如何提取fasta特定长度的序列

小小脑

>scaffold180916
ACACTTGAAATCCCTTTGTCTTTTACCAACTTGTTGTCCATTTAACCCATTTTGCCCAAAGATCCCTTCTACCGTGAATCAAATCGGCCCTACAGCAGCCTTACATAATCACCTCATAGCTTCCTTGACCTGTTTGACCCCATAGCCCAATTTATCTACATCTTGTTATCCAGTTTATGTATTTGATCAGTTTTATCCCTCACAAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTTTTATAAAGAAGAGGAATTAACTACCTTATAACTTATAAGCTGACTCTTTTTTTCAAAACATTATAATATGTATTTTGAATTAATTGGTAATTTGCATTGTGTTAATGTTAAAATAAATATTTCACTTTATAATTTGCAATTATGTAGATCTCAAAAACAATGGCATAATGTATAAAGTTCTTTTTCTTTGTATGTAAGATCATAATAAAATAATGATAATTCTAAAGTACATGAATTTATTTGCATTATACATACAATTAAAATTACAATTACAATCATTTCACAATAAATTAAATATTACAATTACAA
>scaffold180920
TTTCTAAATTTTATTATGTTACAAAACTTCATATTACTCTATTTTTATTATTTTACAAGTTTACAAATTTAAATTTTTTAATAAAATCATTTCACATTATTACAATTAAATTTTTACAAA
TATTTTACATACAATTAGAATTAGAATTACAATTTCACATACAATTACAATTAAAATTACAATTACAATTTTTGAATTTTACATACAATTACAATTACAATAAAAATTTTACAATTACAATCATTTCACAGTAATACAATTAAAATTTTACAAATATTTTACATACAATTAGAATTAGAATTACAATTTTACAATTTCACGTACAATTACAATTACAATTTTAGATTTTTACATACAATTACAATTATAATTTTAGAATTTTACATAAAATTTACAATTACAATTTTAGAATTTTACAAATTTACATATATACTATTACAATTACAATTTTAGAATTTTACATACAATTAGAATTAGAATTAGAATTTTACAATTTTACATATATATATATATATATATAATTACAATTAAAATTACAATTACAATCATTTCACAATAAATTAAATATTACAATTACAATTAAAATTTTACAAATATTTTACATACAATTAAAATTACAATTACAATCATTTCACAATAAATTAAATATTACAATTACAATTTATAAAGAAGAGGAATTAACTACCACATGAATTTATTTGCATTATACATATTTGCAATTAT
如上fasta序列，我想提取每条序列上下游各100bp的长度？如何进行操作呢？

wh7211

回复 1# 小小脑


<<<awk4.0+

1. awk '/^>/{a=NR;b[a]=$0;next}{c[a]=c[a]?c[a]"\n"$0:$0}END{PROCINFO["sorted_in"]="@ind_num_asc";for(i in c){d=length(c[i]);printf("%s|%s|%s|\n",b[i],substr(c[i],1,100),substr(c[i],d-99))}}' file
   
2. >scaffold180916|ACACTTGAAATCCCTTTGTCTTTTACCAACTTGTTGTCCATTTAACCCATTTTGCCCAAAGATCCCTTCTACCGTGAATCAAATCGGCCCTACAGCAGCC|ATAATGATAATTCTAAAGTACATGAATTTATTTGCATTATACATACAATTAAAATTACAATTACAATCATTTCACAATAAATTAAATATTACAATTACAA|
   
3. >scaffold180920|TTTCTAAATTTTATTATGTTACAAAACTTCATATTACTCTATTTTTATTATTTTACAAGTTTACAAATTTAAATTTTTTAATAAAATCATTTCACATTAT|CAATCATTTCACAATAAATTAAATATTACAATTACAATTTATAAAGAAGAGGAATTAACTACCACATGAATTTATTTGCATTATACATATTTGCAATTAT|

复制代码

小小脑

回复 2# wh7211

厉害呀，大神！如果我还是要fasta格式的，就是不要前后的管道，又该如何操作呢

小小脑

回复 2# wh7211

不好意思大神，我刚没仔细看，我知道如何操作了。谢谢大神

wh7211

回复 3# 小小脑

1. awk '/^>/{a=NR;b[a]=$0;next}{c[a]=c[a]?c[a]"\n"$0:$0}END{PROCINFO["sorted_in"]="@ind_num_asc";for(i in c){d=length(c[i]);printf("%s\n%s\n%s\n",b[i],substr(c[i],1,100),substr(c[i],d-99))}}' file
   
2. >scaffold180916
   
3. ACACTTGAAATCCCTTTGTCTTTTACCAACTTGTTGTCCATTTAACCCATTTTGCCCAAAGATCCCTTCTACCGTGAATCAAATCGGCCCTACAGCAGCC
   
4. ATAATGATAATTCTAAAGTACATGAATTTATTTGCATTATACATACAATTAAAATTACAATTACAATCATTTCACAATAAATTAAATATTACAATTACAA
   
5. >scaffold180920
   
6. TTTCTAAATTTTATTATGTTACAAAACTTCATATTACTCTATTTTTATTATTTTACAAGTTTACAAATTTAAATTTTTTAATAAAATCATTTCACATTAT
   
7. CAATCATTTCACAATAAATTAAATATTACAATTACAATTTATAAAGAAGAGGAATTAACTACCACATGAATTTATTTGCATTATACATATTTGCAATTAT

复制代码

小小脑

回复 5# wh7211
awk是4.01 version的
我进行如下代码：
awk '/^>/{a=NR;b[a]=$0;next}{c[a]=c[a]?c[a]"\n"$00}END{PROCINFO["sorted_in"]="@ind_num_asc";for(i in c){d=length(c);printf("%s\n%s%s\n",b,substr(c,1,100),substr(c,d-99))}}' ptaeda_unpaired_filter.fasta|less -S
>C30462902_9_1183
aaccccaaattttgggcgccgcatggaaaccccaaattttgtgcgccgggtggaaacccc
aaattttgggtgccgggtggaaaccccaaattttgggcgaaa
ttttgggcgccgcatggaaaccccaaattttgggcgctaggtgcaaaccccaaattttgg
gcgccgcatggaaaccccaaattttgggcgctagg
>C30487642_123_1263
cccaaattttgggcgctgggtgaaaaccccaaattttgtgcgccgcatggaaaccccaaa
ttttgggcgctcggtggaaaccccaaattttgggcgccgttttggccgccgcatggaaaccccaaattttgggcgc
cgagtggaaaccccaaattttgagcaccgcatggaaaccccaaatttcgggcgccgggtg
g
>C30492480_19_1274
gcgccgcatggaaaccccaaattttggtcgccgagtggaaaccccaaatttgggcgcggc
tggaaaccccaaattttgggcgccgggtggaaaccccaagggtggaaaccccaaattttgggcgccggttggaaaccccaaa
ttttgggcgccgcatggaaaccccaaattttgggcaccgagtggaaaccccaaatt
随后计算长度
awk '/^>/{a=NR;b[a]=$0;next}{c[a]=c[a]?c[a]"\n"$00}END{PROCINFO["sorted_in"]="@ind_num_asc";for(i in c){d=length(c);printf("%s\n%s%s\n",b,substr(c,1,100),substr(c,d-99))}}' ptaeda_unpaired_filter.fasta|awk '{print $1}' | awk '/^>/&&NR>1{print "";}{ printf "%s",/^>/ ? $0" "0 }END{printf("%s\n", $0)}' |awk '{print $1"\t"length($2)}'|less -S
>C30462902_9_1183       197
>C30487642_123_1263     197
>C30492480_19_1274      198

很奇怪不能得到一样的结果。
以下是序列，比较长
>C30462902_9_1183
aaccccaaattttgggcgccgcatggaaaccccaaattttgtgcgccgggtggaaacccc
aaattttgggtgccgggtggaaaccccaaattttgggcgccatggcgctgcatggaaacc
ccaaattctgggtgctctgtggaaaccccaaattttggctgcggcatgcaaaccccaaat
tttgggcgccgagtggaaaccccaaatttggccgtggcatggaatccccaaattttgggc
accggggggaaaccccaaattttgagcgccgcatggaaaccccaaattttgggcgctgga
tggaaaccccaaattttacgcgccgggtggaaaccccaagttttgggcgcagcatggaaa
cccgaaatcttgggcgccgggtggaaaccccaaattttgggcgctctgtggaaacccaaa
attttggccgccacatggaaaccccaaattttcggcgccgagtggaagcctaaattttgg
gcgccgcatggaaaccccaaattttgggcgccggttggaaagcccaaattttgggcgcta
ggtggaaaccctaaatttttggccccgcatggaaaccccaaattttcggcgccgagtcga
aaccccaaatcttgggcgccatgtcgaaaccccaaatttttggcgctgggtggaaacccc
aaattttgggcgccgcatagaaaccccaaattttgggcgccgcatggaaacaccaaattt
tgggcgttgagtggaaaccccaaattttgggcggaaaccccgaattttgtgcggaaaccc
caaattttgggtggaaaccccgaatttgggcgcggcatggaaaacccaaattttgggtgc
cgggtggaaaccccaaatttagggcgctgaggcgccgcatggaaaccccaaattttgggc
gctgggggaaaccccaaattttgggtgccgcatggaaaccccaaattttgggcgttgagt
ggaaaccccaaattttgggcaccgggtggaaacccaaaattttgggcgctgggtggaaac
cccaaattttggccaccgcatagaaaccccaaattttggacaccaagtggaaagcccaaa
ttttgggcgccgcatggaaaccccaaattttgggcgctaggtgcaaaccccaaattttgg
gcgccgcatggaaaccccaaattttgggcgctagg

>C30487642_123_1263
cccaaattttgggcgctgggtgaaaaccccaaattttgtgcgccgcatggaaaccccaaa
ttttgggcgctcggtggaaaccccaaattttgggcgccgggtgtaaaccccaaatttggc
cgcagcatggaaacaccaaattttgggcaccggacggaaaccccaaattttgagcgccgc
atggaaaccccaaattgtgggcaccgggtggaaacctcaaattttgggcgccgggtggaa
accccaaattttgggcgccgggtggaaaccccaaattttgggcgccggggcgccgaatgg
aaacaccaaattttgggcgccaggtggaaaccccaaatttttggcgctaggtgaaagccc
caaattttgggtgccgcatggaaaccccaaattttgggcgccgagtggaaaccccaaatt
ttgggtgctgggtggaagccccaaattttgggcgctgggtggaagccccaaattttgggc
atcgagtgaaaaccccaaagtttgggcgccgcatggaaaccccaaattttgggcaccggg
ttaaaaccccaaattttgggagccgcatggaaaccccaaattttgggcgccgcatgcaaa
ccccaatttttggtcgttggatggaaacgccaaatttgggcgcggcatggaaaccccaaa
ttttgggcgtcgggtggaaaccccaaattttggggccgggtggaaaccccaaattttggg
cgccggctggaaaccccaaattttggcgcgggctggaaaccccaaatttgggcgtggggt
ggaaaccccaaattttgggagccgggtggaaaccccaaattttgggcgctaggtggaaac
cccaaattttgggtgccaggtggaaattgcaaattttgagcaccggatggaaacccccaa
ttttgggtgccgcgtggaaaccccaaattttgggcgccttatggaaatcccaaattttgg
gcggcgggtggaaaccccaaattttcagcgccgtggcgccgcatggaaaccccaaatttt
gggcgctcggcggaaaccccaaattttggccgccgcatggaaaccccaaattttgggcgc
cgagtggaaaccccaaattttgagcaccgcatggaaaccccaaatttcgggcgccgggtg
g

>C30492480_19_1274
gcgccgcatggaaaccccaaattttggtcgccgagtggaaaccccaaatttgggcgcggc
tggaaaccccaaattttgggcgccgggtggaaaccccaaattttgggcgccggctagaaa
ccccaaatttttggcgccagctggaaaccccaaatttgggcgcggggtggaaaccccaaa
cttggggcgcctggtggaaaccccaaattttgggtgccgggtggaaaccccaaaatttga
gcgctgcatggaaaccccaaattttgggcgtcagatggaaaccccaaattttggggccga
gtggaaaccccaatttttgggcgcagggtggaaaccccaaatttgggcgccaggtggaaa
ccccaaattttgggcgccgagtggaaaccccaaattttaggcgccaggtggaaacccgaa
attttgggtgccaagtggaaaccccaaattttgtgtgccgagtggaaaccccaagttttg
ggcgccgcatggaaaccccaaattttgggcgctcggtgggaaccccaaattttggccgcc
gcatggaaaccccaaattttggccaccgagtggaaaccccaaattttgggcgccgcatgt
aaaccccaaattttgggcgccaggtggaagccccaagttttgggcgctaggaggaaagct
caaattttcggccgcatggaaaccccaaattttgggcgccgggtggaaacccaaaatttt
gggcgccacatggaaaccccaaattttgggcgccgggtggaaaccccaaattttgggcac
cgcgtgcaaaccccaaattttgggcgctggctggaaaccccaaattttgggcgccacatg
gaaaccccaaattttgggcgtcgcacggaaaccctaaatttcgggcgccgcatggaaacc
ccaaatttgggcgcggcatggaaaccccaaatgttgggcgcggcatggaaaccccaaatg
ttgggcgcctaggggaaaccccaaattttgggcgccgggtggaaaccccaaattttgggc
accgcatggaaaccccaaattttgggtgcagggtggaaaccccaaattttgggcgcaggg
tggaaaccccaaattttgggcgctgggtggaaaccccaaattttgggcgccgggtggaaa
ccccaaatttgggcacagggtggaaaccccaaattttgggcgccggttggaaaccccaaa
ttttgggcgccgcatggaaaccccaaattttgggcaccgagtggaaaccccaaatt

wh7211

如果你的需求变了，就把需求写清楚再帮你看

小小脑

回复 7# wh7211
麻烦了大神。是这样的我在想截取如下序列上下游各100bp，并计算长度时发现长度不对。
之前的序列截取时并无问题。就很疑惑
>C30462902_9_1183
aaccccaaattttgggcgccgcatggaaaccccaaattttgtgcgccgggtggaaacccc
aaattttgggtgccgggtggaaaccccaaattttgggcgccatggcgctgcatggaaacc
ccaaattctgggtgctctgtggaaaccccaaattttggctgcggcatgcaaaccccaaat
tttgggcgccgagtggaaaccccaaatttggccgtggcatggaatccccaaattttgggc
accggggggaaaccccaaattttgagcgccgcatggaaaccccaaattttgggcgctgga
tggaaaccccaaattttacgcgccgggtggaaaccccaagttttgggcgcagcatggaaa
cccgaaatcttgggcgccgggtggaaaccccaaattttgggcgctctgtggaaacccaaa
attttggccgccacatggaaaccccaaattttcggcgccgagtggaagcctaaattttgg
gcgccgcatggaaaccccaaattttgggcgccggttggaaagcccaaattttgggcgcta
ggtggaaaccctaaatttttggccccgcatggaaaccccaaattttcggcgccgagtcga
aaccccaaatcttgggcgccatgtcgaaaccccaaatttttggcgctgggtggaaacccc
aaattttgggcgccgcatagaaaccccaaattttgggcgccgcatggaaacaccaaattt
tgggcgttgagtggaaaccccaaattttgggcggaaaccccgaattttgtgcggaaaccc
caaattttgggtggaaaccccgaatttgggcgcggcatggaaaacccaaattttgggtgc
cgggtggaaaccccaaatttagggcgctgaggcgccgcatggaaaccccaaattttgggc
gctgggggaaaccccaaattttgggtgccgcatggaaaccccaaattttgggcgttgagt
ggaaaccccaaattttgggcaccgggtggaaacccaaaattttgggcgctgggtggaaac
cccaaattttggccaccgcatagaaaccccaaattttggacaccaagtggaaagcccaaa
ttttgggcgccgcatggaaaccccaaattttgggcgctaggtgcaaaccccaaattttgg
gcgccgcatggaaaccccaaattttgggcgctagg
>C30487642_123_1263
cccaaattttgggcgctgggtgaaaaccccaaattttgtgcgccgcatggaaaccccaaa
ttttgggcgctcggtggaaaccccaaattttgggcgccgggtgtaaaccccaaatttggc
cgcagcatggaaacaccaaattttgggcaccggacggaaaccccaaattttgagcgccgc
atggaaaccccaaattgtgggcaccgggtggaaacctcaaattttgggcgccgggtggaa
accccaaattttgggcgccgggtggaaaccccaaattttgggcgccggggcgccgaatgg
aaacaccaaattttgggcgccaggtggaaaccccaaatttttggcgctaggtgaaagccc
caaattttgggtgccgcatggaaaccccaaattttgggcgccgagtggaaaccccaaatt
ttgggtgctgggtggaagccccaaattttgggcgctgggtggaagccccaaattttgggc
atcgagtgaaaaccccaaagtttgggcgccgcatggaaaccccaaattttgggcaccggg
ttaaaaccccaaattttgggagccgcatggaaaccccaaattttgggcgccgcatgcaaa
ccccaatttttggtcgttggatggaaacgccaaatttgggcgcggcatggaaaccccaaa
ttttgggcgtcgggtggaaaccccaaattttggggccgggtggaaaccccaaattttggg
cgccggctggaaaccccaaattttggcgcgggctggaaaccccaaatttgggcgtggggt
ggaaaccccaaattttgggagccgggtggaaaccccaaattttgggcgctaggtggaaac
cccaaattttgggtgccaggtggaaattgcaaattttgagcaccggatggaaacccccaa
ttttgggtgccgcgtggaaaccccaaattttgggcgccttatggaaatcccaaattttgg
gcggcgggtggaaaccccaaattttcagcgccgtggcgccgcatggaaaccccaaatttt
gggcgctcggcggaaaccccaaattttggccgccgcatggaaaccccaaattttgggcgc
cgagtggaaaccccaaattttgagcaccgcatggaaaccccaaatttcgggcgccgggtg
g
>C30492480_19_1274
gcgccgcatggaaaccccaaattttggtcgccgagtggaaaccccaaatttgggcgcggc
tggaaaccccaaattttgggcgccgggtggaaaccccaaattttgggcgccggctagaaa
ccccaaatttttggcgccagctggaaaccccaaatttgggcgcggggtggaaaccccaaa
cttggggcgcctggtggaaaccccaaattttgggtgccgggtggaaaccccaaaatttga
gcgctgcatggaaaccccaaattttgggcgtcagatggaaaccccaaattttggggccga
gtggaaaccccaatttttgggcgcagggtggaaaccccaaatttgggcgccaggtggaaa
ccccaaattttgggcgccgagtggaaaccccaaattttaggcgccaggtggaaacccgaa
attttgggtgccaagtggaaaccccaaattttgtgtgccgagtggaaaccccaagttttg
ggcgccgcatggaaaccccaaattttgggcgctcggtgggaaccccaaattttggccgcc
gcatggaaaccccaaattttggccaccgagtggaaaccccaaattttgggcgccgcatgt
aaaccccaaattttgggcgccaggtggaagccccaagttttgggcgctaggaggaaagct
caaattttcggccgcatggaaaccccaaattttgggcgccgggtggaaacccaaaatttt
gggcgccacatggaaaccccaaattttgggcgccgggtggaaaccccaaattttgggcac
cgcgtgcaaaccccaaattttgggcgctggctggaaaccccaaattttgggcgccacatg
gaaaccccaaattttgggcgtcgcacggaaaccctaaatttcgggcgccgcatggaaacc
ccaaatttgggcgcggcatggaaaccccaaatgttgggcgcggcatggaaaccccaaatg
ttgggcgcctaggggaaaccccaaattttgggcgccgggtggaaaccccaaattttgggc
accgcatggaaaccccaaattttgggtgcagggtggaaaccccaaattttgggcgcaggg
tggaaaccccaaattttgggcgctgggtggaaaccccaaattttgggcgccgggtggaaa
ccccaaatttgggcacagggtggaaaccccaaattttgggcgccggttggaaaccccaaa
ttttgggcgccgcatggaaaccccaaattttgggcaccgagtggaaaccccaaatt

wh7211

回复 8# 小小脑

麻烦了大神。是这样的我在想截取如下序列上下游各100bp，并计算长度时发现长度不对。
之前的序列截取时并无问题。就很疑惑

你提供的源fasta序列不是一行，都断行了，我帮你连起来了。通过下面的计算，新的fasta序列满足你的需求

1. cat 1
   
2. >C30462902_9_1183
   
3. aaccccaaattttgggcgccgcatggaaaccccaaattttgtgcgccgggtggaaaccccaaattttgggtgccgggtggaaaccccaaattttgggcgccatggcgctgcatggaaaccccaaattctgggtgctctgtggaaaccccaaattttggctgcggcatgcaaaccccaaattttgggcgccgagtggaaaccccaaatttggccgtggcatggaatccccaaattttgggcaccggggggaaaccccaaattttgagcgccgcatggaaaccccaaattttgggcgctggatggaaaccccaaattttacgcgccgggtggaaaccccaagttttgggcgcagcatggaaacccgaaatcttgggcgccgggtggaaaccccaaattttgggcgctctgtggaaacccaaaattttggccgccacatggaaaccccaaattttcggcgccgagtggaagcctaaattttgggcgccgcatggaaaccccaaattttgggcgccggttggaaagcccaaattttgggcgctaggtggaaaccctaaatttttggccccgcatggaaaccccaaattttcggcgccgagtcgaaaccccaaatcttgggcgccatgtcgaaaccccaaatttttggcgctgggtggaaaccccaaattttgggcgccgcatagaaaccccaaattttgggcgccgcatggaaacaccaaattttgggcgttgagtggaaaccccaaattttgggcggaaaccccgaattttgtgcggaaaccccaaattttgggtggaaaccccgaatttgggcgcggcatggaaaacccaaattttgggtgccgggtggaaaccccaaatttagggcgctgaggcgccgcatggaaaccccaaattttgggcgctgggggaaaccccaaattttgggtgccgcatggaaaccccaaattttgggcgttgagtggaaaccccaaattttgggcaccgggtggaaacccaaaattttgggcgctgggtggaaaccccaaattttggccaccgcatagaaaccccaaattttggacaccaagtggaaagcccaaattttgggcgccgcatggaaaccccaaattttgggcgctaggtgcaaaccccaaattttgggcgccgcatggaaaccccaaattttgggcgctagg
   
4. >C30487642_123_1263
   
5. cccaaattttgggcgctgggtgaaaaccccaaattttgtgcgccgcatggaaaccccaaattttgggcgctcggtggaaaccccaaattttgggcgccgggtgtaaaccccaaatttggccgcagcatggaaacaccaaattttgggcaccggacggaaaccccaaattttgagcgccgcatggaaaccccaaattgtgggcaccgggtggaaacctcaaattttgggcgccgggtggaaaccccaaattttgggcgccgggtggaaaccccaaattttgggcgccggggcgccgaatggaaacaccaaattttgggcgccaggtggaaaccccaaatttttggcgctaggtgaaagccccaaattttgggtgccgcatggaaaccccaaattttgggcgccgagtggaaaccccaaattttgggtgctgggtggaagccccaaattttgggcgctgggtggaagccccaaattttgggcatcgagtgaaaaccccaaagtttgggcgccgcatggaaaccccaaattttgggcaccgggttaaaaccccaaattttgggagccgcatggaaaccccaaattttgggcgccgcatgcaaaccccaatttttggtcgttggatggaaacgccaaatttgggcgcggcatggaaaccccaaattttgggcgtcgggtggaaaccccaaattttggggccgggtggaaaccccaaattttgggcgccggctggaaaccccaaattttggcgcgggctggaaaccccaaatttgggcgtggggtggaaaccccaaattttgggagccgggtggaaaccccaaattttgggcgctaggtggaaaccccaaattttgggtgccaggtggaaattgcaaattttgagcaccggatggaaacccccaattttgggtgccgcgtggaaaccccaaattttgggcgccttatggaaatcccaaattttgggcggcgggtggaaaccccaaattttcagcgccgtggcgccgcatggaaaccccaaattttgggcgctcggcggaaaccccaaattttggccgccgcatggaaaccccaaattttgggcgccgagtggaaaccccaaattttgagcaccgcatggaaaccccaaatttcgggcgccgggtgg
   
6. >C30492480_19_1274
   
7. gcgccgcatggaaaccccaaattttggtcgccgagtggaaaccccaaatttgggcgcggctggaaaccccaaattttgggcgccgggtggaaaccccaaattttgggcgccggctagaaaccccaaatttttggcgccagctggaaaccccaaatttgggcgcggggtggaaaccccaaacttggggcgcctggtggaaaccccaaattttgggtgccgggtggaaaccccaaaatttgagcgctgcatggaaaccccaaattttgggcgtcagatggaaaccccaaattttggggccgagtggaaaccccaatttttgggcgcagggtggaaaccccaaatttgggcgccaggtggaaaccccaaattttgggcgccgagtggaaaccccaaattttaggcgccaggtggaaacccgaaattttgggtgccaagtggaaaccccaaattttgtgtgccgagtggaaaccccaagttttgggcgccgcatggaaaccccaaattttgggcgctcggtgggaaccccaaattttggccgccgcatggaaaccccaaattttggccaccgagtggaaaccccaaattttgggcgccgcatgtaaaccccaaattttgggcgccaggtggaagccccaagttttgggcgctaggaggaaagctcaaattttcggccgcatggaaaccccaaattttgggcgccgggtggaaacccaaaattttgggcgccacatggaaaccccaaattttgggcgccgggtggaaaccccaaattttgggcaccgcgtgcaaaccccaaattttgggcgctggctggaaaccccaaattttgggcgccacatggaaaccccaaattttgggcgtcgcacggaaaccctaaatttcgggcgccgcatggaaaccccaaatttgggcgcggcatggaaaccccaaatgttgggcgcggcatggaaaccccaaatgttgggcgcctaggggaaaccccaaattttgggcgccgggtggaaaccccaaattttgggcaccgcatggaaaccccaaattttgggtgcagggtggaaaccccaaattttgggcgcagggtggaaaccccaaattttgggcgctgggtggaaaccccaaattttgggcgccgggtggaaaccccaaatttgggcacagggtggaaaccccaaattttgggcgccggttggaaaccccaaattttgggcgccgcatggaaaccccaaattttgggcaccgagtggaaaccccaaatt
   
8. 
   
9. 打印新的fasta序列
   
10. awk '/^>/{a=NR;b[a]=$0;next}{c[a]=c[a]?c[a]"\n"$0:$0}END{PROCINFO["sorted_in"]="@ind_num_asc";for(i in c){d=length(c[i]);printf("%s\n%s\n%s\n",b[i],substr(c[i],1,100),substr(c[i],d-99))}}' 1                     
    
11. >C30462902_9_1183
    
12. aaccccaaattttgggcgccgcatggaaaccccaaattttgtgcgccgggtggaaaccccaaattttgggtgccgggtggaaaccccaaattttgggcgc
    
13. ccaaattttgggcgccgcatggaaaccccaaattttgggcgctaggtgcaaaccccaaattttgggcgccgcatggaaaccccaaattttgggcgctagg
    
14. >C30487642_123_1263
    
15. cccaaattttgggcgctgggtgaaaaccccaaattttgtgcgccgcatggaaaccccaaattttgggcgctcggtggaaaccccaaattttgggcgccgg
    
16. aattttggccgccgcatggaaaccccaaattttgggcgccgagtggaaaccccaaattttgagcaccgcatggaaaccccaaatttcgggcgccgggtgg
    
17. >C30492480_19_1274
    
18. gcgccgcatggaaaccccaaattttggtcgccgagtggaaaccccaaatttgggcgcggctggaaaccccaaattttgggcgccgggtggaaaccccaaa
    
19. agggtggaaaccccaaattttgggcgccggttggaaaccccaaattttgggcgccgcatggaaaccccaaattttgggcaccgagtggaaaccccaaatt
    
20. 
    
21. 计算长度
    
22. awk '/^>/{a=NR;b[a]=$0;next}{c[a]=c[a]?c[a]"\n"$0:$0}END{PROCINFO["sorted_in"]="@ind_num_asc";for(i in c){d=length(c[i]);printf("%s\n%s\n%s\n",b[i],substr(c[i],1,100),substr(c[i],d-99))}}' 1|awk -F "" '{print NF}'
    
23. 17
    
24. 100
    
25. 100
    
26. 19
    
27. 100
    
28. 100
    
29. 18
    
30. 100
    
31. 100

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回复 9# wh7211

嗯嗯，我明白了。谢谢大神