tests/testthat/_snaps/cmsearch.md

In brendanf/inferrnal: Interface to Call Programs from Infernal RNA Covariance Model Package

cmsearch works

structure(list(target_name = c("seq45", "seq3", "seq2", "seq28", 
"seq23", "seq9", "seq7", "seq48", "seq5", "seq6", "seq11", "seq12", 
"seq13", "seq17", "seq18", "seq19", "seq25", "seq47", "seq14", 
"seq8", "seq21", "seq36", "seq10", "seq22", "seq50", "seq44", 
"seq27", "seq35", "seq15", "seq38", "seq30", "seq26", "seq33", 
"seq46", "seq34", "seq39", "seq16", "seq31", "seq1", "seq41", 
"seq29", "seq49", "seq20", "seq4", "seq32", "seq24", "seq37", 
"seq43", "seq37"), target_accession = c("-", "-", "-", "-", "-", 
"-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", 
"-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", 
"-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", 
"-", "-", "-", "-", "-"), query_name = c("5_8S_rRNA", "5_8S_rRNA", 
"5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", 
"5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", 
"5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", 
"5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", 
"5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", 
"5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", 
"5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", 
"5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", 
"5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", "5_8S_rRNA", 
"5_8S_rRNA", "5_8S_rRNA"), query_accession = c("RF00002", "RF00002", 
"RF00002", "RF00002", "RF00002", "RF00002", "RF00002", "RF00002", 
"RF00002", "RF00002", "RF00002", "RF00002", "RF00002", "RF00002", 
"RF00002", "RF00002", "RF00002", "RF00002", "RF00002", "RF00002", 
"RF00002", "RF00002", "RF00002", "RF00002", "RF00002", "RF00002", 
"RF00002", "RF00002", "RF00002", "RF00002", "RF00002", "RF00002", 
"RF00002", "RF00002", "RF00002", "RF00002", "RF00002", "RF00002", 
"RF00002", "RF00002", "RF00002", "RF00002", "RF00002", "RF00002", 
"RF00002", "RF00002", "RF00002", "RF00002", "RF00002"), mdl = c("cm", 
"cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", 
"cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", 
"cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", 
"cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", "cm", 
"cm", "cm", "cm", "cm"), mdl_from = c(1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 145L), mdl_to = c(154L, 
154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 
154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 
154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 
154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 154L, 
154L, 154L, 154L, 154L), seq_from = c(295L, 236L, 193L, 192L, 
194L, 170L, 191L, 192L, 257L, 257L, 258L, 257L, 256L, 257L, 258L, 
257L, 256L, 257L, 157L, 154L, 256L, 256L, 257L, 256L, 257L, 255L, 
216L, 178L, 258L, 156L, 195L, 188L, 223L, 230L, 219L, 263L, 256L, 
194L, 115L, 258L, 319L, 188L, 234L, 95L, 94L, 95L, 93L, 218L, 
1L), seq_to = c(448L, 389L, 346L, 345L, 347L, 323L, 344L, 345L, 
410L, 410L, 411L, 410L, 409L, 410L, 411L, 410L, 409L, 410L, 310L, 
307L, 409L, 409L, 410L, 409L, 410L, 408L, 368L, 331L, 411L, 309L, 
348L, 340L, 376L, 383L, 371L, 416L, 408L, 346L, 268L, 414L, 475L, 
340L, 388L, 248L, 246L, 246L, 246L, 373L, 10L), strand = c("+", 
"+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", 
"+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", 
"+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", "+", 
"+", "+", "+", "+", "+", "+", "+", "+", "+"), trunc = c("no", 
"no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", 
"no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", 
"no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", 
"no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", 
"no", "no", "no", "5'"), pass = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L), gc = c(0.47, 0.45, 0.48, 
0.48, 0.47, 0.47, 0.5, 0.49, 0.43, 0.43, 0.43, 0.43, 0.43, 0.43, 
0.43, 0.43, 0.43, 0.43, 0.46, 0.47, 0.42, 0.44, 0.44, 0.44, 0.44, 
0.44, 0.46, 0.47, 0.42, 0.47, 0.48, 0.5, 0.5, 0.49, 0.45, 0.44, 
0.43, 0.48, 0.45, 0.44, 0.45, 0.46, 0.57, 0.51, 0.5, 0.5, 0.44, 
0.51, 0.5), bias = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), score = c(171.3, 171, 
170.7, 170.7, 168.5, 167.3, 167.3, 167.1, 165.5, 165.5, 165.5, 
165.5, 165.5, 165.5, 165.5, 165.5, 165.5, 165.5, 165.3, 164.7, 
164.7, 164.1, 163.9, 163.9, 163.7, 163.6, 162.5, 162.4, 161, 
160.6, 160.1, 158.7, 156.6, 156.6, 156.5, 155.7, 154, 153.9, 
151.2, 143.4, 139.6, 121.1, 119.6, 118.1, 115.1, 108.2, 102.4, 
93.5, -5.4), E_value = c(1.9e-27, 2.1e-27, 2.4e-27, 2.4e-27, 
5.3e-27, 7.9e-27, 8.1e-27, 8.7e-27, 1.5e-26, 1.5e-26, 1.5e-26, 
1.5e-26, 1.5e-26, 1.5e-26, 1.5e-26, 1.5e-26, 1.5e-26, 1.5e-26, 
1.6e-26, 2e-26, 2.1e-26, 2.5e-26, 2.7e-26, 2.7e-26, 2.8e-26, 
3e-26, 4.5e-26, 4.6e-26, 7.7e-26, 8.7e-26, 1e-25, 1.7e-25, 3.7e-25, 
3.7e-25, 3.8e-25, 5e-25, 9.2e-25, 9.6e-25, 2.5e-24, 4.1e-23, 
1.6e-22, 1.2e-19, 2.1e-19, 3.6e-19, 1e-18, 1.3e-17, 9.9e-17, 
2.4e-15, 5.9), inc = c("!", "!", "!", "!", "!", "!", "!", "!", 
"!", "!", "!", "!", "!", "!", "!", "!", "!", "!", "!", "!", "!", 
"!", "!", "!", "!", "!", "!", "!", "!", "!", "!", "!", "!", "!", 
"!", "!", "!", "!", "!", "!", "!", "!", "!", "!", "!", "!", "!", 
"!", "?"), description = c("-", "-", "-", "-", "-", "-", "-", 
"-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", 
"-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", 
"-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", 
"-", "-", "-")), class = "data.frame", row.names = c(NA, -49L
))

brendanf/inferrnal documentation built on Sept. 30, 2024, 6:40 a.m.