retrieving attributes of a list generated by read.fasta()

Question

[lech.kaczmarczyk]

Hi All, I am new to R and I struggle with the following: I generated a list with a MusTr <- read.fasta(file = "Mus_musculus.GRCm38.cdna.all.fa", as.string = TRUE) function, which looks like this

$ENSMUST00000177564.1
[1] "atcggagggatacgag"
attr(,"name")
[1] "ENSMUST00000177564.1"
attr(,"Annot")
[1] ">ENSMUST00000177564.1 cdna chromosome:GRCm38:14:54122226:54122241:1 gene:ENSMUSG00000096176.1 gene_biotype:TR_D_gene transcript_biotype:TR_D_gene gene_symbol:Trdd2 description:T cell receptor delta diversity 2 [Source:MGI Symbol;Acc:MGI:4439546]"
attr(,"class")
[1] "SeqFastadna"

$ENSMUST00000196221.1
[1] "atggcatat"
attr(,"name")
[1] "ENSMUST00000196221.1"
attr(,"Annot")
[1] ">ENSMUST00000196221.1 cdna chromosome:GRCm38:14:54113468:54113476:1 gene:ENSMUSG00000096749.2 gene_biotype:TR_D_gene transcript_biotype:TR_D_gene gene_symbol:Trdd1 description:T cell receptor delta diversity 1 [Source:MGI Symbol;Acc:MGI:4439547]"
attr(,"class")
[1] "SeqFastadna"

$ENSMUST00000179664.1
[1] "atggcatatca"
attr(,"name")
[1] "ENSMUST00000179664.1"
attr(,"Annot")
[1] ">ENSMUST00000179664.1 cdna chromosome:GRCm38:14:54113468:54113478:1 gene:ENSMUSG00000096749.2 gene_biotype:TR_D_gene transcript_biotype:processed_transcript gene_symbol:Trdd1 description:T cell receptor delta diversity 1 [Source:MGI Symbol;Acc:MGI:4439547]"
attr(,"class")
[1] "SeqFastadna"

$ENSMUST00000178537.1
[1] "gggacagggggc"
attr(,"name")
[1] "ENSMUST00000178537.1"
attr(,"Annot")
[1] ">ENSMUST00000178537.1 cdna chromosome:GRCm38:6:41533201:41533212:1 gene:ENSMUSG00000095668.1 gene_biotype:TR_D_gene transcript_biotype:TR_D_gene gene_symbol:Trbd1 description:T cell receptor beta, D region 1 [Source:MGI Symbol;Acc:MGI:4439571]"
attr(,"class")
[1] "SeqFastadna"

I would like to retrieve the attributes of each element (e.g. as a vector). For a single element of the list attr works (here to retrieve "Annot" attribute):

attr(MusTr$ENSMUST00000196221.1, "Annot", exact = FALSE)
[1] ">ENSMUST00000196221.1 cdna chromosome:GRCm38:14:54113468:54113476:1 gene:ENSMUSG00000096749.2 gene_biotype:TR_D_gene transcript_biotype:TR_D_gene gene_symbol:Trdd1 description:T cell receptor delta diversity 1 [Source:MGI Symbol;Acc:MGI:4439547]"

How do I achieve the same for multiple/all elements of the list? Thanks in advance for any suggestions.

[Jean-Karim Heriche]

The Ensembl perl API is the tool to use for this kind of job. Any particular reason you need to use R for this ? If you have to, check the biomaRt package or the mygene package. They would give you access to some annotations but are not as flexible or comprehensive as the Ensembl API.

[lech.kaczmarczyk]

I would (potentially) find R helpful in manipulating FASTA files, through converting them to data frames, and then easy exporting with write.fasta. Otherwise, no particular reason. Thanks for your suggestion.

Answer 1

[cpad0112]

little bit late. Try the following in R: I guess you are using seqinR for reading fasta file.

$ lapply(MusTr, function(x) attr(x, "Annot", exact = FALSE)) or $ getAnnot(MusTr)