Question

我有一个如下文件。我想计算每个角色的数量。

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

我尝试了以下代码。

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

上述代码的输出是

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

我想要的输出是

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

如何更改上述代码以获得所需的输出？

Answer 1

这样：

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

请参阅： Sequence length of FASTA file

除了预期的结果，这将处理这些意外的文件格式。

$ 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 2

这是使用awk的一种方式：

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

结果：

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

Answer 3

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

计算文件中的残留数量

3 个答案: