在文本(fasta)文件中向下移动新行字符5位置

Question

我正在尝试转换这样的文本文件(fasta格式)：

>seq1
AAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAA
ATGATGATGGAATGAGGAT
TTAGGAGGGAGGAAAATTC
>seq2
CCCTCCGGGAAAAAAGAGG
TTGCAATGCGCGTATTTAT
TTTTTTTTTTTTTTTTTTT
AAAAAAAAAAAAAGGCTGT
AAAAAAAAAAAAAAAGGGG

目标是在下游替换换行符5位置，但以>开头的行除外。

>seq1
AAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAATGATGATGGAATGA
GGATTTAGGAGGGAGGAAAATTC
>seq2
CCCTCCGGGAAAAAAGAGGTTGCA
ATGCGCGTATTTATTTTTTTTTTT
TTTTTTTTTAAAAAAAAAAAAAGG
CTGTAAAAAAAAAAAAAAAGGGG

我想使用AWK，但我不知道如何进行。我在想一些类似的事情：

awk '{for(i=1;i<=NR;i++){ if($1 ~ /^>/){¿?¿?¿?}}}'

你知道我该怎么解决这个问题吗？

Answer 1

假设：

• 所有数据行将扩展到最多24个字符的

。

awk的一个想法是：

awk -v width=24 '                               # pass width in as awk variable "width"
function print_sequence() {
    if (sequence)                               # if sequence is not blank
       while (sequence) {                       # while sequence is not blank
             print substr(sequence,1,width)     # print 1st 24 characters
             sequence=substr(sequence,width+1)  # remove 1st 24 characters
       }
}

/^>/ { print_sequence()                         # flush previous set of data to stdout
       print                                    # print current input line
       next                                     # process next input line
     }
     { sequence=sequence $1 }                   # append data to our "sequence" variable

END  { print_sequence() }                       # flush last set of data to stdout
' fasta.in > fasta.out

这就产生了：

$ cat fasta.out
>seq1
AAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAATGATGATGGAATGA
GGATTTAGGAGGGAGGAAAATTC
>seq2
CCCTCCGGGAAAAAAGAGGTTGCA
ATGCGCGTATTTATTTTTTTTTTT
TTTTTTTTTAAAAAAAAAAAAAGG
CTGTAAAAAAAAAAAAAAAGGGG

Answer 2

我会这样做，让file.txt内容

>seq1
AAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAA
ATGATGATGGAATGAGGAT
TTAGGAGGGAGGAAAATTC
>seq2
CCCTCCGGGAAAAAAGAGG
TTGCAATGCGCGTATTTAT
TTTTTTTTTTTTTTTTTTT
AAAAAAAAAAAAAGGCTGT
AAAAAAAAAAAAAAAGGGG

然后

awk 'BEGIN{width=24}/>/&&x{print x;x=""}/>/{print;next}{x = x $0}length(x)>=width{print substr(x,1,width);x=substr(x,width+1)}END{print x}' file.txt

给予输出

>seq1
AAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAATGATGATGGAATGA
GGATTTAGGAGGGAGGAAAATTC
>seq2
CCCTCCGGGAAAAAAGAGGTTGCA
ATGCGCGTATTTATTTTTTTTTTT
TTTTTTTTTAAAAAAAAAAAAAGG
CTGTAAAAAAAAAAAAAAAGGGG

说明:我将宽度设置为24，这是所需字符的数量，如果找到了>，并且x中存储了一些内容，请打印该字符，并将x值设置为空字符串，如果遇到>行，请打印它并转到下一行。对于每一行，请将当前行内容附加到x中，如果length of x等于或大于width，请先打印x的width字符，然后从x中删除这些字符。在处理完所有行后，请打印x。免责声明解决方案:此解决方案假定当前宽度与所需宽度之间的比率小于0.5

(GNU Awk 5.0.1)

Answer 3

您还可以尝试另一种方法，使用awk的字段和记录分隔符：

awk -v width=24 '
  BEGIN {
    FS="\n"                            # Set the Field separator to newline
    RS=">"                             # Set the Record separator to ">"
    ORS=OFS=""                         # Set the Output Record and Field separator to an empty string
  }

  NR>1 {                               # Using ">" as a record separator the first record is empty, so skip
    header=$1                          # Using "\n" as the Field separator, $1 contains the header, save it in a variable
    $1=OFS                             # Assign an empty string to $1 so the record gets recalculated and the body becomes $0 i
                                       # with all newlines are removed, since OFS == ""
    gsub(".{" width "}", "&" FS)       # Append every "width" characters with a newline (FS)
    print RS header FS $0 FS           # Print a ">", the header, a newline, the body and a newline
  }
' fasta_in > fasta_out