使用awk修剪multi-fasta文件中的前N个基，并使用最大宽度格式打印

背景

>gi|304322925|ref|YP_003856771.1| NADH [Lynx rufus] SFVGFSSKPSPIYGGFGLIVAGGIGCGIVLNFGGSFLGLMVFLIYLGGMLVVFGYTTAMATEPYPEAWTS NKAVLGMLITGILAELLTACYILKEDEIEVVFKFNGAGDWVIYDTGDSGFFSEEAMGIAALYSYGTWLVV VTGWSLLIGVLVIMEVTRGN >gi|295065592|ref|YP_003587393.1| NADH [Nomascus siki] FVGFSSKPSPIYGGLVLVVSGVVGCAVILNCGGGYLGLMVFLIYLGGMMVVFGYTTAMAIEEYPEAWGSG VEVLVGVLVGLAMEVGLVLWAKECDGLVMVLNFNNMGSWVIYEGEGSGLIREDSIGAGALYDYGRWLVVV TGWTLLVGVYIVIEIARGN >gi|295065550|ref|YP_003587316.1| NADH (mitochondrion) [Symphalangus syndactylus] FVGFSSKPSPIYGGLVLVVSGVVGCAIILDCGGGYLGLMVFLIYLGGMMVVFGYTTAMAIEEYPEAWGSG VEVLVGVLVGLAMEVGLVLWAKEYDGLVVVLNFNNMGSWVIYEGEGSGLIREDSIGAGALYDYGRWLVVV TGWTLLVGVYIVIEIARGN multi fasta格式包含多条序列记录，每条记录以单行描述开始，然后是多条序列行（RNA、DNA、蛋白质）。描述行开头有大于的符号，“>”后面是序列的标识符，其余的行包含记录的描述（两者都是可选的）

在fasta文件中，通常将行序列格式化为最大宽度

输入示例，使用max width=“70”：

---

要回答您的特定问题，您可以使用

*

格式修改器指定输出字段的宽度：

$ awk 'BEGIN{printf "%s\n", "foo"}'
foo
$ awk 'BEGIN{printf "%*s\n", 10, "foo"}'
       foo

不，没有

join

函数将数组重新组合成字符串（与

split（）

相反），但是如果让awk将记录拆分为字段，而不是手动将记录拆分为元素数组，然后，您只需为任何字段分配一个新值，awk就会将这些字段重新编译为$0，因为我在下面的第一个解决方案中使用

$1=“”

删除第一个字段/行时故意产生了副作用

以下是我如何完成任务的方法：

$ cat tst.awk
BEGIN { RS=">"; FS="\n"; OFS="" }
NR>1 {
    print RS $1
    $1 = ""
    for ( start=left_trim+1; start<=length(); start+=width ) {
        print substr($0,start,width)
    }
}

$ awk -v left_trim=15 -v width=70 -f tst.awk file
>gi|304322925|ref|YP_003856771.1| NADH [Lynx rufus]
SFVGFSSKPSPIYGGFGLIVAGGIGCGIVLNFGGSFLGLMVFLIYLGGMLVVFGYTTAMATEPYPEAWTS
NKAVLGMLITGILAELLTACYILKEDEIEVVFKFNGAGDWVIYDTGDSGFFSEEAMGIAALYSYGTWLVV
VTGWSLLIGVLVIMEVTRGN
>gi|295065592|ref|YP_003587393.1| NADH [Nomascus siki]
FVGFSSKPSPIYGGLVLVVSGVVGCAVILNCGGGYLGLMVFLIYLGGMMVVFGYTTAMAIEEYPEAWGSG
VEVLVGVLVGLAMEVGLVLWAKECDGLVMVLNFNNMGSWVIYEGEGSGLIREDSIGAGALYDYGRWLVVV
TGWTLLVGVYIVIEIARGN
>gi|295065550|ref|YP_003587316.1| NADH (mitochondrion) [Symphalangus syndactylus]
FVGFSSKPSPIYGGLVLVVSGVVGCAIILDCGGGYLGLMVFLIYLGGMMVVFGYTTAMAIEEYPEAWGSG
VEVLVGVLVGLAMEVGLVLWAKEYDGLVVVLNFNNMGSWVIYEGEGSGLIREDSIGAGALYDYGRWLVVV
TGWTLLVGVYIVIEIARGN

$cat tst.awk
开始{RS=“>”FS=“\n”OFS=“”}
NR>1{
打印卢比$1
$1 = ""
对于（开始=左微调+1；开始GI | 304322925 |参考| YP | U 003856771.1 | NADH[猞猁rufus]
SFVGFSKPSPIYGFGLIVAGGIGGCGIVLNFGGGSFLGLMVFLYLGMLVGYTTAMATEPEAWTS
NKAVLGMLITGILAELLTACYILKEDEIEVFKFNGDWVIYDTGDSGFSEEAMGIALYSYGTWLVv
VTGWSLIGVLVIMEVTRGN
>gi | 295065592 |参考| YP | U 003587393.1 | NADH[锡基游牧民族]
FvGFSSKPSPIYGLVLVvsgVvgCavinCggylGlmVvFylGmmVvfGytaMaiEyeyPawGSG
VEVLVGLVGLAMEVGLVLWAKECDGLVMVLNFNNMGSWVIYEGGSGLIREDSIGAGALYDYGRWLVVV
tgwtllvgvyivieargn
>gi | 295065550 |参考| YP 003587316.1 | NADH（线粒体）[合趾交趾]
FvGFSSKPSPIYGLVLVvsgVvgCaiIlldCggGyLmVfGlyLyLgMMVfGyTtaMaiEyeyPawGSG
VEVLVGLVGLAMEVGLVLWAKEYDGLVLVNFNNMGSWVIYEGEGGLIREDSIGAGALYDYGRWLVVV
tgwtllvgvyivieargn

或者，如果您愿意：

$ cat tst.awk
/^>/ { prtRec(); rec=""; print; next }
{ rec = rec $0 }
END { prtRec() }
function prtRec(        start) {
    for ( start=left_trim+1; start<=length(rec); start+=width ) {
        print substr(rec,start,width)
    }
}

$ awk -v left_trim=15 -v width=70 -f tst.awk file
>gi|304322925|ref|YP_003856771.1| NADH [Lynx rufus]
SFVGFSSKPSPIYGGFGLIVAGGIGCGIVLNFGGSFLGLMVFLIYLGGMLVVFGYTTAMATEPYPEAWTS
NKAVLGMLITGILAELLTACYILKEDEIEVVFKFNGAGDWVIYDTGDSGFFSEEAMGIAALYSYGTWLVV
VTGWSLLIGVLVIMEVTRGN
>gi|295065592|ref|YP_003587393.1| NADH [Nomascus siki]
FVGFSSKPSPIYGGLVLVVSGVVGCAVILNCGGGYLGLMVFLIYLGGMMVVFGYTTAMAIEEYPEAWGSG
VEVLVGVLVGLAMEVGLVLWAKECDGLVMVLNFNNMGSWVIYEGEGSGLIREDSIGAGALYDYGRWLVVV
TGWTLLVGVYIVIEIARGN
>gi|295065550|ref|YP_003587316.1| NADH (mitochondrion) [Symphalangus syndactylus]
FVGFSSKPSPIYGGLVLVVSGVVGCAIILDCGGGYLGLMVFLIYLGGMMVVFGYTTAMAIEEYPEAWGSG
VEVLVGVLVGLAMEVGLVLWAKEYDGLVVVLNFNNMGSWVIYEGEGSGLIREDSIGAGALYDYGRWLVVV
TGWTLLVGVYIVIEIARGN

$cat tst.awk
/^>/{prtRec（）；rec=“”；打印；下一步}
{rec=rec$0}
结束{prtRec（）}
功能prtRec（启动）{
对于（开始=左微调+1；开始GI | 304322925 |参考| YP | U 003856771.1 | NADH[猞猁rufus]
SFVGFSKPSPIYGFGLIVAGGIGGCGIVLNFGGGSFLGLMVFLYLGMLVGYTTAMATEPEAWTS
NKAVLGMLITGILAELLTACYILKEDEIEVFKFNGDWVIYDTGDSGFSEEAMGIALYSYGTWLVv
VTGWSLIGVLVIMEVTRGN
>gi | 295065592 |参考| YP | U 003587393.1 | NADH[锡基游牧民族]
FvGFSSKPSPIYGLVLVvsgVvgCavinCggylGlmVvFylGmmVvfGytaMaiEyeyPawGSG
VEVLVGLVGLAMEVGLVLWAKECDGLVMVLNFNNMGSWVIYEGGSGLIREDSIGAGALYDYGRWLVVV
tgwtllvgvyivieargn
>gi | 295065550 |参考| YP 003587316.1 | NADH（线粒体）[合趾交趾]
FvGFSSKPSPIYGLVLVvsgVvgCaiIlldCggGyLmVfGlyLyLgMMVfGyTtaMaiEyeyPawGSG
VEVLVGLVGLAMEVGLVLWAKEYDGLVLVNFNNMGSWVIYEGEGGLIREDSIGAGALYDYGRWLVVV
tgwtllvgvyivieargn

$1=“”

只比

sub（/[^\n]+\n/，”）

好，因为

OFS=“”

。如果没有这一点，作业将在行的开头引入一个不需要的空白字符。

$1=“/code>和
OFS=“
的组合使得
gsub（）
不必要-
$1=“”
告诉awk重新编译
$0
，
OFS=“
告诉它在重新编译期间只删除字段之间的换行符（从
FS=“\n”
），而不是用其他字符（默认为空白）替换它们。
sequence=""; 
for(i=2; i<=length(a); i++){
  sequence=sequence a[i];
};

$ awk 'BEGIN{printf "%s\n", "foo"}'
foo
$ awk 'BEGIN{printf "%*s\n", 10, "foo"}'
       foo

$ cat tst.awk
BEGIN { RS=">"; FS="\n"; OFS="" }
NR>1 {
    print RS $1
    $1 = ""
    for ( start=left_trim+1; start<=length(); start+=width ) {
        print substr($0,start,width)
    }
}

$ awk -v left_trim=15 -v width=70 -f tst.awk file
>gi|304322925|ref|YP_003856771.1| NADH [Lynx rufus]
SFVGFSSKPSPIYGGFGLIVAGGIGCGIVLNFGGSFLGLMVFLIYLGGMLVVFGYTTAMATEPYPEAWTS
NKAVLGMLITGILAELLTACYILKEDEIEVVFKFNGAGDWVIYDTGDSGFFSEEAMGIAALYSYGTWLVV
VTGWSLLIGVLVIMEVTRGN
>gi|295065592|ref|YP_003587393.1| NADH [Nomascus siki]
FVGFSSKPSPIYGGLVLVVSGVVGCAVILNCGGGYLGLMVFLIYLGGMMVVFGYTTAMAIEEYPEAWGSG
VEVLVGVLVGLAMEVGLVLWAKECDGLVMVLNFNNMGSWVIYEGEGSGLIREDSIGAGALYDYGRWLVVV
TGWTLLVGVYIVIEIARGN
>gi|295065550|ref|YP_003587316.1| NADH (mitochondrion) [Symphalangus syndactylus]
FVGFSSKPSPIYGGLVLVVSGVVGCAIILDCGGGYLGLMVFLIYLGGMMVVFGYTTAMAIEEYPEAWGSG
VEVLVGVLVGLAMEVGLVLWAKEYDGLVVVLNFNNMGSWVIYEGEGSGLIREDSIGAGALYDYGRWLVVV
TGWTLLVGVYIVIEIARGN

$ cat tst.awk
/^>/ { prtRec(); rec=""; print; next }
{ rec = rec $0 }
END { prtRec() }
function prtRec(        start) {
    for ( start=left_trim+1; start<=length(rec); start+=width ) {
        print substr(rec,start,width)
    }
}

$ awk -v left_trim=15 -v width=70 -f tst.awk file
>gi|304322925|ref|YP_003856771.1| NADH [Lynx rufus]
SFVGFSSKPSPIYGGFGLIVAGGIGCGIVLNFGGSFLGLMVFLIYLGGMLVVFGYTTAMATEPYPEAWTS
NKAVLGMLITGILAELLTACYILKEDEIEVVFKFNGAGDWVIYDTGDSGFFSEEAMGIAALYSYGTWLVV
VTGWSLLIGVLVIMEVTRGN
>gi|295065592|ref|YP_003587393.1| NADH [Nomascus siki]
FVGFSSKPSPIYGGLVLVVSGVVGCAVILNCGGGYLGLMVFLIYLGGMMVVFGYTTAMAIEEYPEAWGSG
VEVLVGVLVGLAMEVGLVLWAKECDGLVMVLNFNNMGSWVIYEGEGSGLIREDSIGAGALYDYGRWLVVV
TGWTLLVGVYIVIEIARGN
>gi|295065550|ref|YP_003587316.1| NADH (mitochondrion) [Symphalangus syndactylus]
FVGFSSKPSPIYGGLVLVVSGVVGCAIILDCGGGYLGLMVFLIYLGGMMVVFGYTTAMAIEEYPEAWGSG
VEVLVGVLVGLAMEVGLVLWAKEYDGLVVVLNFNNMGSWVIYEGEGSGLIREDSIGAGALYDYGRWLVVV
TGWTLLVGVYIVIEIARGN