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我正在尝试操作 Fastq 文件。它看起来像这样：

@HWUSI-EAS610:1:1:3:1131#0/1
GATGCTAAGCCCCTAAGGTCATAAGACTGNNANGTC
+
B<ABA<;B@=4A9@:6@96:1??9;>##########
@HWUSI-EAS610:1:1:3:888#0/1
GATAGGACCAAACATCTAACATCTTCCCGNNGNTTC
+
B9>>ABA@B7BB:7?@####################
@HWUSI-EAS610:1:1:4:941#0/1
GCTTAGGAAGGAAGGAAGGAAGGGGTGTTCTGTAGT
+
BBBB:CB=@CB@?BA/@BA;6>BBA8A6A<?A4?B=
...
...
...
@HWUSI-EAS610:1:1:7:1951#0/1
TGATAGATAAGTGCCTACCTGCTTACGTTACTCTCC
+
BB=A6A9>BBB9B;B:B?B@BA@AB@B:74:;8=>7

我的预期输出是：

@HWUSI-EAS610:1:1:3:1131#0/1
GACNTNNCAGTCTTATGACCTTAGGGGCTTAGCATC
@HWUSI-EAS610:1:1:3:888#0/1
GAANCNNCGGGAAGATGTTAGATGTTTGGTCCTATC
@HWUSI-EAS610:1:1:4:941#0/1
ACTACAGAACACCCCTTCCTTCCTTCCTTCCTAAGC

因此，ID 行是以@HWUSI 开头的行（即@HWUSI-EAS610:1:1:7:1951#0/1）。每个ID 之后都有一行及其序列。现在，我想获得一个仅包含每个 ID 及其对应序列的文件，并且该序列应该是反向和互补的。(A=T, T=A, C=G, G=C) 用 Sed I 可以得到所有与命令反向互补的序列

sed -n '2~4p' MYFILE.fq | rev | tr ATCG TAGC

我怎样才能获得相应的ID？

4

2 回答 2

1

使用 sed：

sed -n '/@HWUSI/ { p; s/.*//; N; :a /\n$/! { s/\n\(.*\)\(.\)/\2\n\1/; ba }; y/ATCG/TAGC/; p }' filename

这工作如下：

/@HWUSI/ {                     # If a line starts with @HWUSI
  p                            # print it
  s/.*//                       # empty the pattern space
  N                            # fetch the sequence line. It is now preceded
                               # by a newline in the pattern space. That is
                               # going to be our cursor
  :a                           # jump label for looping
  /\n$/! {                     # while the cursor has not arrived at the end
    s/\n\(.*\)\(.\)/\2\n\1/    # move the last character before the cursor
    ba                         # go back to a. This loop reverses the sequence
  }
  y/ATCG/TAGC/                 # then invert it
  p                            # and print it.
}

我故意将换行符留在那里以获得更可读的间距；如果不需要，请将最后一个替换为pa P（大写而不是小写）。wherep打印整个模式空间，P仅打印第一个换行符之前的内容。

于 2015-03-20T12:19:22.530 回答
0 
$ sed -n '/^[^@]/y/ATCG/TAGC/;/^@/p;/^[ATCGN]*$/p' file
@HWUSI-EAS610:1:1:3:1131#0/1
CTACGATTCGGGGATTCCAGTATTCTGACNNTNCAG
@HWUSI-EAS610:1:1:3:888#0/1
CTATCCTGGTTTGTAGATTGTAGAAGGGCNNCNAAG
@HWUSI-EAS610:1:1:4:941#0/1
CGAATCCTTCCTTCCTTCCTTCCCCACAAGACATCA
@HWUSI-EAS610:1:1:7:1951#0/1
ACTATCTATTCACGGATGGACGAATGCAATGAGAGG

解释

/^[^@]/y/ATCG/TAGC/  # Translate bases on lines that don't start with an @    
/^@/p                # Print IDs
/^[ATCGN]*$/p        # Print sequence lines
于 2015-03-20T12:29:47.063 回答