将多个文件，不同的计数值 [英] Combine multiple files with different count values

问题描述

我想从每个文件采取第二列96合并文件，并保持第一列是所有文件之间相似。我试图做到这一点的R，但figued它会在终端上更好。它的工作原理用awk？

示例数据：

  DMED7013：RFAM robinm $头Rfam_Counts_combined_SplitRfam_Counts_combinedhtseq_Rfamoutput402R.sam
SEQ _ .. /修剪/ 402R.tally.fasta __not_aligned
__too_low_aQual 3
MIR-10 5
Y_RNA 4
__too_low_aQual 0
__too_low_aQual 0
__not_aligned 1
MIR-8 2
MIR-671 3
MIR-671 16
 

中的文件：

  DMED7013：RFAM robinm $ ls -l命令
-rw-R  -  R-- 1 robinm人员1711388 9月22日19:12 Rfam_Counts_combined_SplitRfam_Counts_combinedhtseq_Rfamoutput100G.sam
-rw-R  -  R-- 1 robinm人员1712778 9月22日19:12 Rfam_Counts_combined_SplitRfam_Counts_combinedhtseq_Rfamoutput100R.sam
-rw-R  -  R-- 1 robinm人员1709703 9月22日19:12 Rfam_Counts_combined_SplitRfam_Counts_combinedhtseq_Rfamoutput106G.sam
-rw-R  -  R-- 1 robinm人员1707486 9月22日19:12 Rfam_Counts_combined_SplitRfam_Counts_combinedhtseq_Rfamoutput106R.sam
-rw-R  -  R-- 1 robinm人员1704757 9月22日19:12 Rfam_Counts_combined_SplitRfam_Counts_combinedhtseq_Rfamoutput122G.sam
-rw-R  -  R-- 1 robinm人员1705471 9月22日19:12 Rfam_Counts_combined_SplitRfam_Counts_combinedhtseq_Rfamoutput122R.sam
.....
 

解决方案

您可以尝试（如果我理解正确的）

 的awk'（在D $ 1）{D [$ 1 = $ 2！;下一个}
     {D [$ 1] + = $ 2}
     END {为（以D键）打印键，D [关键] }'* .SAM
 

您可以：

__too_low_aQual 3
MIR-671 19
MIR-8 2
__not_aligned 1
Y_RNA 4
MIR-10 5

I would like to combine 96 files by taking the second column from each files and keep the first column which is similar between all files. I tried to do this in R, but figued it would be better in the terminal. Does it work using awk?

Sample data:

DMED7013:Rfam robinm$ head Rfam_Counts_combined_SplitRfam_Counts_combinedhtseq_Rfamoutput402R.sam
Seq_../trimmed/402R.tally.fasta __not_aligned
__too_low_aQual 3
mir-10 5
Y_RNA 4
__too_low_aQual 0
__too_low_aQual 0
__not_aligned 1
mir-8 2
mir-671 3
mir-671 16

The files:

DMED7013:Rfam robinm$ ls -l  
-rw-r--r--   1 robinm  staff  1711388 Sep 22 19:12 Rfam_Counts_combined_SplitRfam_Counts_combinedhtseq_Rfamoutput100G.sam
-rw-r--r--   1 robinm  staff  1712778 Sep 22 19:12 Rfam_Counts_combined_SplitRfam_Counts_combinedhtseq_Rfamoutput100R.sam
-rw-r--r--   1 robinm  staff  1709703 Sep 22 19:12 Rfam_Counts_combined_SplitRfam_Counts_combinedhtseq_Rfamoutput106G.sam
-rw-r--r--   1 robinm  staff  1707486 Sep 22 19:12 Rfam_Counts_combined_SplitRfam_Counts_combinedhtseq_Rfamoutput106R.sam
-rw-r--r--   1 robinm  staff  1704757 Sep 22 19:12 Rfam_Counts_combined_SplitRfam_Counts_combinedhtseq_Rfamoutput122G.sam
-rw-r--r--   1 robinm  staff  1705471 Sep 22 19:12 Rfam_Counts_combined_SplitRfam_Counts_combinedhtseq_Rfamoutput122R.sam
.....

解决方案

you can try (if, I understood correctly)

awk '!($1 in d){d[$1]=$2; next}
     {d[$1]+=$2}
     END{for(key in d) print key, d[key]; }' *.sam

you get:

__too_low_aQual 3
mir-671 19
mir-8 2
__not_aligned 1
Y_RNA 4
mir-10 5

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