sed:重命名文件中的选择性字符串

Question

我有一个名为protein.faa的文件，其内容是：

>WP_004066472.1 MULTISPECIES: NADH-quinone oxidoreductase subunit K [Thermococcus]
MIPLQFVTAFLMIFMGIYAFLYKRNLIKLILALNLI
LVLTSIVIGVCVLSLAMALTINAYRHYGTLDVNKLRRLRG
>WP_004066568.1 MULTISPECIES: DNA-directed RNA polymerase subunit P [Thermococcus]
MVEALYKCAKCGKEF
>WP_004066764.1 MULTISPECIES: Lrp/AsnC ligand binding domain-containing protein [Thermococcus]
MVTAFILMVTAAGKEREVMEKLLTYPEVKEAYVVYG
>WP_004067064.1 MULTISPECIES: hypothetical protein [Thermococcus]
MEITIEKFKPKVTRPFKRKNEYWVKL
PSAKELVDEYFSE

我只想在每个之后将名称重命名为filename+its订单号，即：

>protein_1 MULTISPECIES: NADH-quinone oxidoreductase subunit K [Thermococcus]
MIPLQFVTAFLMIFMGIYAFLYKRNLIKLILALNLI
LVLTSIVIGVCVLSLAMALTINAYRHYGTLDVNKLRRLRG
>protein_2 MULTISPECIES: DNA-directed RNA polymerase subunit P [Thermococcus]
MVEALYKCAKCGKEF
>protein_3 MULTISPECIES: Lrp/AsnC ligand binding domain-containing protein [Thermococcus]
MVTAFILMVTAAGKEREVMEKLLTYPEVKEAYVVYG
>protein_4 MULTISPECIES: hypothetical protein [Thermococcus]
MEITIEKFKPKVTRPFKRKNEYWVKL
PSAKELVDEYFSE

我的代码是

name="$(echo protein.faa | sed 's/....$//')"
sed "s/>.*/>${name}/" protein.faa 

这让我只能

>protein
MIPLQFVTAFLMIFMGIYAFLYKRNLIKLILALNLI
LVLTSIVIGVCVLSLAMALTINAYRHYGTLDVNKLRRLRG
>protein
MVEALYKCAKCGKEF
>protein
MVTAFILMVTAAGKEREVMEKLLTYPEVKEAYVVYG
>protein
MEITIEKFKPKVTRPFKRKNEYWVKL
PSAKELVDEYFSE

如何添加订单编号并保留>protein_i后面的任何内容

Answer 1

此职务套餐gnu awk更多：

awk -i inplace 'BEGINFILE {fn=FILENAME; sub(/\..*$/, "", fn); i=0} $1 ~ /^>/{$1 = ">" fn "_" ++i} 1' *.faa

>protein_1 MULTISPECIES: NADH-quinone oxidoreductase subunit K [Thermococcus]
MIPLQFVTAFLMIFMGIYAFLYKRNLIKLILALNLI
LVLTSIVIGVCVLSLAMALTINAYRHYGTLDVNKLRRLRG
>protein_2 MULTISPECIES: DNA-directed RNA polymerase subunit P [Thermococcus]
MVEALYKCAKCGKEF
>protein_3 MULTISPECIES: Lrp/AsnC ligand binding domain-containing protein [Thermococcus]
MVTAFILMVTAAGKEREVMEKLLTYPEVKEAYVVYG
>protein_4 MULTISPECIES: hypothetical protein [Thermococcus]
MEITIEKFKPKVTRPFKRKNEYWVKL
PSAKELVDEYFSE

使gnu awk更易读

awk -i inplace 'BEGINFILE {
   fn = FILENAME
   sub(/\..*$/, "", fn)
   i = 0
}
$1 ~ /^>/{
   $1 = ">" fn "_" ++i
} 1' *.faa

对于non-gnu awk：

for f in *.faa; do
   awk 'BEGINFILE {fn=FILENAME; sub(/\..*$/, "", fn)} $1 ~ /^>/{$1 = ">" fn "_" ++i} 1' "$f" > _tmp && mv _tmp "$f"
done

Answer 2

使用这个Perl一行程序：

perl -pe 'BEGIN { $i = 1; chomp( $basename = `basename $ARGV[0] .faa` ); } s{^>\S+}{>${basename}_${i}} and $i++; ' in.faa > out.faa

若要就地更改文件：

perl -i.bak -pe 'BEGIN { $i = 1; chomp( $basename = `basename $ARGV[0] .faa` ); } s{^>\S+}{>${basename}_${i}} and $i++; ' in.faa

Perl一行程序使用以下命令行标志：

-e：告诉Perl在行中查找代码，而不是在文件中。

-p：每次循环输入一行，默认情况下将其分配给$_。在每个循环迭代之后添加print $_。

-i.bak：就地编辑输入文件(覆盖输入文件).在重写之前，将扩展名.bak附加到原始文件的备份副本中。

还请参见：

perldoc perlrun: how to execute the Perl interpreter: command line switches

perldoc perlre: Perl regular expressions (regexes)

perldoc perlrequick: Perl regular expressions quick start