tests/testthat/_snaps/pairwise_aligment.md
In currocam/HMMERutils: HMMERutils
Test that pairwise_alignment_sequence_identity works with missing values
structure(list(from = c(".", ".", ".", ".", ".", ".", ".", ".",
".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".",
".", ".", ".", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY",
"ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY",
"ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY",
"ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY",
"ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "GRB2_RAT",
"GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT",
"GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT",
"GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT",
"GRB2_RAT", "GRB2_RAT", "GRB2_RAT", ".1", ".1", ".1", ".1", ".1",
".1", ".1", ".1", ".1", ".1", ".1", ".1", ".1", ".1", ".1", ".1",
".1", ".1", ".1", ".1", ".1", ".2", ".2", ".2", ".2", ".2", ".2",
".2", ".2", ".2", ".2", ".2", ".2", ".2", ".2", ".2", ".2", ".2",
".2", ".2", ".2", ".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3",
".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3",
".4", ".4", ".4", ".4", ".4", ".4", ".4", ".4", ".4", ".4", ".4",
".4", ".4", ".4", ".4", ".4", ".4", ".4", "MYO1_NEUCR", "MYO1_NEUCR",
"MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR",
"MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR",
"MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR",
"SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN",
"SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN",
"SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN",
"SRC_HUMAN", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA",
"SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA",
"SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA",
"SRK2_SPOLA", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN",
"BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN",
"BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN",
"YES_HUMAN", "YES_HUMAN", "YES_HUMAN", "YES_HUMAN", "YES_HUMAN",
"YES_HUMAN", "YES_HUMAN", "YES_HUMAN", "YES_HUMAN", "YES_HUMAN",
"YES_HUMAN", "YES_HUMAN", "YES_HUMAN", ".5", ".5", ".5", ".5",
".5", ".5", ".5", ".5", ".5", ".5", ".5", ".5", "YES_RAT", "YES_RAT",
"YES_RAT", "YES_RAT", "YES_RAT", "YES_RAT", "YES_RAT", "YES_RAT",
"YES_RAT", "YES_RAT", "YES_RAT", ".6", ".6", ".6", ".6", ".6",
".6", ".6", ".6", ".6", ".6", "SH2B3_HUMAN", "SH2B3_HUMAN", "SH2B3_HUMAN",
"SH2B3_HUMAN", "SH2B3_HUMAN", "SH2B3_HUMAN", "SH2B3_HUMAN", "SH2B3_HUMAN",
"SH2B3_HUMAN", "SH3R2_MOUSE", "SH3R2_MOUSE", "SH3R2_MOUSE", "SH3R2_MOUSE",
"SH3R2_MOUSE", "SH3R2_MOUSE", "SH3R2_MOUSE", "SH3R2_MOUSE", "FYN_BOVIN",
"FYN_BOVIN", "FYN_BOVIN", "FYN_BOVIN", "FYN_BOVIN", "FYN_BOVIN",
"FYN_BOVIN", "CRK_HUMAN", "CRK_HUMAN", "CRK_HUMAN", "CRK_HUMAN",
"CRK_HUMAN", "CRK_HUMAN", ".7", ".7", ".7", ".7", ".7", "LYN_MOUSE",
"LYN_MOUSE", "LYN_MOUSE", "LYN_MOUSE", "SH34A_DANRE", "SH34A_DANRE",
"SH34A_DANRE", ".8", ".8", "SH2B2_MOUSE", "ABL_FSVHY", "GRB2_RAT",
".1", ".2", ".3", ".4", "MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA",
"BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN",
"SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE",
".8", "SH2B2_MOUSE", ".9", "GRB2_RAT", ".1", ".2", ".3", ".4",
"MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA", "BCAR3_BOVIN", "YES_HUMAN",
".5", "YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN",
"CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE",
".9", ".1", ".2", ".3", ".4", "MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA",
"BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN",
"SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE",
".8", "SH2B2_MOUSE", ".9", ".2", ".3", ".4", "MYO1_NEUCR", "SRC_HUMAN",
"SRK2_SPOLA", "BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6",
"SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7",
"LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", ".3",
".4", "MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA", "BCAR3_BOVIN",
"YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE",
"FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE", ".8",
"SH2B2_MOUSE", ".9", ".4", "MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA",
"BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN",
"SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE",
".8", "SH2B2_MOUSE", ".9", "MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA",
"BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN",
"SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE",
".8", "SH2B2_MOUSE", ".9", "SRC_HUMAN", "SRK2_SPOLA", "BCAR3_BOVIN",
"YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE",
"FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE", ".8",
"SH2B2_MOUSE", ".9", "SRK2_SPOLA", "BCAR3_BOVIN", "YES_HUMAN",
".5", "YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN",
"CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE",
".9", "BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN",
"SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE",
".8", "SH2B2_MOUSE", ".9", "YES_HUMAN", ".5", "YES_RAT", ".6",
"SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7",
"LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", ".5",
"YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN",
".7", "LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9",
"YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN",
".7", "LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9",
".6", "SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN",
".7", "LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9",
"SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7",
"LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", "SH3R2_MOUSE",
"FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE", ".8",
"SH2B2_MOUSE", ".9", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE",
"SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", "CRK_HUMAN", ".7",
"LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", ".7",
"LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", "LYN_MOUSE",
"SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", "SH34A_DANRE", ".8",
"SH2B2_MOUSE", ".9", ".8", "SH2B2_MOUSE", ".9", "SH2B2_MOUSE",
".9", ".9"), to = c("ABL_FSVHY", "GRB2_RAT", ".1", ".2", ".3",
".4", "MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA", "BCAR3_BOVIN",
"YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE",
"FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE", ".8",
"SH2B2_MOUSE", ".9", "GRB2_RAT", ".1", ".2", ".3", ".4", "MYO1_NEUCR",
"SRC_HUMAN", "SRK2_SPOLA", "BCAR3_BOVIN", "YES_HUMAN", ".5",
"YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN",
".7", "LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9",
".1", ".2", ".3", ".4", "MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA",
"BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN",
"SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE",
".8", "SH2B2_MOUSE", ".9", ".2", ".3", ".4", "MYO1_NEUCR", "SRC_HUMAN",
"SRK2_SPOLA", "BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6",
"SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7",
"LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", ".3",
".4", "MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA", "BCAR3_BOVIN",
"YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE",
"FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE", ".8",
"SH2B2_MOUSE", ".9", ".4", "MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA",
"BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN",
"SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE",
".8", "SH2B2_MOUSE", ".9", "MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA",
"BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN",
"SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE",
".8", "SH2B2_MOUSE", ".9", "SRC_HUMAN", "SRK2_SPOLA", "BCAR3_BOVIN",
"YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE",
"FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE", ".8",
"SH2B2_MOUSE", ".9", "SRK2_SPOLA", "BCAR3_BOVIN", "YES_HUMAN",
".5", "YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN",
"CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE",
".9", "BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN",
"SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE",
".8", "SH2B2_MOUSE", ".9", "YES_HUMAN", ".5", "YES_RAT", ".6",
"SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7",
"LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", ".5",
"YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN",
".7", "LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9",
"YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN",
".7", "LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9",
".6", "SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN",
".7", "LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9",
"SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7",
"LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", "SH3R2_MOUSE",
"FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE", ".8",
"SH2B2_MOUSE", ".9", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE",
"SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", "CRK_HUMAN", ".7",
"LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", ".7",
"LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", "LYN_MOUSE",
"SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", "SH34A_DANRE", ".8",
"SH2B2_MOUSE", ".9", ".8", "SH2B2_MOUSE", ".9", "SH2B2_MOUSE",
".9", ".9", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".",
".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".",
".", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY",
"ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY",
"ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY",
"ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY",
"ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "GRB2_RAT", "GRB2_RAT",
"GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT",
"GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT",
"GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT",
"GRB2_RAT", "GRB2_RAT", ".1", ".1", ".1", ".1", ".1", ".1", ".1",
".1", ".1", ".1", ".1", ".1", ".1", ".1", ".1", ".1", ".1", ".1",
".1", ".1", ".1", ".2", ".2", ".2", ".2", ".2", ".2", ".2", ".2",
".2", ".2", ".2", ".2", ".2", ".2", ".2", ".2", ".2", ".2", ".2",
".2", ".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3",
".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3", ".4", ".4",
".4", ".4", ".4", ".4", ".4", ".4", ".4", ".4", ".4", ".4", ".4",
".4", ".4", ".4", ".4", ".4", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR",
"MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR",
"MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR",
"MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "SRC_HUMAN",
"SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN",
"SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN",
"SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN",
"SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA",
"SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA",
"SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA",
"BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN",
"BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN",
"BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "YES_HUMAN",
"YES_HUMAN", "YES_HUMAN", "YES_HUMAN", "YES_HUMAN", "YES_HUMAN",
"YES_HUMAN", "YES_HUMAN", "YES_HUMAN", "YES_HUMAN", "YES_HUMAN",
"YES_HUMAN", "YES_HUMAN", ".5", ".5", ".5", ".5", ".5", ".5",
".5", ".5", ".5", ".5", ".5", ".5", "YES_RAT", "YES_RAT", "YES_RAT",
"YES_RAT", "YES_RAT", "YES_RAT", "YES_RAT", "YES_RAT", "YES_RAT",
"YES_RAT", "YES_RAT", ".6", ".6", ".6", ".6", ".6", ".6", ".6",
".6", ".6", ".6", "SH2B3_HUMAN", "SH2B3_HUMAN", "SH2B3_HUMAN",
"SH2B3_HUMAN", "SH2B3_HUMAN", "SH2B3_HUMAN", "SH2B3_HUMAN", "SH2B3_HUMAN",
"SH2B3_HUMAN", "SH3R2_MOUSE", "SH3R2_MOUSE", "SH3R2_MOUSE", "SH3R2_MOUSE",
"SH3R2_MOUSE", "SH3R2_MOUSE", "SH3R2_MOUSE", "SH3R2_MOUSE", "FYN_BOVIN",
"FYN_BOVIN", "FYN_BOVIN", "FYN_BOVIN", "FYN_BOVIN", "FYN_BOVIN",
"FYN_BOVIN", "CRK_HUMAN", "CRK_HUMAN", "CRK_HUMAN", "CRK_HUMAN",
"CRK_HUMAN", "CRK_HUMAN", ".7", ".7", ".7", ".7", ".7", "LYN_MOUSE",
"LYN_MOUSE", "LYN_MOUSE", "LYN_MOUSE", "SH34A_DANRE", "SH34A_DANRE",
"SH34A_DANRE", ".8", ".8", "SH2B2_MOUSE"), PID = c(NaN, NaN,
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, 20.6018518518519,
NaN, NaN, NaN, NaN, 16.557911908646, 39.1554702495202, 39.6788990825688,
21.1042944785276, 38.4191176470588, NaN, 38.3763837638376, NaN,
20.4116638078902, 19.2737430167598, 37.8531073446328, 23.0434782608696,
NaN, 39.1472868217054, 18.7702265372168, NaN, 22.1705426356589,
NaN, NaN, NaN, NaN, NaN, 10.3684661525278, 21.3836477987421,
18.9265536723164, 13.5757575757576, 18.5321100917431, NaN, 18.4162062615101,
NaN, 17.3913043478261, 15.4794520547945, 20.9643605870021, 22.2950819672131,
NaN, 18.7134502923977, 12.2026887280248, NaN, 15.6351791530945,
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
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NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, 17.8747940691928, 15.0943396226415, 20.5350118017309, 18.6290322580645,
NaN, 18.1964573268921, NaN, 17.5762439807384, 20.2614379084967,
17.566478646253, 12.8744939271255, NaN, 17.440912795436, 21.1746522411128,
NaN, 19.0325138778747, NaN, 62.2282608695652, 21.7129071170084,
75.3676470588235, NaN, 74.8175182481752, NaN, 23.0182926829268,
21.5968586387435, 69.4139194139194, 21.5469613259669, NaN, 53.9179104477612,
20.7106598984772, NaN, 22.6299694189602, NaN, 18.1044957472661,
43.75, NaN, 45.1866404715128, NaN, 20.6185567010309, 18.9265536723164,
63.3152173913044, 21.4659685863874, NaN, 45.2586206896552, 17.5054704595186,
NaN, 20.7792207792208, NaN, 21.6248506571087, NaN, 20.8085612366231,
NaN, 22.5501770956316, 24.0950226244344, 20.2127659574468, 18.2519280205656,
NaN, 21.7964071856287, 22.0100502512563, NaN, 22.4157955865273,
NaN, NaN, 95.5801104972376, NaN, 21.40625, 20.5804749340369,
73.4545454545455, 18, NaN, 55.3308823529412, 21.1597151576806,
NaN, 22.4163027656477, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, NaN, NaN, NaN, 21.4285714285714, 20.4485488126649,
73.224043715847, 18.2481751824818, NaN, 55.7798165137615, 21.6326530612245,
NaN, 22.0740740740741, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, 21.9195849546044, 21.0776545166403, 19.4295900178253,
NaN, 19.1275167785235, 19.1446028513238, NaN, 38.0809595202399,
NaN, 19.4666666666667, 17.7027027027027, NaN, 20.6391478029294,
20.99609375, NaN, 23.4015345268542, NaN, 21.6014897579143, NaN,
55.7407407407407, 19.6704428424305, NaN, 22.7810650887574, NaN,
NaN, 19.1938579654511, 15.2965660770031, NaN, 18.8498402555911,
NaN, NaN, NaN, NaN, NaN, NaN, 19.3679918450561, NaN, 22.8441754916793,
NaN, NaN, 19.6969696969697, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, 20.6018518518519, NaN,
NaN, NaN, NaN, 16.557911908646, 39.1554702495202, 39.6788990825688,
21.1042944785276, 38.4191176470588, NaN, 38.3763837638376, NaN,
20.4116638078902, 19.2737430167598, 37.8531073446328, 23.0434782608696,
NaN, 39.1472868217054, 18.7702265372168, NaN, 22.1705426356589,
NaN, NaN, NaN, NaN, NaN, 10.3684661525278, 21.3836477987421,
18.9265536723164, 13.5757575757576, 18.5321100917431, NaN, 18.4162062615101,
NaN, 17.3913043478261, 15.4794520547945, 20.9643605870021, 22.2950819672131,
NaN, 18.7134502923977, 12.2026887280248, NaN, 15.6351791530945,
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
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NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, 17.8747940691928, 15.0943396226415, 20.5350118017309, 18.6290322580645,
NaN, 18.1964573268921, NaN, 17.5762439807384, 20.2614379084967,
17.566478646253, 12.8744939271255, NaN, 17.440912795436, 21.1746522411128,
NaN, 19.0325138778747, NaN, 62.2282608695652, 21.7129071170084,
75.3676470588235, NaN, 74.8175182481752, NaN, 23.0182926829268,
21.5968586387435, 69.4139194139194, 21.5469613259669, NaN, 53.9179104477612,
20.7106598984772, NaN, 22.6299694189602, NaN, 18.1044957472661,
43.75, NaN, 45.1866404715128, NaN, 20.6185567010309, 18.9265536723164,
63.3152173913044, 21.4659685863874, NaN, 45.2586206896552, 17.5054704595186,
NaN, 20.7792207792208, NaN, 21.6248506571087, NaN, 20.8085612366231,
NaN, 22.5501770956316, 24.0950226244344, 20.2127659574468, 18.2519280205656,
NaN, 21.7964071856287, 22.0100502512563, NaN, 22.4157955865273,
NaN, NaN, 95.5801104972376, NaN, 21.40625, 20.5804749340369,
73.4545454545455, 18, NaN, 55.3308823529412, 21.1597151576806,
NaN, 22.4163027656477, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, NaN, NaN, NaN, 21.4285714285714, 20.4485488126649,
73.224043715847, 18.2481751824818, NaN, 55.7798165137615, 21.6326530612245,
NaN, 22.0740740740741, NaN, NaN, NaN, NaN, NaN, NaN, NaN, NaN,
NaN, NaN, NaN, 21.9195849546044, 21.0776545166403, 19.4295900178253,
NaN, 19.1275167785235, 19.1446028513238, NaN, 38.0809595202399,
NaN, 19.4666666666667, 17.7027027027027, NaN, 20.6391478029294,
20.99609375, NaN, 23.4015345268542, NaN, 21.6014897579143, NaN,
55.7407407407407, 19.6704428424305, NaN, 22.7810650887574, NaN,
NaN, 19.1938579654511, 15.2965660770031, NaN, 18.8498402555911,
NaN, NaN, NaN, NaN, NaN, NaN, 19.3679918450561, NaN, 22.8441754916793,
NaN, NaN, 19.6969696969697, NaN, NaN, NaN, NaN)), class = c("tbl_df",
"tbl", "data.frame"), row.names = c(NA, -600L))
currocam/HMMERutils documentation built on Feb. 15, 2023, 8:41 p.m.
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Test that pairwise_alignment_sequence_identity works with missing values
structure(list(from = c(".", ".", ".", ".", ".", ".", ".", ".",
".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".",
".", ".", ".", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY",
"ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY",
"ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY",
"ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY",
"ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "ABL_FSVHY", "GRB2_RAT",
"GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT",
"GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT",
"GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT", "GRB2_RAT",
"GRB2_RAT", "GRB2_RAT", "GRB2_RAT", ".1", ".1", ".1", ".1", ".1",
".1", ".1", ".1", ".1", ".1", ".1", ".1", ".1", ".1", ".1", ".1",
".1", ".1", ".1", ".1", ".1", ".2", ".2", ".2", ".2", ".2", ".2",
".2", ".2", ".2", ".2", ".2", ".2", ".2", ".2", ".2", ".2", ".2",
".2", ".2", ".2", ".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3",
".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3", ".3",
".4", ".4", ".4", ".4", ".4", ".4", ".4", ".4", ".4", ".4", ".4",
".4", ".4", ".4", ".4", ".4", ".4", ".4", "MYO1_NEUCR", "MYO1_NEUCR",
"MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR",
"MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR",
"MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR", "MYO1_NEUCR",
"SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN",
"SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN",
"SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN", "SRC_HUMAN",
"SRC_HUMAN", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA",
"SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA",
"SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA", "SRK2_SPOLA",
"SRK2_SPOLA", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN",
"BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN",
"BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN", "BCAR3_BOVIN",
"YES_HUMAN", "YES_HUMAN", "YES_HUMAN", "YES_HUMAN", "YES_HUMAN",
"YES_HUMAN", "YES_HUMAN", "YES_HUMAN", "YES_HUMAN", "YES_HUMAN",
"YES_HUMAN", "YES_HUMAN", "YES_HUMAN", ".5", ".5", ".5", ".5",
".5", ".5", ".5", ".5", ".5", ".5", ".5", ".5", "YES_RAT", "YES_RAT",
"YES_RAT", "YES_RAT", "YES_RAT", "YES_RAT", "YES_RAT", "YES_RAT",
"YES_RAT", "YES_RAT", "YES_RAT", ".6", ".6", ".6", ".6", ".6",
".6", ".6", ".6", ".6", ".6", "SH2B3_HUMAN", "SH2B3_HUMAN", "SH2B3_HUMAN",
"SH2B3_HUMAN", "SH2B3_HUMAN", "SH2B3_HUMAN", "SH2B3_HUMAN", "SH2B3_HUMAN",
"SH2B3_HUMAN", "SH3R2_MOUSE", "SH3R2_MOUSE", "SH3R2_MOUSE", "SH3R2_MOUSE",
"SH3R2_MOUSE", "SH3R2_MOUSE", "SH3R2_MOUSE", "SH3R2_MOUSE", "FYN_BOVIN",
"FYN_BOVIN", "FYN_BOVIN", "FYN_BOVIN", "FYN_BOVIN", "FYN_BOVIN",
"FYN_BOVIN", "CRK_HUMAN", "CRK_HUMAN", "CRK_HUMAN", "CRK_HUMAN",
"CRK_HUMAN", "CRK_HUMAN", ".7", ".7", ".7", ".7", ".7", "LYN_MOUSE",
"LYN_MOUSE", "LYN_MOUSE", "LYN_MOUSE", "SH34A_DANRE", "SH34A_DANRE",
"SH34A_DANRE", ".8", ".8", "SH2B2_MOUSE", "ABL_FSVHY", "GRB2_RAT",
".1", ".2", ".3", ".4", "MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA",
"BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN",
"SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE",
".8", "SH2B2_MOUSE", ".9", "GRB2_RAT", ".1", ".2", ".3", ".4",
"MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA", "BCAR3_BOVIN", "YES_HUMAN",
".5", "YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN",
"CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE",
".9", ".1", ".2", ".3", ".4", "MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA",
"BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN",
"SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE",
".8", "SH2B2_MOUSE", ".9", ".2", ".3", ".4", "MYO1_NEUCR", "SRC_HUMAN",
"SRK2_SPOLA", "BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6",
"SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7",
"LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", ".3",
".4", "MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA", "BCAR3_BOVIN",
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"FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE", ".8",
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"BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN",
"SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE",
".8", "SH2B2_MOUSE", ".9", "MYO1_NEUCR", "SRC_HUMAN", "SRK2_SPOLA",
"BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN",
"SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE",
".8", "SH2B2_MOUSE", ".9", "SRC_HUMAN", "SRK2_SPOLA", "BCAR3_BOVIN",
"YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE",
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"SH2B2_MOUSE", ".9", "SRK2_SPOLA", "BCAR3_BOVIN", "YES_HUMAN",
".5", "YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN",
"CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE",
".9", "BCAR3_BOVIN", "YES_HUMAN", ".5", "YES_RAT", ".6", "SH2B3_HUMAN",
"SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN", ".7", "LYN_MOUSE", "SH34A_DANRE",
".8", "SH2B2_MOUSE", ".9", "YES_HUMAN", ".5", "YES_RAT", ".6",
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"LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9", ".5",
"YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN",
".7", "LYN_MOUSE", "SH34A_DANRE", ".8", "SH2B2_MOUSE", ".9",
"YES_RAT", ".6", "SH2B3_HUMAN", "SH3R2_MOUSE", "FYN_BOVIN", "CRK_HUMAN",
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"SH2B2_MOUSE", ".9", ".8", "SH2B2_MOUSE", ".9", "SH2B2_MOUSE",
".9", ".9"), to = c("ABL_FSVHY", "GRB2_RAT", ".1", ".2", ".3",
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