如何在linux中創建一個包含來自不同多個文件的所需列的新文件？

我有一個目錄ballgown，其中有大約 1000 個子目錄作為範例名稱。每個子目錄都有一個文件t_data.ctab。所有子目錄中的文件名都相同。

ballgown
     |_______TCGA-A2-A0T3-01A
                  |___________ t_data.ctab
     |_______TCGA-A7-A4SA-01A
                  |___________ t_data.ctab
     |_______TCGA-A7-A6VW-01A
                  |___________ t_data.ctab

像上面一樣ballgown有 1000 個子目錄。所有這 1000 個子目錄中的t_data.ctab文件如下所示：

t_id    chr     strand  start   end     t_name  num_exons       length  gene_id gene_name       cov     FPKM
1       1       -       10060   10614   MSTRG.1.1       1       555     MSTRG.1 .       0.000000        0.000000
2       1       +       11140   30023   MSTRG.10.1      12      3981    MSTRG.10        .       2.052715        0.284182
3       1       -       11694   29342   MSTRG.11.1      8       6356    MSTRG.11        .       0.557588        0.077194
4       1       +       11869   14409   ENST00000456328.2       3       1657    MSTRG.10        DDX11L1 0.000000        0.000000
5       1       +       11937   29347   MSTRG.10.3      12      3544    MSTRG.10        .       0.000000        0.000000
6       1       -       11959   30203   MSTRG.11.2      11      4547    MSTRG.11        .       0.369929        0.051214
7       1       +       12010   13670   ENST00000450305.2       6       632     MSTRG.10        DDX11L1 0.000000        0.000000
8       1       +       12108   26994   MSTRG.10.5      10      5569    MSTRG.10        .       0.057091        0.007904
9       1       +       12804   199997  MSTRG.10.6      12      3567    MSTRG.10        .       0.000000        0.000000
10      1       +       13010   31097   MSTRG.10.7      12      4375    MSTRG.10        .       0.000000        0.000000
11      1       -       13068   26832   MSTRG.11.3      9       5457    MSTRG.11        .       0.995280        0.137788

從t_data.ctab我只想提取的所有文件中t_name，FPKM列並創建一個新文件。在新文件中，該FPKM列應該是樣品名稱。它應該如下所示：

t_name         TCGA-A2-A0T3-01A TCGA-A7-A4SA-01A    TCGA-A7-A6VW-01A
MSTRG.1.1              0            0.028181                 0
MSTRG.10.1         0.284182         0.002072             0.046302
MSTRG.11.1         0.077194         0.685535             0.105849
ENST00000456328.2      0            0.307315             0.038961
MSTRG.10.3             0            0.446015             0.009946
MSTRG.11.2         0.051214         0.053577             0.036081
ENST00000450305.2      0            0.110438             0.040319
MSTRG.10.5         0.007904             0                1.430825
MSTRG.10.6             0                0                0.221105
MSTRG.10.7             0            0.199354                 0
MSTRG.11.3         0.137788         0.004792                 0

如果是兩個或三個文件，我可以cut在每個文件上使用 -f6,12 然後加入它們。但我現在有大約 1000 個文件。

試試這個簡單的方法：

首先做：

awk 'FNR==1 { print substr(FILENAME,1,16) >substr(FILENAME,1,16)".tmp" }
    FNR >1 { print $12 > substr(FILENAME,1,16)".tmp" }
    NR==FNR{ print $6  >"first_column.tmp" }' TCGA-A*/t_data.ctab

然後paste將它們與逗號分隔的文件一起（-d,如果你想要 Tab 而不是刪除）：

paste -d, *.tmp
t_name,TCGA-A2-A0T3-01A,TCGA-A7-A4SA-01A,TCGA-A7-A6VW-01A
MSTRG.1.1,0.000000,0.00000,0.0000
MSTRG.10.1,0.284182,0.28418,0.2841
MSTRG.11.1,0.077194,0.07719,0.0771
ENST00000456328.2,0.000000,0.00000,0.0000
MSTRG.10.3,0.000000,0.00000,0.0000
MSTRG.11.2,0.051214,0.05121,0.0512
ENST00000450305.2,0.000000,0.00000,0.0000
MSTRG.10.5,0.007904,0.00790,0.0079
MSTRG.10.6,0.000000,0.00000,0.0000
MSTRG.10.7,0.000000,0.00000,0.0000
MSTRG.11.3,0.137788,0.13778,0.1377

引用自：https://unix.stackexchange.com/questions/465464