SB Hash IDs

--hash_ids, -hi

Description

Rename all sequence IDs to a hash string selected randomly from the ascii_letters set.

A hash-map table is written to stderr above the sequences which are written to stdout. This can be silenced with the -q flag

For developers; an attribute is appended to the SeqBuddy object named hash_map. It is an OrderedDict(), of the form {hash: original_id}

Argument

Hash length ( int )

Optional. Specify the length of the new hash strings IDs (default = 10). If the number of possible hashes is smaller than twice the total number of sequences, then a warning will be printed to stderr and the hash length will be increased automatically until it meets this criteria.

Examples

Input file: Drosophila.nex

#NEXUS
begin data;
    dimensions ntax=8 nchar=316;
    format datatype=protein missing=? gap=-;
matrix
'Dme-Panxδ3' -----GFI---K----IDNMVFRCHYRITAILFTC-CIIVTANNLIGDPISCI--IPMHVINTFCWITYTYTV---A--GPGLE-K--HSYYQWVPFVLFFQGLMFYVPHWVWKM-D-GKIRMITG--VDDRDRIL-KYFVNNT--HNGYSFYFFCELLNFINVIVNIFMVDKFLGGAFMSYGTDVLKFSNMDQ-DRFDPMIEIFPRLTKCTFHKFGPSGSVQKHDTLCVLALNILNEKIYIFLWFWFIILATISGVAVLYSVVI---TR-TIR----------K--EGDFLILHFLSQNLSTRSYSDML-Q----
'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-Panxδ2' MDVFGSVKGLLKIDQV-DNNVFRMHYKATVIILIAFSLLVTSRQYIGDPIDCIVEIPLGVMDTYCWIYSTFTVPEGRDVQP--GSEKYHKYYQWVCFVLFFQAILFYVPRYLWKSWEGGRLKMLVDLSVNDKDRKIVDYFG-NLNRHNFYAFFFVCEALNFVNVIGQIYFVDFFLDGEFSTYGSDVLKFTELEPDERIDPMARVFPKVTKCTFHKYGPSGSVQTHDGLCVLPLNIVNEKIYVFLWFWFIILSIMSI-SLIYRIAVAPKLRHLLLRARSRAESEVEVAIGDWFLLYQLGKNIDPLIYKEVISDLEMG
'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-Panxδ4' MAAVKPLSKYLQFKVHIYDAIFTLHSKVTVALLLACTFLLSSKQYFGDPIQCF-G-D-KDMDAFCWIYGAYL-QCAVSK--VVEN--YITYYQWVVLVLLLESFVFYMPAFLWKIWEGGRLKHLCDFKRTHRV--LVNYFETHFR----YFVYVFCEILNLSISILNFLLLDVFFGGFWGRYRNALY-------NQWI-AV---FPKCAKCEYKG-GPSGSSNIYDYLCLLPLNILNEKIFAFLWIWFI-LAMLISLKFLYRLAVLYPMRLQLLRPKKHLQVALNCSFGDWFVLMRVGNNISPELFRKLLEEL---
'Dme-Panxδ1' YKLLGSLKSYLKWQIQTDNAVFRLHNSFTTVLLLTCSLIITATQYVGQPISCIVGVP-HVVNTFCWIHSTFTMPDRREVHPGVDF-KYYTYYQWVCFVLFFQAMACYTPKFLWNKFEGGLMRMIVGLNITRKRDALLDYLIKHVKRHKLY-AYWACEFLCCINIIVQMYLMNRFFDGEFLSYGTNIMKLSDVPQEQRVDPMVYVFPRVTKCTFHKYGPSGSLQKHDSLCILPLNIVNEKTYVFIWFWFWILLVLLGL--VFRCIIFPKFRPRLLNASNRIPMECRLDIGDWWLIYMLGRNLDPVIYKDVMSEFQVP
'Dme-Panxδ8' LDIFRGLKNLVKVSVKTDSIVFRLHYSITVMILMSFSLIITTRQYVGNPIDCVTDIP-DVLNTYCWIQSTYTLKSLVSVYPGIGNKKHYKYYQWVCFCLFFQAILFYTPRWLWKSWEGGKIHALIDLDISEKKKLLLDYLWENLRYHNWW-AYYVCELLALINVIGQMFLMNRFFDGEFITFGLKVIDYMETDQEDRMDPMIYIFPRMTKCTFFKYGSSGEVEKHDAICILPLNVVNEKIYIFLWFWFILLTFLTLLTLIYRVIIFPRMRVYLFRMRFRVRRDIEIKMGDWFLLYLLGENIDTVIFRDVVQDLRL-
;
end;

Usage example 1

$: sb Drosophila.nex -hi

Output

# Hash table
AOWbwXrHoH,Dme-Panxδ3
0MCIfy1A22,Dme-Panxδ7
YYVKzOc2mA,Dme-Panxδ2
euQWHu839C,Dme-Panxδ5
6yf3HRiqPH,Dme-Panxδ6
vXZcyssJwI,Dme-Panxδ4
OWMQHsQpbD,Dme-Panxδ1
DuqM1wgjFe,Dme-Panxδ8

#NEXUS
begin data;
	dimensions ntax=8 nchar=316;
	format datatype=protein missing=? gap=-;
matrix
AOWbwXrHoH -----GFI---K----IDNMVFRCHYRITAILFTC-CIIVTANNLIGDPISCI--IPMHVINTFCWITYTYTV---A--GPGLE-K--HSYYQWVPFVLFFQGLMFYVPHWVWKM-D-GKIRMITG--VDDRDRIL-KYFVNNT--HNGYSFYFFCELLNFINVIVNIFMVDKFLGGAFMSYGTDVLKFSNMDQ-DRFDPMIEIFPRLTKCTFHKFGPSGSVQKHDTLCVLALNILNEKIYIFLWFWFIILATISGVAVLYSVVI---TR-TIR----------K--EGDFLILHFLSQNLSTRSYSDML-Q----
0MCIfy1A22 --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
YYVKzOc2mA MDVFGSVKGLLKIDQV-DNNVFRMHYKATVIILIAFSLLVTSRQYIGDPIDCIVEIPLGVMDTYCWIYSTFTVPEGRDVQP--GSEKYHKYYQWVCFVLFFQAILFYVPRYLWKSWEGGRLKMLVDLSVNDKDRKIVDYFG-NLNRHNFYAFFFVCEALNFVNVIGQIYFVDFFLDGEFSTYGSDVLKFTELEPDERIDPMARVFPKVTKCTFHKYGPSGSVQTHDGLCVLPLNIVNEKIYVFLWFWFIILSIMSI-SLIYRIAVAPKLRHLLLRARSRAESEVEVAIGDWFLLYQLGKNIDPLIYKEVISDLEMG
euQWHu839C MSAVKPLSKYLQFKIRIYDSVFTIHSRCTVVILLTCSLLLSARQYFGDPIQCI-S-EEKNIESYCWTMGTYYNEASIAE--GVEIRQYLRYYQWVIILLLFQSFVFYFPSCLWKVWEGRRLKQLCEVDNTRRM--LVKYFDMHFC----YMAYVFCEVLNFLISVVNIIVLEVFLNGFWSKYLRALW-------DRWV-SV---FPKIAKCELKF-GGSGTANVMDNLCILPLNILNEKIFVFLWAWFL-LALMSGLNLLCRLAICSRLREQMIRTKRHVKRALDLTIGDWFLMMKVSVNVNPMLFRDLMQEL---
6yf3HRiqPH MAAVKPLSNYLRLKVRIYDPIFTLHSKCTIVILLTCTFLLSAKQYFGEPILCL-S-SERQADSYCWTMGTYWNEQSIAE--GVETRMYLRYYQWVFMILLFQSLLFYFPSFLWKVWEGQRMEQLCEVDRTRQM--LTRYFPIHWC----YSIYAFCELLNVFISILNFWLMDVVFNGFWYKYIHALW-------NLWM-RV---FPKVAKCEFVY-GPSGTPNIMDILCVLPLNILNEKIFAVLYVWFL-FALLAIMNILYRLLICCPLRLQLLNPKSHVREVLSAGYGDWFVLMCVSINVNPTLFRELLEQL--D
vXZcyssJwI MAAVKPLSKYLQFKVHIYDAIFTLHSKVTVALLLACTFLLSSKQYFGDPIQCF-G-D-KDMDAFCWIYGAYL-QCAVSK--VVEN--YITYYQWVVLVLLLESFVFYMPAFLWKIWEGGRLKHLCDFKRTHRV--LVNYFETHFR----YFVYVFCEILNLSISILNFLLLDVFFGGFWGRYRNALY-------NQWI-AV---FPKCAKCEYKG-GPSGSSNIYDYLCLLPLNILNEKIFAFLWIWFI-LAMLISLKFLYRLAVLYPMRLQLLRPKKHLQVALNCSFGDWFVLMRVGNNISPELFRKLLEEL---
OWMQHsQpbD YKLLGSLKSYLKWQIQTDNAVFRLHNSFTTVLLLTCSLIITATQYVGQPISCIVGVP-HVVNTFCWIHSTFTMPDRREVHPGVDF-KYYTYYQWVCFVLFFQAMACYTPKFLWNKFEGGLMRMIVGLNITRKRDALLDYLIKHVKRHKLY-AYWACEFLCCINIIVQMYLMNRFFDGEFLSYGTNIMKLSDVPQEQRVDPMVYVFPRVTKCTFHKYGPSGSLQKHDSLCILPLNIVNEKTYVFIWFWFWILLVLLGL--VFRCIIFPKFRPRLLNASNRIPMECRLDIGDWWLIYMLGRNLDPVIYKDVMSEFQVP
DuqM1wgjFe LDIFRGLKNLVKVSVKTDSIVFRLHYSITVMILMSFSLIITTRQYVGNPIDCVTDIP-DVLNTYCWIQSTYTLKSLVSVYPGIGNKKHYKYYQWVCFCLFFQAILFYTPRWLWKSWEGGKIHALIDLDISEKKKLLLDYLWENLRYHNWW-AYYVCELLALINVIGQMFLMNRFFDGEFITFGLKVIDYMETDQEDRMDPMIYIFPRMTKCTFFKYGSSGEVEKHDAICILPLNVVNEKIYIFLWFWFILLTFLTLLTLIYRVIIFPRMRVYLFRMRFRVRRDIEIKMGDWFLLYLLGENIDTVIFRDVVQDLRL-
;
end;

Usage example 2

Here we are pulling in the input file three times (i.e., triplicate of each sequence) for a total of 24 sequences, and then trying to apply a hash length of '1'. SeqBuddy will complain that this hash length is too short for the dataset size, and will automatically increase the hash length to a valid minimum (in this case, '2').

$: sb Drosophila.nex Drosophila.nex Drosophila.nex -hi 1

Output

Warning: The hash_length parameter was passed in with the value 1. This is too small to properly cover all sequences, so it has been increased to 2.

# Hash table
om,Dme-Panxδ3
LF,Dme-Panxδ7
ws,Dme-Panxδ2
........

#NEXUS
begin data;
	dimensions ntax=24 nchar=316;
	format datatype=protein missing=? gap=-;
matrix
om -----GFI---K----IDNMVFRCHYRITAILFTC-CIIVTANNLIGDPISCI--IPMHVINTFCWITYTYTV---A--GPGLE-K--HSYYQWVPFVLFFQGLMFYVPHWVWKM-D-GKIRMITG--VDDRDRIL-KYFVNNT--HNGYSFYFFCELLNFINVIVNIFMVDKFLGGAFMSYGTDVLKFSNMDQ-DRFDPMIEIFPRLTKCTFHKFGPSGSVQKHDTLCVLALNILNEKIYIFLWFWFIILATISGVAVLYSVVI---TR-TIR----------K--EGDFLILHFLSQNLSTRSYSDML-Q----
LF --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
ws MDVFGSVKGLLKIDQV-DNNVFRMHYKATVIILIAFSLLVTSRQYIGDPIDCIVEIPLGVMDTYCWIYSTFTVPEGRDVQP--GSEKYHKYYQWVCFVLFFQAILFYVPRYLWKSWEGGRLKMLVDLSVNDKDRKIVDYFG-NLNRHNFYAFFFVCEALNFVNVIGQIYFVDFFLDGEFSTYGSDVLKFTELEPDERIDPMARVFPKVTKCTFHKYGPSGSVQTHDGLCVLPLNIVNEKIYVFLWFWFIILSIMSI-SLIYRIAVAPKLRHLLLRARSRAESEVEVAIGDWFLLYQLGKNIDPLIYKEVISDLEMG
........