統計文件中的殘差數

Question

我有一個文件如下。我想統計每個角色的數量。

>1DMLA 
MTDSPGGVAPASPVEDASDASLGQPEEGAPCQVVLQGAELNGILQAFAPLRTSLLDSLLVMGDRGILIHNTIFGEQVFLP 
LEHSQFSRYRWRGPTAAFLSLVDQKRSLLSVFRANQYPDLRRVELAITGQAPFRTLVQRIWTTTSDGEAVELASETLMKR 
ELTSFVVLVPQGTPDVQLRLTRPQLTKVLNATGADSATPTTFELGVNGKFSVFTTSTCVTFAAREEGVSSSTSTQVQILS 
NALTKAGQAAANAKTVYGENTHRTFSVVVDDCSMRAVLRRLQVGGGTLKFFLTTPVPSLCVTATGPNAVSAVFLLKPQK 
>1DMLB 
DDVAARLRAAGFGAVGAGATAEETRRMLHRAFDTLA 
>2BHDC 
MTDSPGGVAPASPVEDASDASLGQPEEGAPCQVVLQGAELNGILQAFAPLRTSLLDSLLVMGDRGILIHNTIFGEQVFLP 
LEHSQFSRYRWRGPTAAFLSLVDQKRSLLSVFRANQYPDLRRVELAITGQAPFRTLVQRIWTTTSDGEAVELASETLMKR 
ELTSFVVLVPQGTPDVQLRLTRPQLTKVLNATGADSATPTTFELGVNGKFSVFTTSTCVTFAAREEGVSSSTSTQVQILS 

我試了下面的代碼。

awk '/^>/ { res=substr($0, 2); } /^[^>]/ { print res " - " length($0); }' <file 

上述代碼的輸出是

1DMLA - 80 
1DMLA - 80 
1DMLA - 80 
1DMLA - 79 
1DMLB - 36 
2BHDC - 80 
2BHDC - 80 
2BHDC - 80 

我期望的輸出是

1DMLA - 319 
1DMLB - 36 
2BHDC - 240 

如何改變讓我的期望輸出上面的代碼？

Answer 1

下面是使用awk單程：

awk '/^>/ && r { print r, "-", s; r=s="" } /^>/ { r = substr($0, 2); next } { s += length } END { print r, "-", s }' file 

結果：

1DMLA - 319 
1DMLB - 36 
2BHDC - 240 

Answer 2

這樣：

awk -F\> '/^>/ {if (seqlen != ""){print seqlen}printf("%s - ",$2);seqlen=0;next}seqlen != ""{seqlen +=length($0)}END{print seqlen}' infile 

或格式化：

awk -F\> '/^>/ { if (seqlen != "") 
        print seqlen 
       printf("%s - ",$2) 
       seqlen=0 
       next } 
      seqlen != ""{seqlen+=length($0)} 
      END{ 
      print seqlen}' infile 

見： Sequence length of FASTA file

從預期的結果

除此之外，這將處理這些意外的文件格式。

$ cat infile 
MTDSPGGVAPASPVEDASDASLGQPEEGAPCQVVLQGAELNGILQAFAPLRTSLLDSLLVMGDRGILIHNTIFGEQVFLP 
LEHSQFSRYRWRGPTAAFLSLVDQKRSLLSVFRANQYPDLRRVELAITGQAPFRTLVQRIWTTTSDGEAVELASETLMKR 
ELTSFVVLVPQGTPDVQLRLTRPQLTKVLNATGADSATPTTFELGVNGKFSVFTTSTCVTFAAREEGVSSSTSTQVQILS 
NALTKAGQAAANAKTVYGENTHRTFSVVVDDCSMRAVLRRLQVGGGTLKFFLTTPVPSLCVTATGPNAVSAVFLLKPQK 
>1DMLB 
>2BHDC 
MTDSPGGVAPASPVEDASDASLGQPEEGAPCQVVLQGAELNGILQAFAPLRTSLLDSLLVMGDRGILIHNTIFGEQVFLP 
LEHSQFSRYRWRGPTAAFLSLVDQKRSLLSVFRANQYPDLRRVELAITGQAPFRTLVQRIWTTTSDGEAVELASETLMKR 
ELTSFVVLVPQGTPDVQLRLTRPQLTKVLNATGADSATPTTFELGVNGKFSVFTTSTCVTFAAREEGVSSSTSTQVQILS 


$ awk -F\> '/^>/ {if (seqlen != ""){print seqlen}printf("%s - ",$2);seqlen=0;next}seqlen != ""{seqlen +=length($0)}END{print seqlen}' kk2 
1DMLB - 0 
2BHDC - 240 

Answer 3

awk -vRS='>' '$1{gsub("[\r]", "",$1); 
       printf "%s - %d\n", $1, length($0) - length($1) - NF + 1}' input