVTVALLLACTFLLSSKQYFGDPIQCF-G-D-KDMDAFCWIYGAYL-QCAVSK--VVEN--YITYYQWVVLVLLLESFVFYMPAFLWKIWEGGRLKHLCDFKRTHRV--LVNYFETHFR----YFVYVFCEILNLSISILNFLLLDVFFGGFWGRYRNALY-------NQWI-AV---FPKCAKCEYKG-GPSGSSNIYDYLCLLPLNILNEKIFAFLWIWFI-LAMLISLKFLYRLAVLYPMRLQLLRPKKHLQVALNCSFGDWFVLMRVGNNISPELFRKLLEEL---
'Dme-Panxδ7' --L--SV----R-Q-RIDNIVFKLHYRWTVILLVA-TLLITSRQYIGEHIQCL--VVSPVINTFCFFTPTF-VD--P---PGI--D-RHAYYQWVPFVLFFQALCFYIPHALWKW-EGGRIKALVK--LG-MERVKD---IRDM--RLNWG-HVFAEVLNLINLLLQITWTNRFLGGQFLTLG------HALKN-RSDEVV---FPKITKCKFHKFGDSGSIQMHDALCVMALNIMNEKIYIILWFWYAFLLIVTVLGLLWRLCF---VR-WSL----------P-LASNWMFLFFLRSNLS-----E-L----DN
;
end;

Usage example 2

$: sb Drosophila.nex -prg 150 -q

output

#NEXUS
begin data;
	dimensions ntax=1 nchar=316;
	format datatype=protein missing=? gap=-;
matrix
'Dme-Panxδ1' YKLLGSLKSYLKWQIQTDNAVFRLHNSFTTVLLLTCSLIITATQYVGQPISCIVGVP-HVVNTFCWIHSTFTMPDRREVHPGVDF-KYYTYYQWVCFVLFFQAMACYTPKFLWNKFEGGLMRMIVGLNITRKRDALLDYLIKHVKRHKLY-AYWACEFLCCINIIVQMYLMNRFFDGEFLSYGTNIMKLSDVPQEQRVDPMVYVFPRVTKCTFHKYGPSGSLQKHDSLCILPLNIVNEKTYVFIWFWFWILLVLLGL--VFRCIIFPKFRPRLLNASNRIPMECRLDIGDWWLIYMLGRNLDPVIYKDVMSEFQVP
;
end;