makrez
commented
2 years ago Here is the data:
gff_subs <- structure(list(seq_id = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("LBN7-1_scf1",
"LMX7-1_scf1", "LMX7-1_scf2"), class = "factor"), source = structure(c(4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L), .Label = c("cmsearch", "GeneMarkS-2+", "Local", "Protein Homology",
"tRNAscan-SE"), class = "factor"), type = structure(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), .Label = c("CDS", "exon", "gene", "pseudogene", "pseudogenic_tRNA",
"region", "riboswitch", "RNase_P_RNA", "rRNA", "SRP_RNA", "tmRNA",
"tRNA"), class = "factor"), start = c(0L, 871L, 2092L, 3598L,
4028L, 4649L, 6013L, 6689L, 7387L, 9567L, 10918L, 12472L, 13217L,
14839L, 15972L, 17521L, 18636L, 19642L, 21049L, 22577L, 24119L,
24806L, 0L, 758L, 2145L, 3548L, 4852L, 7184L, 7734L, 8477L, 9819L,
10422L, 11074L, 12472L, 13565L), end = c(866L, 1947L, 3348L,
3987L, 4591L, 5851L, 6681L, 7231L, 9564L, 10877L, 12299L, 13095L,
14461L, 15936L, 17483L, 18582L, 19598L, 20595L, 22431L, 23773L,
24574L, 25141L, 335L, 1972L, 3527L, 4849L, 7029L, 7726L, 8402L,
9763L, 10382L, 10811L, 12330L, 13527L, 14431L), score = c(NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_),
strand = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L,
1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("-",
"+"), class = "factor"), phase = structure(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), .Label = c("0", "1", "2"), class = "factor"), ID = c("cds-LBN7-1.2_001106",
"cds-LBN7-1.2_001107", "cds-LBN7-1.2_001108", "cds-LBN7-1.2_001109",
"cds-LBN7-1.2_001110", "cds-LBN7-1.2_001111", "cds-LBN7-1.2_001112",
"cds-LBN7-1.2_001113", "cds-LBN7-1.2_001114", "cds-LBN7-1.2_001115",
"cds-LBN7-1.2_001116", "cds-LBN7-1.2_001117", "cds-LBN7-1.2_001118",
"cds-LBN7-1.2_001119", "cds-LBN7-1.2_001120", "cds-LBN7-1.2_001121",
"cds-LBN7-1.2_001122", "cds-LBN7-1.2_001123", "cds-LBN7-1.2_001124",
"cds-LBN7-1.2_001125", "cds-LBN7-1.2_001126", "cds-LBN7-1.2_001127",
"cds-LMX7-1.2_002664", "cds-LMX7-1.2_002665", "cds-LMX7-1.2_002666",
"cds-LMX7-1.2_002667", "cds-LMX7-1.2_002668", "cds-LMX7-1.2_002669",
"cds-LMX7-1.2_002670", "cds-LMX7-1.2_002671", "cds-LMX7-1.2_002672",
"cds-LMX7-1.2_002673", "cds-LMX7-1.2_002674", "cds-LMX7-1.2_002675",
"cds-LMX7-1.2_002676"), Dbxref = c(NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_), Name = c("extdb:LBN7-1.2_001106", "extdb:LBN7-1.2_001107",
"extdb:LBN7-1.2_001108", "extdb:LBN7-1.2_001109", "extdb:LBN7-1.2_001110",
"extdb:LBN7-1.2_001111", "extdb:LBN7-1.2_001112", "extdb:LBN7-1.2_001113",
"extdb:LBN7-1.2_001114", "extdb:LBN7-1.2_001115", NA, "extdb:LBN7-1.2_001117",
"extdb:LBN7-1.2_001118", "extdb:LBN7-1.2_001119", "extdb:LBN7-1.2_001120",
"extdb:LBN7-1.2_001121", "extdb:LBN7-1.2_001122", "extdb:LBN7-1.2_001123",
"extdb:LBN7-1.2_001124", "extdb:LBN7-1.2_001125", "extdb:LBN7-1.2_001126",
"extdb:LBN7-1.2_001127", "extdb:LMX7-1.2_002664", "extdb:LMX7-1.2_002665",
"extdb:LMX7-1.2_002666", "extdb:LMX7-1.2_002667", "extdb:LMX7-1.2_002668",
"extdb:LMX7-1.2_002669", "extdb:LMX7-1.2_002670", "extdb:LMX7-1.2_002671",
"extdb:LMX7-1.2_002672", "extdb:LMX7-1.2_002673", "extdb:LMX7-1.2_002674",
"extdb:LMX7-1.2_002675", "extdb:LMX7-1.2_002676"), gbkey = c("CDS",
"CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS",
"CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS",
"CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS",
"CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS"), genome = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), mol_type = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), strain = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), gene_biotype = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), feat_id = c("LBN7-1.2_001106",
"LBN7-1.2_001107", "LBN7-1.2_001108", "LBN7-1.2_001109",
"LBN7-1.2_001110", "LBN7-1.2_001111", "LBN7-1.2_001112",
"LBN7-1.2_001113", "LBN7-1.2_001114", "LBN7-1.2_001115",
"LBN7-1.2_001116", "LBN7-1.2_001117", "LBN7-1.2_001118",
"LBN7-1.2_001119", "LBN7-1.2_001120", "LBN7-1.2_001121",
"LBN7-1.2_001122", "LBN7-1.2_001123", "LBN7-1.2_001124",
"LBN7-1.2_001125", "LBN7-1.2_001126", "LBN7-1.2_001127",
"LMX7-1.2_002664", "LMX7-1.2_002665", "LMX7-1.2_002666",
"LMX7-1.2_002667", "LMX7-1.2_002668", "LMX7-1.2_002669",
"LMX7-1.2_002670", "LMX7-1.2_002671", "LMX7-1.2_002672",
"LMX7-1.2_002673", "LMX7-1.2_002674", "LMX7-1.2_002675",
"LMX7-1.2_002676"), partial = c(NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_), start_range = c(NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_), Parent = c("gene-LBN7-1.2_001106", "gene-LBN7-1.2_001107",
"gene-LBN7-1.2_001108", "gene-LBN7-1.2_001109", "gene-LBN7-1.2_001110",
"gene-LBN7-1.2_001111", "gene-LBN7-1.2_001112", "gene-LBN7-1.2_001113",
"gene-LBN7-1.2_001114", "gene-LBN7-1.2_001115", "gene-LBN7-1.2_001116",
"gene-LBN7-1.2_001117", "gene-LBN7-1.2_001118", "gene-LBN7-1.2_001119",
"gene-LBN7-1.2_001120", "gene-LBN7-1.2_001121", "gene-LBN7-1.2_001122",
"gene-LBN7-1.2_001123", "gene-LBN7-1.2_001124", "gene-LBN7-1.2_001125",
"gene-LBN7-1.2_001126", "gene-LBN7-1.2_001127", "gene-LMX7-1.2_002664",
"gene-LMX7-1.2_002665", "gene-LMX7-1.2_002666", "gene-LMX7-1.2_002667",
"gene-LMX7-1.2_002668", "gene-LMX7-1.2_002669", "gene-LMX7-1.2_002670",
"gene-LMX7-1.2_002671", "gene-LMX7-1.2_002672", "gene-LMX7-1.2_002673",
"gene-LMX7-1.2_002674", "gene-LMX7-1.2_002675", "gene-LMX7-1.2_002676"
), inference = c("COORDINATES: similar to AA sequence:RefSeq:WP_019180136.1",
"COORDINATES: protein motif:HMM:NF012742.2", "COORDINATES: similar to AA sequence:RefSeq:WP_007542666.1",
"COORDINATES: protein motif:HMM:NF013228.2", "COORDINATES: similar to AA sequence:RefSeq:WP_013585224.1",
"COORDINATES: protein motif:HMM:NF019640.2", "COORDINATES: similar to AA sequence:RefSeq:WP_019482283.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_019482282.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_019180140.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_019482280.1",
"COORDINATES: protein motif:HMM:NF012398.2", "COORDINATES: similar to AA sequence:RefSeq:WP_012865089.1",
"COORDINATES: protein motif:HMM:NF019640.2", "COORDINATES: protein motif:HMM:NF024799.2",
"COORDINATES: protein motif:HMM:NF012235.2", "COORDINATES: protein motif:HMM:NF014684.2",
"COORDINATES: protein motif:HMM:NF019474.2", "COORDINATES: similar to AA sequence:RefSeq:WP_010156141.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_020145555.1",
"COORDINATES: protein motif:HMM:NF019640.2", "COORDINATES: protein motif:HMM:NF019498.2",
"COORDINATES: protein motif:HMM:NF013228.2", "COORDINATES: protein motif:HMM:NF013228.2",
"COORDINATES: protein motif:HMM:NF019640.2", "COORDINATES: similar to AA sequence:RefSeq:WP_020075570.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_019617933.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_019180140.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_019482282.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_019482283.1",
"COORDINATES: protein motif:HMM:NF019640.2", "COORDINATES: similar to AA sequence:RefSeq:WP_017197468.1",
"COORDINATES: protein motif:HMM:NF013228.2", "COORDINATES: similar to AA sequence:RefSeq:WP_007542666.1",
"COORDINATES: protein motif:HMM:NF012742.2", "COORDINATES: similar to AA sequence:RefSeq:WP_019180136.1"
), product = c("NAD(P)-dependent oxidoreductase", "LacI family transcriptional regulator",
"Xaa-Pro peptidase family protein", "RidA family protein",
"flavin reductase family protein", "acyl-CoA dehydrogenase family protein",
"GntR family transcriptional regulator", "VOC family protein",
"thiamine pyrophosphate-dependent enzyme", "2-oxo acid dehydrogenase subunit E2",
"aldehyde dehydrogenase family protein", "NADPH-dependent F420 reductase",
"acyl-CoA dehydrogenase family protein", "sugar ABC transporter substrate-binding protein",
"sugar ABC transporter ATP-binding protein", "ABC transporter permease",
"alpha/beta hydrolase", "DMT family transporter", "Xaa-Pro peptidase family protein",
"acyl-CoA dehydrogenase family protein", "cupin domain-containing protein",
"RidA family protein", "RidA family protein", "acyl-CoA dehydrogenase family protein",
"aldehyde dehydrogenase family protein", "2-oxo acid dehydrogenase subunit E2",
"thiamine pyrophosphate-dependent enzyme", "VOC family protein",
"GntR family transcriptional regulator", "acyl-CoA dehydrogenase family protein",
"flavin reductase family protein", "RidA family protein",
"M24 family metallopeptidase", "LacI family transcriptional regulator",
"NAD(P)-dependent oxidoreductase"), protein_id = c("extdb:LBN7-1.2_001106",
"extdb:LBN7-1.2_001107", "extdb:LBN7-1.2_001108", "extdb:LBN7-1.2_001109",
"extdb:LBN7-1.2_001110", "extdb:LBN7-1.2_001111", "extdb:LBN7-1.2_001112",
"extdb:LBN7-1.2_001113", "extdb:LBN7-1.2_001114", "extdb:LBN7-1.2_001115",
NA, "extdb:LBN7-1.2_001117", "extdb:LBN7-1.2_001118", "extdb:LBN7-1.2_001119",
"extdb:LBN7-1.2_001120", "extdb:LBN7-1.2_001121", "extdb:LBN7-1.2_001122",
"extdb:LBN7-1.2_001123", "extdb:LBN7-1.2_001124", "extdb:LBN7-1.2_001125",
"extdb:LBN7-1.2_001126", "extdb:LBN7-1.2_001127", "extdb:LMX7-1.2_002664",
"extdb:LMX7-1.2_002665", "extdb:LMX7-1.2_002666", "extdb:LMX7-1.2_002667",
"extdb:LMX7-1.2_002668", "extdb:LMX7-1.2_002669", "extdb:LMX7-1.2_002670",
"extdb:LMX7-1.2_002671", "extdb:LMX7-1.2_002672", "extdb:LMX7-1.2_002673",
"extdb:LMX7-1.2_002674", "extdb:LMX7-1.2_002675", "extdb:LMX7-1.2_002676"
), transl_table = c("11", "11", "11", "11", "11", "11", "11",
"11", "11", "11", "11", "11", "11", "11", "11", "11", "11",
"11", "11", "11", "11", "11", "11", "11", "11", "11", "11",
"11", "11", "11", "11", "11", "11", "11", "11"), Ontology_term = c(NA,
NA, NA, NA, NA, NA, NA, NA, "GO:0016624", NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "GO:0016624",
NA, NA, NA, NA, NA, NA, NA, NA), go_function = c(NA, NA,
NA, NA, NA, NA, NA, NA, "oxidoreductase activity%2C acting on the aldehyde or oxo group of donors%2C disulfide as acceptor|0016624||IEA",
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, "oxidoreductase activity%2C acting on the aldehyde or oxo group of donors%2C disulfide as acceptor|0016624||IEA",
NA, NA, NA, NA, NA, NA, NA, NA), gene_name = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), go_process = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), go_component = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), Note = c(NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, "frameshifted", NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA), pseudo = c(NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, "true", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA), anticodon = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), bound_moiety = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), regulatory_class = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), gene_synonym = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), end_range = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), gene_number = c(1106, 1107,
1108, 1109, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117,
1118, 1119, 1120, 1121, 1122, 1123, 1124, 1125, 1126, 1127,
2664, 2665, 2666, 2667, 2668, 2669, 2670, 2671, 2672, 2673,
2674, 2675, 2676), width = c(866L, 1076L, 1256L, 389L, 563L,
1202L, 668L, 542L, 2177L, 1310L, 1381L, 623L, 1244L, 1097L,
1511L, 1061L, 962L, 953L, 1382L, 1196L, 455L, 335L, 335L,
1214L, 1382L, 1301L, 2177L, 542L, 668L, 1286L, 563L, 389L,
1256L, 1055L, 866L), length = c(866L, 1076L, 1256L, 389L,
563L, 1202L, 668L, 542L, 2177L, 1310L, 1381L, 623L, 1244L,
1097L, 1511L, 1061L, 962L, 953L, 1382L, 1196L, 455L, 335L,
335L, 1214L, 1382L, 1301L, 2177L, 542L, 668L, 1286L, 563L,
389L, 1256L, 1055L, 866L)), row.names = c(NA, -35L), class = c("tbl_df",
"tbl", "data.frame"))
gff_subs_seqs <- structure(list(seq_id = structure(1:2, .Label = c("LBN7-1_scf1",
"LMX7-1_scf1", "LMX7-1_scf2"), class = "factor"), start = c(0L,
0L), end = c(25141L, 14431L), length = c(25141L, 14431L)), class = "data.frame", row.names = c(NA,
-2L))
gene_links <- structure(list(feat_id = c("LBN7-1.2_001106", "LBN7-1.2_001107",
"LBN7-1.2_001108", "LBN7-1.2_001109", "LBN7-1.2_001109", "LBN7-1.2_001110",
"LBN7-1.2_001111", "LBN7-1.2_001111", "LBN7-1.2_001112", "LBN7-1.2_001113",
"LBN7-1.2_001114", "LBN7-1.2_001115", "LBN7-1.2_001118", "LBN7-1.2_001118",
"LBN7-1.2_001124", "LBN7-1.2_001125", "LBN7-1.2_001125", "LBN7-1.2_001127",
"LBN7-1.2_001127"), feat_id2 = c("LMX7-1.2_002676", "LMX7-1.2_002675",
"LMX7-1.2_002674", "LMX7-1.2_002673", "LMX7-1.2_002664", "LMX7-1.2_002672",
"LMX7-1.2_002671", "LMX7-1.2_002665", "LMX7-1.2_002670", "LMX7-1.2_002669",
"LMX7-1.2_002668", "LMX7-1.2_002667", "LMX7-1.2_002665", "LMX7-1.2_002671",
"LMX7-1.2_002674", "LMX7-1.2_002671", "LMX7-1.2_002665", "LMX7-1.2_002664",
"LMX7-1.2_002673"), pident = c(82.6, 76.6, 97.6, 94.6, 47.8,
95.2, 92, 29.6, 91, 92.8, 96, 87.4, 93.6, 32.9, 52.9, 66, 32.6,
86.5, 48.3), length = c(288L, 351L, 418L, 129L, 115L, 187L, 400L,
402L, 222L, 180L, 725L, 436L, 404L, 395L, 427L, 400L, 390L, 111L,
116L), mismatch = c(50L, 81L, 10L, 7L, 55L, 9L, 32L, 252L, 20L,
13L, 29L, 52L, 26L, 248L, 179L, 134L, 252L, 15L, 55L), gapopen = c(0L,
1L, 0L, 0L, 1L, 0L, 0L, 7L, 0L, 0L, 0L, 1L, 0L, 6L, 2L, 1L, 3L,
0L, 1L), start = c(0L, 871L, 2092L, 3598L, 3598L, 4028L, 4649L,
4649L, 6013L, 6689L, 7387L, 9567L, 13217L, 13217L, 21049L, 22577L,
22577L, 24806L, 24806L), end = c(866L, 1947L, 3348L, 3987L, 3987L,
4591L, 5851L, 5851L, 6681L, 7231L, 9564L, 10877L, 14461L, 14461L,
22431L, 23773L, 23773L, 25141L, 25141L), start2 = c(13565L, 12472L,
11074L, 10422L, 0L, 9819L, 8477L, 758L, 7734L, 7184L, 4852L,
3548L, 758L, 8477L, 11074L, 8477L, 758L, 0L, 10422L), end2 = c(14431L,
13527L, 12330L, 10811L, 335L, 10382L, 9763L, 1972L, 8402L, 7726L,
7029L, 4849L, 1972L, 9763L, 12330L, 9763L, 1972L, 335L, 10811L
), evalue = c(6.7e-126, 6.4e-150, 8e-245, 1.5e-64, 6.9e-22, 2.7e-99,
2.3e-209, 3e-47, 2.1e-111, 3.4e-99, 0, 8.7e-202, 7.2e-222, 2.4e-52,
1.1e-130, 6.8e-153, 1.1e-57, 6.8e-50, 2.4e-23), bitscore = c(444.1,
524.2, 839.7, 239.2, 97.4, 355.1, 721.8, 183.3, 395.6, 354.8,
1402.5, 696.8, 763.5, 200.3, 460.7, 534.3, 218, 190.3, 102.1),
seq_id = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("LBN7-1_scf1",
"LMX7-1_scf1", "LMX7-1_scf2"), class = "factor"), seq_id2 = structure(c(2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L), .Label = c("LBN7-1_scf1", "LMX7-1_scf1", "LMX7-1_scf2"
), class = "factor"), start_feat_id1 = c(0L, 871L, 2092L,
3598L, 3598L, 4028L, 4649L, 4649L, 6013L, 6689L, 7387L, 9567L,
13217L, 13217L, 21049L, 22577L, 22577L, 24806L, 24806L),
end_feat_id1 = c(866L, 1947L, 3348L, 3987L, 3987L, 4591L,
5851L, 5851L, 6681L, 7231L, 9564L, 10877L, 14461L, 14461L,
22431L, 23773L, 23773L, 25141L, 25141L), start_feat_id2 = c(13565L,
12472L, 11074L, 10422L, 0L, 9819L, 8477L, 758L, 7734L, 7184L,
4852L, 3548L, 758L, 8477L, 11074L, 8477L, 758L, 0L, 10422L
), end_feat_id2 = c(14431L, 13527L, 12330L, 10811L, 335L,
10382L, 9763L, 1972L, 8402L, 7726L, 7029L, 4849L, 1972L,
9763L, 12330L, 9763L, 1972L, 335L, 10811L)), row.names = c(NA,
-19L), class = c("tbl_df", "tbl", "data.frame"))
thackl
Hello
Thank you very much for this package, it really fills a gap in the biology
gg-universe.I managed to make a plot with links, but when I try to flip one genome, the links do not get flipped. I suppose that this has to do with a missing specification in either the links-file or I am missing another command.
I am using a BLAST output for creating the links. I did not use the 'read_sublinks(..., parser="read_blast")
command, since I had to further manipulate the dataframe. Thus I just used theread.table()` instead and then renamed the columns. It would be helpful if there was a minmal example published, in which it is shown how to use a BLAST output for creating the links.Anyways, I though it's easiest if I add a specific reprex here with which I am working at the moment.
I would be very happy to get some help here.
Created on 2022-05-05 by the reprex package (v2.0.1)