Alison,
You've got two geneids with two periods (instead of just one period).
gene.list <- strsplit(as.character(Rumino_Reps_agreeWalign$geneid),"\\.")
Rumino_Reps_agreeWalign[sapply(gene.list, length)!=2, ]
geneid count_Conser count_NonCons count_ConsSubst
count_NCSubst
7 411470.DS231493.G14 1 0 0 0
154 411470.DS231491.G186 1 2 0 1
Your method had an error, because it couldn't deal with the different
lengths of vectors in the list created by strsplit.
My method ran without error because it just pulled of the first two parts
of the geneid,
411470.DS231493 and 411470.DS231491
and ignored the third part of the geneid
G14 and G186.
However, you may need to come up with a different method or a workaround,
if you want the full geneid from these two records.
Jean
alison waller <alison.wal...@embl.de> wrote on 04/12/2012 03:00:26 AM:
> Thanks - I checked through and it looks as if all of the geneids are
> formatted similarily so I don't know which one would be causing an
error.
> Interestingly, your sapply method works on the same data. So I'm
> happy although still confused, because the strsplit method worked
> the other day with a similarly generated dataset.
>
> I dumped my entire dataframe below. Incase anyone wants to investigate.
>
> Alison
>
> Rumino_Reps_agreeWalign$geneid.prefix <- sapply(gene.list, "[", 1)
> Rumino_Reps_agreeWalign$geneid.suffix <- sapply(gene.list, "[", 2)
> > dput(Rumino_Reps_agreeWalign)
> structure(list(geneid = c("657313.locus_tag:RTO_08940",
"457412.251848018",
> "657314.locus_tag:CK5_20630", "657323.locus_tag:CK1_33060",
> "657313.locus_tag:RTO_09690",
> "471875.197297106", "411470.DS231493.G14", "411459.149830627",
> "657313.locus_tag:RTO_09720", "411460.145845997", "411459.
> 149831369",
> "657321.locus_tag:RBR_01830", "411460.145846414", "457412.
> 251848805",
> "657321.locus_tag:RBR_08030", "471875.197296907", "457412.
> 251847995",
> "657314.locus_tag:CK5_20840", "411460.145846423",
> "657314.locus_tag:CK5_25030",
> "457412.251847990", "471875.197297117", "471875.197299322", "411459.
> 149831093",
> "411459.149831815", "411460.145846434",
> "213810.locus_tag:RUM_09700",
> "657314.locus_tag:CK5_09460", "657323.locus_tag:CK1_18840", "471875.
> 197297108",
> "411460.145846680", "411459.149831368",
> "657314.locus_tag:CK5_19120",
> "657321.locus_tag:RBR_09560", "411460.145846435",
> "657323.locus_tag:CK1_11530",
> "457412.251850723", "213810.locus_tag:RUM_12960",
> "213810.locus_tag:RUM_14740",
> "213810.locus_tag:RUM_07030", "471875.197296936", "411459.
> 149831092",
> "471875.197297110", "471875.197298135", "411460.145846430",
> "657314.locus_tag:CK5_20370",
> "657313.locus_tag:RTO_09790", "657323.locus_tag:CK1_33050", "411460.
> 145846407",
> "457412.251849909", "411460.145846340",
> "657313.locus_tag:RTO_14810",
> "457412.251848010", "457412.251850599",
> "657323.locus_tag:CK1_33200",
> "657323.locus_tag:CK1_33190", "213810.locus_tag:RUM_03050",
> "657314.locus_tag:CK5_09880",
> "213810.locus_tag:RUM_15180", "657313.locus_tag:RTO_14610",
> "657313.locus_tag:RTO_23930",
> "411459.149830473", "657313.locus_tag:RTO_18090",
> "657323.locus_tag:CK1_27940",
> "657314.locus_tag:CK5_20720", "411459.149831855", "471875.
> 197297691",
> "411459.149833320", "457412.251849358",
> "657321.locus_tag:RBR_13130",
> "411459.149831077", "471875.197297272",
> "657314.locus_tag:CK5_09370",
> "457412.251847994", "411459.149831080",
> "657314.locus_tag:CK5_20730",
> "457412.251850579", "213810.locus_tag:RUM_14870",
> "657321.locus_tag:RBR_01750",
> "657313.locus_tag:RTO_09660", "657314.locus_tag:CK5_28910", "411460.
> 145846907",
> "657313.locus_tag:RTO_09860", "457412.251847996",
> "657323.locus_tag:CK1_38480",
> "411460.145846417", "471875.197297592", "411459.149831814", "457412.
> 251848016",
> "411459.149831804", "657323.locus_tag:CK1_32880",
> "657321.locus_tag:RBR_08130",
> "411460.145846429", "657313.locus_tag:RTO_09880",
> "213810.locus_tag:RUM_03410",
> "657313.locus_tag:RTO_09740", "657313.locus_tag:RTO_09840", "457412.
> 251848009",
> "657323.locus_tag:CK1_33090", "657323.locus_tag:CK1_25000", "411459.
> 149831095",
> "411459.149830934", "457412.251847970", "457412.251848000",
> "657314.locus_tag:CK5_20680",
> "411459.149831088", "657323.locus_tag:CK1_19350",
> "657321.locus_tag:RBR_08670",
> "471875.197299547", "411459.149831081",
> "657323.locus_tag:CK1_32550",
> "411459.149831091", "657313.locus_tag:RTO_24580", "457412.
> 251848004",
> "471875.197297195", "411460.145846602",
> "657321.locus_tag:RBR_06200",
> "213810.locus_tag:RUM_19570", "411460.145846361", "411459.
> 149833804",
> "657323.locus_tag:CK1_32930", "471875.197296906", "411459.
> 149831078",
> "657321.locus_tag:RBR_09900", "411460.145846496",
> "657321.locus_tag:RBR_08260",
> "411459.149833021", "657313.locus_tag:RTO_02600",
> "657323.locus_tag:CK1_33030",
> "657313.locus_tag:RTO_09750", "213810.locus_tag:RUM_14790", "457412.
> 251848017",
> "457412.251848806", "457412.251847640",
> "657314.locus_tag:CK5_20620",
> "411459.149830474", "657323.locus_tag:CK1_11750",
> "213810.locus_tag:RUM_09690",
> "457412.251847999", "657321.locus_tag:RBR_05870", "411460.
> 145846409",
> "657313.locus_tag:RTO_16220", "657321.locus_tag:RBR_10630", "411459.
> 149833026",
> "457412.251847997", "657313.locus_tag:RTO_09650", "471875.
> 197297129",
> "471875.197297112", "213810.locus_tag:RUM_14720", "457412.
> 251847991",
> "657313.locus_tag:RTO_09730", "471875.197297132",
> "657313.locus_tag:RTO_14650",
> "411470.DS231491.G186", "457412.251849520",
> "657323.locus_tag:CK1_04710",
> "657323.locus_tag:CK1_04510", "411460.145846182", "411460.
> 145846883",
> "657321.locus_tag:RBR_08040", "411459.149833983", "457412.
> 251849519",
> "471875.197297124", "457412.251849906",
> "657321.locus_tag:RBR_08010",
> "657321.locus_tag:RBR_03380", "657323.locus_tag:CK1_20230", "471875.
> 197297115",
> "657323.locus_tag:CK1_13100", "657323.locus_tag:CK1_32950", "411460.
> 145846428",
> "471875.197297120", "213810.locus_tag:RUM_13040",
> "657314.locus_tag:CK5_25080",
> "411459.149831096", "411459.149831090", "411459.149833331", "411459.
> 149831370",
> "657313.locus_tag:RTO_26330", "411459.149833340",
> "657314.locus_tag:CK5_20590",
> "411460.145846458", "471875.197297290",
> "657313.locus_tag:RTO_09850",
> "213810.locus_tag:RUM_12130", "657323.locus_tag:CK1_32910",
> "213810.locus_tag:RUM_09770",
> "657313.locus_tag:RTO_09640", "657313.locus_tag:RTO_09830", "457412.
> 251849013",
> "411460.145847544", "657323.locus_tag:CK1_33040",
> "213810.locus_tag:RUM_23250",
> "657314.locus_tag:CK5_20580", "411459.149831082", "471875.
> 197297125",
> "657314.locus_tag:CK5_14780", "657321.locus_tag:RBR_03820",
> "213810.locus_tag:RUM_06600",
> "657314.locus_tag:CK5_20610", "657321.locus_tag:RBR_08120",
> "657314.locus_tag:CK5_20770",
> "471875.197297119", "657313.locus_tag:RTO_10610",
> "657321.locus_tag:RBR_08270",
> "657323.locus_tag:CK1_32920", "457412.251849800", "411460.
> 145846603",
> "411459.149830653", "411459.149833020", "411459.149831085", "411459.
> 149833803",
> "657323.locus_tag:CK1_32990", "471875.197297121", "411459.
> 149833164",
> "657313.locus_tag:RTO_14600", "457412.251848005",
> "657314.locus_tag:CK5_10670",
> "213810.locus_tag:RUM_14730", "411459.149831367",
> "657314.locus_tag:CK5_20640",
> "657321.locus_tag:RBR_15140", "411460.145847269",
> "657323.locus_tag:CK1_04820",
> "457412.251848673", "471875.197296932", "411459.149831083",
> "657323.locus_tag:CK1_33080",
> "657321.locus_tag:RBR_08170", "657314.locus_tag:CK5_20740",
> "657321.locus_tag:RBR_08100",
> "657314.locus_tag:CK5_20850", "471875.197297111",
> "657313.locus_tag:RTO_17750",
> "471875.197297308", "657314.locus_tag:CK5_00900",
> "657313.locus_tag:RTO_03810",
> "471875.197297779", "411460.145848384",
> "657313.locus_tag:RTO_29320",
> "657314.locus_tag:CK5_20780", "471875.197299321", "411460.
> 145846431",
> "471875.197298831", "471875.197297131",
> "657323.locus_tag:CK1_30770",
> "457412.251848007", "657314.locus_tag:CK5_25320",
> "213810.locus_tag:RUM_03700",
> "657313.locus_tag:RTO_19560", "411460.145846432",
> "657314.locus_tag:CK5_29790",
> "411460.145848483", "657323.locus_tag:CK1_32890", "411460.
> 145846406",
> "657321.locus_tag:RBR_15270", "657321.locus_tag:RBR_18050",
> "657314.locus_tag:CK5_20650",
> "657323.locus_tag:CK1_33210", "411459.149831086", "457412.
> 251847993",
> "411459.149831051", "411460.145846418",
> "657321.locus_tag:RBR_07990",
> "411459.149830912", "471875.197298686", "457412.251850588", "457412.
> 251848006",
> "657314.locus_tag:CK5_17510", "657313.locus_tag:RTO_05370", "457412.
> 251849359",
> "471875.197297105", "657313.locus_tag:RTO_09820",
> "657323.locus_tag:CK1_25830",
> "471875.197297130", "657314.locus_tag:CK5_09290", "457412.
> 251848019",
> "471875.197297928", "657314.locus_tag:CK5_14710", "411460.
> 145847612",
> "457412.251849367", "657314.locus_tag:CK5_20860", "471875.
> 197297907",
> "657321.locus_tag:RBR_07980"), count_Conser = c(7L, 1L, 2L, 1L,
> 3L, 0L, 1L, 0L, 4L, 0L, 3L, 4L, 1L, 3L, 0L, 5L, 2L, 2L, 1L, 0L,
> 0L, 2L, 3L, 0L, 2L, 1L, 1L, 4L, 0L, 0L, 0L, 1L, 1L, 5L, 0L, 0L,
> 2L, 0L, 1L, 1L, 2L, 0L, 1L, 1L, 1L, 3L, 1L, 2L, 0L, 0L, 0L, 1L,
> 0L, 0L, 2L, 1L, 1L, 0L, 1L, 4L, 0L, 1L, 1L, 4L, 0L, 7L, 0L, 4L,
> 1L, 1L, 2L, 0L, 1L, 0L, 0L, 2L, 3L, 0L, 4L, 0L, 1L, 0L, 1L, 4L,
> 1L, 0L, 5L, 4L, 0L, 6L, 2L, 1L, 3L, 1L, 0L, 2L, 3L, 0L, 1L, 12L,
> 1L, 1L, 2L, 0L, 0L, 2L, 1L, 2L, 1L, 3L, 2L, 0L, 2L, 0L, 0L, 0L,
> 0L, 0L, 0L, 0L, 0L, 3L, 0L, 2L, 0L, 1L, 0L, 2L, 1L, 1L, 1L, 1L,
> 0L, 2L, 0L, 2L, 2L, 5L, 2L, 18L, 0L, 4L, 2L, 0L, 3L, 0L, 1L,
> 0L, 1L, 1L, 1L, 3L, 3L, 1L, 1L, 2L, 0L, 1L, 0L, 1L, 0L, 2L, 0L,
> 0L, 1L, 1L, 2L, 1L, 0L, 1L, 2L, 1L, 0L, 1L, 1L, 2L, 3L, 2L, 0L,
> 0L, 0L, 3L, 3L, 1L, 1L, 0L, 0L, 3L, 1L, 1L, 0L, 0L, 1L, 0L, 6L,
> 0L, 3L, 8L, 1L, 3L, 0L, 0L, 3L, 5L, 0L, 1L, 0L, 0L, 1L, 0L, 4L,
> 3L, 1L, 2L, 0L, 0L, 0L, 4L, 0L, 6L, 6L, 0L, 1L, 2L, 0L, 2L, 3L,
> 1L, 3L, 0L, 2L, 4L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 2L, 2L, 2L,
> 0L, 0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 4L, 0L,
> 0L, 3L, 3L, 1L, 0L, 1L, 1L, 2L, 0L, 0L, 1L, 3L, 0L, 2L, 5L, 0L,
> 0L, 1L, 0L, 8L, 1L, 8L, 2L, 0L, 1L), count_NonCons = c(5L, 4L,
> 4L, 0L, 0L, 2L, 0L, 2L, 0L, 2L, 4L, 0L, 0L, 2L, 1L, 1L, 2L, 0L,
> 0L, 0L, 3L, 1L, 1L, 2L, 1L, 0L, 0L, 4L, 1L, 0L, 4L, 2L, 2L, 15L,
> 2L, 0L, 2L, 0L, 1L, 0L, 1L, 0L, 3L, 0L, 0L, 8L, 0L, 0L, 0L, 0L,
> 1L, 2L, 4L, 0L, 0L, 0L, 1L, 3L, 5L, 2L, 0L, 0L, 6L, 0L, 2L, 1L,
> 1L, 4L, 1L, 4L, 1L, 8L, 5L, 1L, 6L, 1L, 5L, 0L, 11L, 0L, 0L,
> 0L, 2L, 1L, 0L, 0L, 6L, 1L, 0L, 10L, 2L, 1L, 0L, 1L, 1L, 3L,
> 2L, 1L, 3L, 4L, 1L, 0L, 12L, 0L, 0L, 1L, 3L, 15L, 9L, 4L, 12L,
> 2L, 4L, 2L, 0L, 0L, 0L, 2L, 2L, 3L, 1L, 1L, 1L, 0L, 0L, 1L, 0L,
> 5L, 0L, 0L, 1L, 0L, 3L, 4L, 1L, 1L, 2L, 0L, 0L, 0L, 1L, 3L, 9L,
> 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 10L, 2L, 0L, 12L, 0L, 1L,
> 1L, 2L, 0L, 1L, 1L, 3L, 3L, 1L, 4L, 0L, 2L, 1L, 1L, 4L, 0L, 2L,
> 5L, 5L, 4L, 0L, 0L, 0L, 2L, 0L, 3L, 0L, 2L, 3L, 2L, 3L, 1L, 4L,
> 2L, 2L, 0L, 6L, 2L, 1L, 2L, 3L, 0L, 7L, 0L, 0L, 6L, 2L, 2L, 1L,
> 2L, 0L, 6L, 0L, 0L, 3L, 0L, 0L, 0L, 2L, 2L, 1L, 0L, 2L, 2L, 0L,
> 0L, 4L, 0L, 2L, 1L, 3L, 2L, 0L, 1L, 0L, 1L, 0L, 6L, 1L, 1L, 1L,
> 2L, 2L, 4L, 1L, 0L, 0L, 2L, 3L, 2L, 0L, 1L, 0L, 0L, 0L, 1L, 2L,
> 1L, 0L, 16L, 1L, 3L, 0L, 5L, 10L, 1L, 2L, 4L, 0L, 6L, 0L, 0L,
> 0L, 1L, 2L, 0L, 0L, 0L, 0L, 0L, 0L, 11L, 1L, 4L, 5L, 1L, 1L),
> count_ConsSubst = c(5, 3, 1, 1, 3, 1, 0, 1, 1, 0, 0, 2, 0,
> 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 3, 0, 1, 0, 0,
> 0, 6, 1, 1, 1, 0, 0, 0, 1, 2, 1, 0, 0, 4, 0, 0, 1, 0, 0,
> 4, 1, 0, 0, 0, 0, 1, 0, 3, 0, 1, 0, 2, 1, 3, 0, 3, 0, 3,
> 2, 0, 1, 1, 3, 4, 2, 0, 9, 0, 1, 1, 1, 0, 2, 0, 1, 1, 0,
> 1, 1, 3, 0, 2, 0, 1, 0, 2, 2, 1, 3, 0, 6, 0, 0, 0, 2, 7,
> 3, 1, 5, 1, 0, 2, 0, 0, 0, 0, 1, 0, 0, 0, 5, 0, 0, 1, 0,
> 0, 0, 1, 0, 0, 3, 1, 0, 1, 1, 2, 0, 2, 0, 5, 2, 0, 0, 0,
> 0, 2, 0, 2, 0, 0, 3, 0, 0, 2, 0, 2, 0, 2, 1, 1, 0, 2, 1,
> 1, 1, 0, 0, 1, 1, 4, 0, 1, 0, 1, 5, 0, 0, 0, 5, 2, 1, 0,
> 0, 1, 0, 0, 0, 4, 0, 2, 1, 1, 1, 2, 1, 1, 1, 4, 1, 2, 1,
> 1, 2, 0, 0, 0, 1, 0, 1, 0, 0, 2, 0, 0, 1, 1, 0, 3, 1, 1,
> 2, 2, 1, 1, 1, 1, 0, 2, 1, 1, 0, 0, 0, 1, 0, 0, 0, 3, 2,
> 0, 1, 1, 0, 0, 0, 0, 2, 1, 1, 0, 0, 0, 0, 0, 3, 1, 0, 0,
> 3, 4, 0, 5, 1, 0, 4, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 4,
> 1, 4, 0, 0, 0), count_NCSubst = c(1, 0, 0, 0, 1, 1, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 1,
> 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0,
> 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 2, 0, 0, 1, 0, 0, 1, 0, 0,
> 0, 1, 1, 1, 0, 0, 1, 3, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0,
> 1, 0, 1, 0, 5, 0, 0, 3, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 2, 0, 0,
> 0, 1, 1, 1, 0, 2, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 0, 1, 0,
> 0, 1, 0, 0, 0, 0, 1, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2,
> 1, 0, 1, 0, 0, 0, 1, 0, 2, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0,
> 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1,
> 0, 0, 0, 0, 0, 1, 1, 0, 0, 0)), .Names = c("geneid", "count_Conser",
> "count_NonCons", "count_ConsSubst", "count_NCSubst"), class =
> "data.frame", row.names = c(NA,
> -284L))
>
> On 04/11/2012 08:01 PM, Jean V Adams wrote:
>
> Alison,
>
> Your code works fine on the first six lines of the data that you
provided.
>
> Rumino_Reps_agreeWalign <- data.frame(
> geneid = c("657313.locus_tag:RTO_08940",
> "457412.251848018",
> "657314.locus_tag:CK5_20630",
> "657323.locus_tag:CK1_33060",
> "657313.locus_tag:RTO_09690",
> "471875.197297106"),
> count_Conser = c(7, 1, 2, 1, 3, 0),
> count_NonCons = c(5, 4, 4, 0, 0, 2),
> count_ConsSubst = c(5, 3, 1, 1, 3, 1),
> count_NCSubst = c(1, 0, 0, 0, 1, 1))
> gene.list <- strsplit(as.character(Rumino_Reps_agreeWalign$geneid),
"\\.")
> Rumino_Reps_agreeWalignTR <- transform(Rumino_Reps_agreeWalign,
> taxid=do.call(rbind, gene.list))
>
> Perhaps in later rows of the data there are cases where there is no
> "." in geneid? If not, can you provide a subset of your data that
> results in the warning? Use the dput() function.
>
> It's not a good idea to create an object named "strsplit". That
> will only mask the function strsplit() in later runs.
>
> If time is an issue, a slightly faster way to do this, after the
> strsplit() function is:
> Rumino_Reps_agreeWalign$geneid.prefix <- sapply(gene.list, "[", 1)
> Rumino_Reps_agreeWalign$geneid.suffix <- sapply(gene.list, "[", 2)
>
> Jean
>
>
> alison waller wrote on 04/11/2012 08:23:29 AM:
>
> > Dear all,
> >
> > I want to use string split to parse column names, however, I am having
> > some errors that I don't understand.
> > I see a problem when I try to rbind the output from strsplit.
> >
> > please let me know if I'm missing something obvious,
> >
> > thanks,
> > alison
> >
> > here are my commands:
> >
>strsplit<-strsplit(as.character(Rumino_Reps_agreeWalign$geneid),"\\.")
> > >
> > Rumino_Reps_agreeWalignTR<-transform
> > (Rumino_Reps_agreeWalign,taxid=do.call(rbind,
> > strsplit))
> > Warning message:
> > In function (..., deparse.level = 1) :
> > number of columns of result is not a multiple of vector length (arg
1)
> >
> >
> > here is my data:
> >
> > > head(Rumino_Reps_agreeWalign)
> > geneid count_Conser count_NonCons
count_ConsSubst
> > 1 657313.locus_tag:RTO_08940 7 5 5
> > 2 457412.251848018 1 4 3
> > 3 657314.locus_tag:CK5_20630 2 4 1
> > 4 657323.locus_tag:CK1_33060 1 0 1
> > 5 657313.locus_tag:RTO_09690 3 0 3
> > 6 471875.197297106 0 2 1
> > count_NCSubst
> > 1 1
> > 2 0
> > 3 0
> > 4 0
> > 5 1
> > 6 1
> >
> > here are the results from strsplit:
> > > head(strsplit)
> > [[1]]
> > [1] "657313" "locus_tag:RTO_08940"
> >
> > [[2]]
> > [1] "457412" "251848018"
> >
> > [[3]]
> > [1] "657314" "locus_tag:CK5_20630"
> >
> > [[4]]
> > [1] "657323" "locus_tag:CK1_33060"
> >
> > [[5]]
> > [1] "657313" "locus_tag:RTO_09690"
> >
> > [[6]]
> > [1] "471875" "197297106"
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