Question

我有这样的输入文件，其中 KO ID，例如K00001，K00002 K00006，01100metabolicpathway，01523Antifolateresistance(7)

等特定类别下的01522Endocrineresistance(7)等

01100Metabolicpathways(812)
K00001
Ca_19344,Ca_19730
K00002
Ca_09433,Ca_23715,Ca_15858,Ca_19929,Ca_26670
K00008
Ca_20904
K00011
Ca_15431
K00012
Ca_10466,Ca_23867,Ca_06574
K00013
Ca_08009
K00016
Ca_02357,Ca_16304
K00020
Ca_08005
K00021
Ca_10251,Ca_09868
01523Antifolateresistance(7)
K00297
Ca_26773
K00600
Ca_00054,Ca_00455,Ca_14951,Ca_11397,Ca_08538,Ca_11540,Ca_11173
01522Endocrineresistance(7)
K04650
Ca_20380,Ca_04277

这样的期望输出：

K00001  Ca_19344,Ca_19730   01100Metabolicpathways(812)
K00002  Ca_09433,Ca_23715,Ca_15858,Ca_19929,Ca_26670    01100Metabolicpathways(812)
K00006  Ca_14695,Ca_21671,Ca_07219,Ca_24024,Ca_23566,Ca_27084   01100Metabolicpathways(812)
K00008  Ca_20904    01100Metabolicpathways(812)
K00011  Ca_15431    01100Metabolicpathways(812)
K00012  Ca_10466,Ca_23867,Ca_06574  01100Metabolicpathways(812)
K00013  Ca_08009    01100Metabolicpathways(812)
K00016  Ca_02357,Ca_16304   01100Metabolicpathways(812)
K00020  Ca_08005    01100Metabolicpathways(812)
K00021  Ca_10251,Ca_09868   01100Metabolicpathways(812)
K00297  Ca_26773    01523Antifolateresistance(7)
K00600  Ca_00054,Ca_00455,Ca_14951,Ca_11397,Ca_08538,Ca_11540,Ca_11173  01523Antifolateresistance(7)    
K04650  Ca_20380,Ca_04277   01522Endocrineresistance(7)

我通过将 KO ID带入KO_list.txt文件，

写了类似的内容

K00001
K00002
K00006
K00008
K00011
K00012
K00013
K00016
K00020
K00021
for n in `cat KO_list.txt`
do
x=$(cat $2 | grep  -w -A1 "^$n"  | head -2 | sed ':a;N;$!ba;s/\n/\t/g')
echo -e "$x" | awk 'NF' >> output.txt
done

但它只给我这样的输出

K00001  Ca_19344,Ca_19730   
K00002  Ca_09433,Ca_23715,Ca_15858,Ca_19929,Ca_26670    
K00006  Ca_14695,Ca_21671,Ca_07219,Ca_24024,Ca_23566,Ca_27084   
K00008  Ca_20904    
K00011  Ca_15431    
K00012  Ca_10466,Ca_23867,Ca_06574  
K00013  Ca_08009    
K00016  Ca_02357,Ca_16304   
K00020  Ca_08005
K00021  Ca_10251,Ca_09868   
K00297  Ca_26773    
K00600  Ca_00054,Ca_00455,Ca_14951,Ca_11397,Ca_08538,Ca_11540,Ca_11173  
K04650  Ca_20380,Ca_04277

任何帮助人员

＃＃＃＃＃＃＃＃＃第二部分

谢谢大家，我真的很欣赏你所有的valubale评论，它还有第二部分是否有任何方法可以根据Ca-ID进行输出，其中Ca-ID位于第一列并且每个Ca-id分别有信息而不是直接来自输入文件或KO-ID在第一列的所需输出文件中的KO-id，我正在从任何相同的文件中寻找这样的输出。

来自此输入文件

01100Metabolicpathways(812)
K00001
Ca_19344,Ca_19730
01522Endocrineresistance(7)
K04650
Ca_20380,Ca_04277

或从输入文件

创建的输出文件

K00001  Ca_19344,Ca_19730   01100Metabolicpathways(812)
K04650  Ca_20380,Ca_04277   01522Endocrineresistance(7)

新的理想输出应该是这样的

Ca_19344    K00001  01100Metabolicpathways(812)
Ca_19730    K00001  01100Metabolicpathways(812)
Ca_20380    K04650  01522Endocrineresistance(7)
Ca_04277    K04650  01522Endocrineresistance(7)

提前致谢

Answer 1

这是一个便宜的解决方案，但它适用于您的输入：

awk '/^[0-9].*/{ h = $0; next }/^K/{ k = $0; next }{ print k, $0, h }' yourfile

输出：

K00001 Ca_19344,Ca_19730 01100Metabolicpathways(812)
K00002 Ca_09433,Ca_23715,Ca_15858,Ca_19929,Ca_26670 01100Metabolicpathways(812)
K00008 Ca_20904 01100Metabolicpathways(812)
K00011 Ca_15431 01100Metabolicpathways(812)
K00012 Ca_10466,Ca_23867,Ca_06574 01100Metabolicpathways(812)
K00013 Ca_08009 01100Metabolicpathways(812)
K00016 Ca_02357,Ca_16304 01100Metabolicpathways(812)
K00020 Ca_08005 01100Metabolicpathways(812)
K00021 Ca_10251,Ca_09868 01100Metabolicpathways(812)
K00297 Ca_26773 01523Antifolateresistance(7)
K00600 Ca_00054,Ca_00455,Ca_14951,Ca_11397,Ca_08538,Ca_11540,Ca_11173 01523Antifolateresistance(7)

所以，这个班轮基本上做的是将某些行捕获到变量中。因此，第一部分/^[0-9].*/{ h = $0; next }会捕获以类别标识符之类的数字开头的行。 Awk看到行01100metabolicpathway并将其存储到变量h中。然后执行next命令并且awk读取下一行。当一行以K开头时，第二部分/^K/{ k = $0; next }执行。就像你的KO id一样。 awk再次将整行存储到变量中并继续下一个变量。现在，当一条线不符合任何提到的标准（以K或数字开头）时，执行las部分{ print k, $0, h }。然后是变量k的内容，整个当前行和变量h的内容。这导致了期望的输出。

Answer 2

awk -v OFS=, '/^K/{k=$0;next}/^C/{ print k, $0 " " c; k=""; next}{c=$0}' infile

解释

awk -v OFS=, '                            # set output field separator
              /^K/{                       # if line starts with K
                    k=$0;                 # variable k = current line/record
                    next                  # go to next line
              } 
             /^C/{                        # if line starts with C 
                    print k, $0 " " c;    # print variable k, current row and variable c
                    k="";                 # nullify variable k
                    next                  # go to next line
              }
              {
                    c=$0                  # if from above statement line not
                                          # skipped then variable c will be category
              }
            ' infile

输入

$ cat infile
01100Metabolicpathways(812)
K00001
Ca_19344,Ca_19730
K00002
Ca_09433,Ca_23715,Ca_15858,Ca_19929,Ca_26670
K00008
Ca_20904
K00011
Ca_15431
K00012
Ca_10466,Ca_23867,Ca_06574
K00013
Ca_08009
K00016
Ca_02357,Ca_16304
K00020
Ca_08005
K00021
Ca_10251,Ca_09868
01523Antifolateresistance(7)
K00297
Ca_26773
K00600
Ca_00054,Ca_00455,Ca_14951,Ca_11397,Ca_08538,Ca_11540,Ca_11173
01522Endocrineresistance(7)
K04650
Ca_20380,Ca_04277

输出

$ awk -v OFS=, '/^K/{k=$0;next}/^C/{ print k,$0" "c ; k=""; next}{c=$0}' infile
K00001,Ca_19344,Ca_19730 01100Metabolicpathways(812)
K00002,Ca_09433,Ca_23715,Ca_15858,Ca_19929,Ca_26670 01100Metabolicpathways(812)
K00008,Ca_20904 01100Metabolicpathways(812)
K00011,Ca_15431 01100Metabolicpathways(812)
K00012,Ca_10466,Ca_23867,Ca_06574 01100Metabolicpathways(812)
K00013,Ca_08009 01100Metabolicpathways(812)
K00016,Ca_02357,Ca_16304 01100Metabolicpathways(812)
K00020,Ca_08005 01100Metabolicpathways(812)
K00021,Ca_10251,Ca_09868 01100Metabolicpathways(812)
K00297,Ca_26773 01523Antifolateresistance(7)
K00600,Ca_00054,Ca_00455,Ca_14951,Ca_11397,Ca_08538,Ca_11540,Ca_11173 01523Antifolateresistance(7)
K04650,Ca_20380,Ca_04277 01522Endocrineresistance(7)

- 编辑 -

For new input

$ cat infile_new
K00001  Ca_19344,Ca_19730   01100Metabolicpathways(812)
K04650  Ca_20380,Ca_04277   01522Endocrineresistance(7)

$ awk  '{split($2,a,/,/); for(i=1; i in a; i++)print a[i], $1,  $3}' infile_new
Ca_19344 K00001 01100Metabolicpathways(812)
Ca_19730 K00001 01100Metabolicpathways(812)
Ca_20380 K04650 01522Endocrineresistance(7)
Ca_04277 K04650 01522Endocrineresistance(7)

Answer 3

短 awk 解决方案：

awk '/^[0-9]/{ cat=$0;next }cat{ printf "%s %s",$0,(/^Ca/)? cat"\n":"" }' file

输出：

K00001 Ca_19344,Ca_19730 01100Metabolicpathways(812)
K00002 Ca_09433,Ca_23715,Ca_15858,Ca_19929,Ca_26670 01100Metabolicpathways(812)
K00008 Ca_20904 01100Metabolicpathways(812)
K00011 Ca_15431 01100Metabolicpathways(812)
K00012 Ca_10466,Ca_23867,Ca_06574 01100Metabolicpathways(812)
K00013 Ca_08009 01100Metabolicpathways(812)
K00016 Ca_02357,Ca_16304 01100Metabolicpathways(812)
K00020 Ca_08005 01100Metabolicpathways(812)
K00021 Ca_10251,Ca_09868 01100Metabolicpathways(812)
K00297 Ca_26773 01523Antifolateresistance(7)
K00600 Ca_00054,Ca_00455,Ca_14951,Ca_11397,Ca_08538,Ca_11540,Ca_11173 01523Antifolateresistance(7)
K04650 Ca_20380,Ca_04277 01522Endocrineresistance(7)

新条件的

奖金解决方案（第二部分）：

awk '/^[0-9]/{ cat=$0;next }cat{ if(/^K/){ k=$0;next } 
     if(/^Ca/){ split($0,a,","); for(i in a) print a[i],k,cat } }' file

输出：

Ca_19344 K00001 01100Metabolicpathways(812)
Ca_19730 K00001 01100Metabolicpathways(812)
Ca_09433 K00002 01100Metabolicpathways(812)
Ca_23715 K00002 01100Metabolicpathways(812)
Ca_15858 K00002 01100Metabolicpathways(812)
Ca_19929 K00002 01100Metabolicpathways(812)
Ca_26670 K00002 01100Metabolicpathways(812)
Ca_20904 K00008 01100Metabolicpathways(812)
Ca_15431 K00011 01100Metabolicpathways(812)
Ca_10466 K00012 01100Metabolicpathways(812)
Ca_23867 K00012 01100Metabolicpathways(812)
Ca_06574 K00012 01100Metabolicpathways(812)
Ca_08009 K00013 01100Metabolicpathways(812)
Ca_02357 K00016 01100Metabolicpathways(812)
Ca_16304 K00016 01100Metabolicpathways(812)
Ca_08005 K00020 01100Metabolicpathways(812)
Ca_10251 K00021 01100Metabolicpathways(812)
Ca_09868 K00021 01100Metabolicpathways(812)
Ca_26773 K00297 01523Antifolateresistance(7)
Ca_00054 K00600 01523Antifolateresistance(7)
Ca_00455 K00600 01523Antifolateresistance(7)
Ca_14951 K00600 01523Antifolateresistance(7)
Ca_11397 K00600 01523Antifolateresistance(7)
Ca_08538 K00600 01523Antifolateresistance(7)
Ca_11540 K00600 01523Antifolateresistance(7)
Ca_11173 K00600 01523Antifolateresistance(7)
Ca_20380 K04650 01522Endocrineresistance(7)
Ca_04277 K04650 01522Endocrineresistance(7)

Answer 4

$ cat tst.awk
BEGIN { OFS="\t" }
/\(/ { cat=$0; cnt=0; next }
++cnt % 2 { kid=$0; next }
{ print kid, $0, cat }

$ awk -f tst.awk file
K00001  Ca_19344,Ca_19730       01100Metabolicpathways(812)
K00002  Ca_09433,Ca_23715,Ca_15858,Ca_19929,Ca_26670    01100Metabolicpathways(812)
K00008  Ca_20904        01100Metabolicpathways(812)
K00011  Ca_15431        01100Metabolicpathways(812)
K00012  Ca_10466,Ca_23867,Ca_06574      01100Metabolicpathways(812)
K00013  Ca_08009        01100Metabolicpathways(812)
K00016  Ca_02357,Ca_16304       01100Metabolicpathways(812)
K00020  Ca_08005        01100Metabolicpathways(812)
K00021  Ca_10251,Ca_09868       01100Metabolicpathways(812)
K00297  Ca_26773        01523Antifolateresistance(7)
K00600  Ca_00054,Ca_00455,Ca_14951,Ca_11397,Ca_08538,Ca_11540,Ca_11173  01523Antifolateresistance(7)
K04650  Ca_20380,Ca_04277       01522Endocrineresistance(7)

根据标题的类别

4 个答案: