Question

我正在尝试使用awk使用一个隔离ID以及一个从1到n的contig编号在fasta文件中重命名contig。

Fastafile：

  >NODE_1_length_172477_cov_46.1343
  GCAGGGCGCAGTTTTTGGAGGCTTGGCAAACCCGTGAGGGAAATTTGGCAGGCAAAATTT
  TGGCGGTCGTGCCGAAAAAAGCGGAGGCGATTTCAAATAAATTGTTTTTCACACATCATC
  CCAAGCGGCAGACGGAGTTTGCAGTCGGACAAATCAGGCAAGGGCGCGCAGAGTAAGTCA

隔离ID是一个变量，因为我想对多个文件执行此操作。我可以打印出isolateIDnumber，但是我需要> isolateID_number

    for file in /dir/*.fasta
    do
        name=$(basename "$file" .fasta)
        awk '/^>/{print "'"$name"'" ++i; next}{print}' $file > rename.fasta
    done;

这给了我

 15AR07771
 GCAGGGCGCAGTTTTTGGAGGCTTGGCAAACCCGTGAGGGAAATTTGGCAGGCAAAATTT
 TGGCGGTCGTGCCGAAAAAAGCGGAGGCGATTTCAAATAAATTGTTTTTCACACATCATC
 CCAAGCGGCAGACGGAGTTTGCAGTCGGACAAATCAGGCAAGGGCGCGCAGAGTAAGTCA

所需的输出：

 >15AR0777_1
 GCAGGGCGCAGTTTTTGGAGGCTTGGCAAACCCGTGAGGGAAATTTGGCAGGCAAAATTT
 TGGCGGTCGTGCCGAAAAAAGCGGAGGCGATTTCAAATAAATTGTTTTTCACACATCATC
 CCAAGCGGCAGACGGAGTTTGCAGTCGGACAAATCAGGCAAGGGCGCGCAGAGTAAGTCA

问题是，我应该在哪里放置字符串，以便它将显示> 15AR0777_1而不是15AR07771

我尝试了以下几种变体，但没有奏效

  awk '/^>/{print ">'"$name"'" "_" ++i; next}{print}' $file > rename.fasta
  awk '/^>/{print ">'"$name"'" _++i; next}{print}' $file > rename.fasta

谢谢！

Answer 1

使用onHandleIntent()将Shell变量传输到awk脚本中。 awk -v awk_var="$bash_bar"

man awk:

即：

-v var=val
--assign var=val
       Assign the value val to the variable var, before execution of the program begins.  Such variable values are available to the
       BEGIN rule of an AWK program.

这里是全awk版本：

for file in dir/*.fasta
do         
    name=$(basename "$file" .fasta)
    awk -v name="$name" '/^>/{print ">" name "_" ++i; next}{print}' $file > rename.fasta
done

如果有文件awk ' FNR==1 { # new file, close old and make name for new close(f) # close the old output file n=FILENAME # get filename of the new file gsub(/^.*\/|\.fasta$/,"",n) # remove path and .fasta f="rename_" n ".fasta" # new output file } /^>/ { $0=">" n "_" ++i # >name_number } { print > f # print to output file }' dir/*.fasta # process .fasta files in dir，脚本将生成其中的文件dir/15AR07771.fasta。（您的版本将所有输出文件写入./rename_15AR07771.fasta，甚至没有追加，您可能要修复它。）

AWK打印字符串+ bash变量+字符串的组合

1 个答案: