AWK：从 4 位数字中添加一个序列号

Question

我如何通过关注 string.ext

>Lipoprotein releasing system transmembrane protein LolC
MKWLWFAYQNVIRNRRRSLMTILIIAVGTAAILLSNGFALYTYDNLREGSALASGHVIIAHVDHFDKEEEIPMEYGLSDYEDIERHIAADDRVRMAIPRLQFSGLISNGDKSVIFMGTGVDPEGEFDIGGVLTNVLTGNTLSTHSAPDAVPEVMLAKDLAKQLHADIGGLLTLLATTADGALNALDVQVRGIFSTGVPEMDKRMLAVALPTAQELIMTDKVGTLSVYLHEIEQTDAMWAVLAEWYPNFATQPWWEQASFYFKVRALYDIIFGVMGVIILLIVFFTITNTLSMTIVERTRETGTLLALGTLPRQIMRNFALEALLIGLAGALLGMLIAGFTSITLFIAEIQMPPPPGSTEGYPLYIYFSPWLYGITSLLVVTLSIAAAFLTSRKAARKPIVEALAHV
>Phosphoserine phosphatase (EC 3.1.3.3)
MFQEHALTLAIFDLDNTLLAGDSDFLWGVFLVERGIVDGDEFERENERFYRAYQEGDLDIFEFLRFAFRPLRDNRLEDLKRWRQDFLREKIEPAILPMACELVEHHRAAGDTLLIITSTNEFVTAPIAEQLGIPNLIATVPEQLHGCYTGEAAGTPAFQAGKVKRLLDWLEETSTELAGSTFYSDSHNDIPLLEWVDHPVATDPDDRLRGYARDRGWPIISLREEIAP

将string后的序号改为4位数字（以0001开头），并用|和[=14=分开]，这样 output 就会像这样返回：

>string|0001|Lipoprotein_releasing_system_transmembrane_protein_LolC
MKWLWFAYQNVIRNRRRSLMTILIIAVGTAAILLSNGFALYTYDNLREGSALASGHVIIAHVDHFDKEEEIPMEYGLSDYEDIERHIAADDRVRMAIPRLQFSGLISNGDKSVIFMGTGVDPEGEFDIGGVLTNVLTGNTLSTHSAPDAVPEVMLAKDLAKQLHADIGGLLTLLATTADGALNALDVQVRGIFSTGVPEMDKRMLAVALPTAQELIMTDKVGTLSVYLHEIEQTDAMWAVLAEWYPNFATQPWWEQASFYFKVRALYDIIFGVMGVIILLIVFFTITNTLSMTIVERTRETGTLLALGTLPRQIMRNFALEALLIGLAGALLGMLIAGFTSITLFIAEIQMPPPPGSTEGYPLYIYFSPWLYGITSLLVVTLSIAAAFLTSRKAARKPIVEALAHV
>string|0002|Phosphoserine_phosphatase_(EC_3_1_3_3)
MFQEHALTLAIFDLDNTLLAGDSDFLWGVFLVERGIVDGDEFERENERFYRAYQEGDLDIFEFLRFAFRPLRDNRLEDLKRWRQDFLREKIEPAILPMACELVEHHRAAGDTLLIITSTNEFVTAPIAEQLGIPNLIATVPEQLHGCYTGEAAGTPAFQAGKVKRLLDWLEETSTELAGSTFYSDSHNDIPLLEWVDHPVATDPDDRLRGYARDRGWPIISLREEIAP

我到这里为止的命令是（$faa 指的是文件名 string.ext）

faa=
var=$(basename "$faa" .ext)

awk '!/^>/ { printf "%s", [=12=]; n = "\n" } /^>/ { print n [=12=]; n = "" } END { printf "%s", n }' $faa >$faa.tmp
sed 's/ /_/g' $faa.tmp >$faa.tmp2
awk -v var="$var" '/>/{sub(">","&"var"|");sub(/\.ext/,x)}1' $faa.tmp2 >$faa.tmp3
awk '/>/{sub(/\|/,++i"|")}1' $faa.tmp3 >$faa.tmp4
tr '\.' '_' <$faa.tmp4 | tr '\:' '_' | sed 's/__/_/g' >$faa.tmp5

编辑：我还想将以下字符更改为 1 个下划线：/ . :

Answer 1

在 awk 中。

$ awk '/^>/{n=sprintf("%04d",++i);sub(/^>/,">string|" n "|")}1' file
>string|0001|Lipoprotein releasing system transmembrane protein LolC
MKWLWFAYQNVIRNRRRSLMTILIIAVGTAAILLSNGFALYTYDNLREGSALASGHVIIAHVDHFDKEEEIPMEYGLSDYEDIERHIAADDRVRMAIPRLQFSGLISNGDKSVIFMGTGVDPEGEFDIGGVLTNVLTGNTLSTHSAPDAVPEVMLAKDLAKQLHADIGGLLTLLATTADGALNALDVQVRGIFSTGVPEMDKRMLAVALPTAQELIMTDKVGTLSVYLHEIEQTDAMWAVLAEWYPNFATQPWWEQASFYFKVRALYDIIFGVMGVIILLIVFFTITNTLSMTIVERTRETGTLLALGTLPRQIMRNFALEALLIGLAGALLGMLIAGFTSITLFIAEIQMPPPPGSTEGYPLYIYFSPWLYGITSLLVVTLSIAAAFLTSRKAARKPIVEALAHV
>string|0002|Phosphoserine phosphatase (EC 3.1.3.3)
MFQEHALTLAIFDLDNTLLAGDSDFLWGVFLVERGIVDGDEFERENERFYRAYQEGDLDIFEFLRFAFRPLRDNRLEDLKRWRQDFLREKIEPAILPMACELVEHHRAAGDTLLIITSTNEFVTAPIAEQLGIPNLIATVPEQLHGCYTGEAAGTPAFQAGKVKRLLDWLEETSTELAGSTFYSDSHNDIPLLEWVDHPVATDPDDRLRGYARDRGWPIISLREEIAP

解释：

$ awk '
/^>/ {                          # if string starts with >
    n=sprintf("%04d",++i)       # iterate i from 1 and zeropad
    sub(/^>/,">string|" n "|")  # replace the > with stuff
}1' file                        # implicit output

不要在 string 中包含 &（见评论）。

Answer 2

awk -F'[ \.]' 'BEGIN{a=1;OFS="_"}/^>/{=sprintf(">String|%04d",a);++a;print [=10=]; next;}{print [=10=]}' filename

Answer 3

$ awk '
    FNR==1 {base=FILENAME; sub(/\.[^.]+$/,"",base) }
    sub(/^>/,"") { gsub(/[\/ .:]+/,"_"); [=10=]=sprintf(">%s|%04d|%s",base,++c,[=10=]) }
1' string.ext
>string|0001|Lipoprotein_releasing_system_transmembrane_protein_LolC
MKWLWFAYQNVIRNRRRSLMTILIIAVGTAAILLSNGFALYTYDNLREGSALASGHVIIAHVDHFDKEEEIPMEYGLSDYEDIERHIAADDRVRMAIPRLQFSGLISNGDKSVIFMGTGVDPEGEFDIGGVLTNVLTGNTLSTHSAPDAVPEVMLAKDLAKQLHADIGGLLTLLATTADGALNALDVQVRGIFSTGVPEMDKRMLAVALPTAQELIMTDKVGTLSVYLHEIEQTDAMWAVLAEWYPNFATQPWWEQASFYFKVRALYDIIFGVMGVIILLIVFFTITNTLSMTIVERTRETGTLLALGTLPRQIMRNFALEALLIGLAGALLGMLIAGFTSITLFIAEIQMPPPPGSTEGYPLYIYFSPWLYGITSLLVVTLSIAAAFLTSRKAARKPIVEALAHV
>string|0002|Phosphoserine_phosphatase_(EC_3_1_3_3)
MFQEHALTLAIFDLDNTLLAGDSDFLWGVFLVERGIVDGDEFERENERFYRAYQEGDLDIFEFLRFAFRPLRDNRLEDLKRWRQDFLREKIEPAILPMACELVEHHRAAGDTLLIITSTNEFVTAPIAEQLGIPNLIATVPEQLHGCYTGEAAGTPAFQAGKVKRLLDWLEETSTELAGSTFYSDSHNDIPLLEWVDHPVATDPDDRLRGYARDRGWPIISLREEIAP

根据您发布的示例和代码，我假设您实际上想要将空格、句点、正斜杠 and/or 的任意组合的每个连续序列转换为单个下划线。

Answer 4

我会在这里使用 perl:

perl -pe '
    next unless /^>/;     # only transform the "header" lines
    s/[\h.]/_/g;          # change dots and horizontal whitespace
    substr($_,1,0) = sprintf("string|%04d|", ++$n)  # insert the counter
' file

AWK：从 4 位数字中添加一个序列号

AWK: add a sequential number out of 4 digits

awk

sed

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