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  • Splitting the fasta file into 2 columns

    Hi,

    I have read the fasta file using "read.fasta" from "seqinr" pacakge. The file like like as follows:

    Code:
    >dg_TM_254_2_1
    MASDHAGUWHJAHSHHGAZAGHSGBAHSHGASHJAJAWWQWDSDASJDHKHASK
    ASDASDGASJGZDSGDDHASDHASGD
    >dg_TM_656_2_1
    MJIAKJIEQWIHAASDASJDHASHDKJASDWQOWIOQIWQLAJLSJWIOQUZZEWASD
    >dg_TM_543_1_2
    MUZTREQWERNBVXCYMNMVHZTOPOPOEURDASDOPOQWEUZQUIZRZIRIEIWUEWASDHASHDAHSDHAKHHSDHASHDJASHDAHUWIEUROWUOERUOWEUROOWWWW
    >dg_TM_212_0_2
    MQWUEGSPOZBYCVDVRFTEVWBVRVRVVSDSZTTASDZUZUZUZUADUS
    I would like split the file into the names of the sequence in one column and the corresponding the sequence in another column. I tried like creating data.frame and adding names of fasta_sequences in column and the corresponding sequences in another column, but it failed in R

    Can anyone please guide me.

    Thanks in advance

  • #2
    Assuming the output of read.fasta() is an object "f"
    Code:
    data.frame(Fragments=names(f), Seqs=unlist(getSequence(f, as.string=T)))

    Comment


    • #3
      Originally posted by dpryan View Post
      Assuming the output of read.fasta() is an object "f"
      Code:
      data.frame(Fragments=names(f), Seqs=unlist(getSequence(f, as.string=T)))
      Thanks Ryan..It worked.

      Comment

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