Converting .faa file into a data frame
1
0
Entering edit mode
8 weeks ago
Samet • 0

I'm trying to scan an element in a .csv file, for example "NP_000005.3", within the .faa file, and combine the matches into the table with the relevant information.

.faa file does not have column names or titles. Therefore, I have tried converting it into a .cvs and data frame, yet, I was not successful.

The data from ncbi

library(seqinr)
data2_asfaa <- read.fasta("GCF_000001405.40_GRCh38.p14_protein.faa")
> summary(data2_asfaa)
               Length Class       Mode     
NP_000005.3     1474  SeqFastadna character
NP_000006.2      290  SeqFastadna character
NP_000007.1      421  SeqFastadna character
NP_000008.1      412  SeqFastadna character
NP_000009.1      655  SeqFastadna character
NP_000010.1      427  SeqFastadna character
NP_000011.2      503  SeqFastadna character
NP_000012.1      467  SeqFastadna character
NP_000013.2      363  SeqFastadna character
NP_000014.1      387  SeqFastadna character

> head(data2_asfaa)
$NP_000005.3
   [1] "m" "g" "k" "n" "k" "l" "l" "h" "p" "s" "l" "v" "l" "l" "l" "l" "v" "l" "l" "p" "t" "d" "a" "s" "v" "s" "g" "k"
  [29] "p" "q" "y" "m" "v" "l" "v" "p" "s" "l" "l" "h" "t" "e" "t" "t" "e" "k" "g" "c" "v" "l" "l" "s" "y" "l" "n" "e"
  [57] "t" "v" "t" "v" "s" "a" "s" "l" "e" "s" "v" "r" "g" "n" "r" "s" "l" "f" "t" "d" "l" "e" "a" "e" "n" "d" "v" "l"
  [85] ### shortened it while entering the post
 [ reached getOption("max.print") -- omitted 474 entries ]
attr(,"name")
[1] "NP_000005.3"
attr(,"Annot")
[1] ">NP_000005.3 alpha-2-macroglobulin isoform a precursor [Homo sapiens]"
attr(,"class")
[1] "SeqFastadna"
fasta r • 279 views
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1
Entering edit mode

This data format not intuitve when you are new to it.

You can access the following way

assuming you have the name: attr(data2_asfaa[['NP_000005.3']],'Annot')

or the ID attr(data2_asfaa[[1]],'Annot')

collapse the sequence: paste0(data2_asfaa[[1]],collapse = '')

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3
Entering edit mode
8 weeks ago
ATpoint 68k

Biostrings:

library(Biostrings)

fa <- Biostrings::readAAStringSet("~/Downloads/GCF_000001405.40_GRCh38.p14_protein.faa.gz")

head(data.frame(names=names(fa), sequence=as.character(fa), width=width(fa)))
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