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Asked: 2021-05-29 00:17:47 +0800 CST

多列CSV的后处理：删除重复行+排序

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我正在处理由几个 CSV 的串联（通过 cat）生成的 csv：

ID(Prot),   ID(lig),    ID(cluster),    dG(rescored),   dG(before), POP(before)
1000,   lig40,  1,  0.805136,   -5.5200,    79
1000,   lig868, 1,  0.933209,   -5.6100,    42
1000,   lig278, 1,  0.933689,   -5.7600,    40
1000,   lig619, 3,  0.946354,   -7.6100,    20
1000,   lig211, 1,  0.960048,   -5.2800,    39
1000,   lig40,  2,  0.971051,   -4.9900,    40
1000,   lig868, 3,  0.986384,   -5.5000,    29
1000,   lig12,  3,  0.988506,   -6.7100,    16
1000,   lig800, 16, 0.995574,   -4.5300,    40
1000,   lig800, 1,  0.999935,   -5.7900,    22
1000,   lig619, 1,  1.00876,    -7.9000,    3
1000,   lig619, 2,  1.02254,    -7.6400,    1
1000,   lig12,  1,  1.02723,    -6.8600,    5
1000,   lig12,  2,  1.03273,    -6.8100,    4
1000,   lig211, 2,  1.03722,    -5.2000,    19
1000,   lig211, 3,  1.03738,    -5.0400,    21
ID(Prot),   ID(lig),    ID(cluster),    dG(rescored),   dG(before), POP(before)
10V1,   lig40,  1,  0.513472,   -6.4600,    150
10V1,   lig211, 2,  0.695981,   -6.8200,    91
10V1,   lig278, 1,  0.764432,   -7.0900,    70
10V1,   lig868, 1,  0.787698,   -7.3100,    62
10V1,   lig211, 1,  0.83416,    -6.8800,    54
10V1,   lig868, 3,  0.888408,   -6.4700,    44
10V1,   lig278, 2,  0.915932,   -6.6600,    35
10V1,   lig12,  1,  0.922741,   -9.3600,    19
10V1,   lig12,  8,  0.934144,   -7.4600,    24
10V1,   lig40,  2,  0.949955,   -5.9000,    34
10V1,   lig800, 5,  0.964194,   -5.9200,    30
10V1,   lig868, 2,  0.966243,   -6.9100,    20
10V1,   lig12,  2,  0.972575,   -8.3000,    10
10V1,   lig619, 6,  0.979168,   -8.1600,    9
10V1,   lig619, 4,  0.986202,   -8.7800,    5
10V1,   lig800, 2,  0.989599,   -6.2400,    20
10V1,   lig619, 1,  0.989725,   -9.2900,    3
10V1,   lig12,  7,  0.991535,   -7.5800,    9
ID(Prot),   ID(lig),    ID(cluster),    dG(rescored),   dG(before), POP(before)
10V2,   lig40,  1,  0.525767,   -6.4600,    146
10V2,   lig211, 2,  0.744702,   -6.8200,    78
10V2,   lig278, 1,  0.749015,   -7.0900,    74
10V2,   lig868, 1,  0.772025,   -7.3100,    66
10V2,   lig211, 1,  0.799829,   -6.8700,    63
10V2,   lig12,  1,  0.899345,   -9.1600,    25
10V2,   lig12,  4,  0.899606,   -7.5500,    32
10V2,   lig868, 3,  0.903364,   -6.4800,    40
10V2,   lig278, 3,  0.913145,   -6.6300,    36
10V2,   lig800, 5,  0.94576,    -5.9100,    35

要后处理此 CSV，我需要 1) 删除标题行的重复

ID(Prot),   ID(lig),    ID(cluster),    dG(rescored),   dG(before), POP(before)

仅将标题保留在融合 csv 的开头（在第一行！）

然后我需要根据第 4 (dG(rescored)) 列中的数字对所有行（忽略第一行标题）进行排序。

为了完成第一项任务，我尝试使用以下 awk one-liner 它正在寻找第一行，然后删除其重复

 awk '{first=$1;gsub("ID(Prot)","");print first,$0}' mycsv.csv > csv_without_repeats.csv

但是它无法识别标题行，这意味着模式定义不正确。

然后根据我使用的第 4 列中的值对数据进行排序：

LC_ALL=C sort -k4,4g

如何将它通过管道传输到我的 AWK 代码或其他由 AWK 直接完成的所有事情？

例如我试过

awk '{first=$1;gsub(/ID(Prot)?(\([-azA-Z]+\))?/,"");print first,$0}' | LC_ALL=C sort -k4,4g input.csv > sorted_and_without_repeats.csv

但是脚本可以被终止，同时正确地生成分类的 CSV（由于 awk 部分的问题，仍然有重复）。

csv sorting

1 个回答

  1. Best Answer

    这是使用 GNU awk 的一种方法：

    解析.awk

    BEGIN { 
  # Arrays should be sorted numerically by their index
  PROCINFO["sorted_in"] = "@ind_num_asc" 

  # Set field-separator to comma followed by optional space
  FS = ",[ \t]*"
}

# Print the header
NR==1 { print; next }

# Collect lines into the `h` hashmap
NR>1 && $1 !~ /^ID/ { 
  h[$4] = $0
} 

# Print the sorted hashmap `h`
END { 
  for(k in h) print h[k]
}

    像这样运行它：

    awk -f parse.awk infile

    输出：

    ID(Prot),   ID(lig),    ID(cluster),    dG(rescored),   dG(before), POP(before)
10V1,   lig40,  1,  0.513472,   -6.4600,    150
10V2,   lig40,  1,  0.525767,   -6.4600,    146
10V1,   lig211, 2,  0.695981,   -6.8200,    91
10V2,   lig211, 2,  0.744702,   -6.8200,    78
10V2,   lig278, 1,  0.749015,   -7.0900,    74
10V1,   lig278, 1,  0.764432,   -7.0900,    70
10V2,   lig868, 1,  0.772025,   -7.3100,    66
10V1,   lig868, 1,  0.787698,   -7.3100,    62
10V2,   lig211, 1,  0.799829,   -6.8700,    63
1000,   lig40,  1,  0.805136,   -5.5200,    79
10V1,   lig211, 1,  0.83416,    -6.8800,    54
10V1,   lig868, 3,  0.888408,   -6.4700,    44
10V2,   lig12,  1,  0.899345,   -9.1600,    25
10V2,   lig12,  4,  0.899606,   -7.5500,    32
10V2,   lig868, 3,  0.903364,   -6.4800,    40
10V2,   lig278, 3,  0.913145,   -6.6300,    36
10V1,   lig278, 2,  0.915932,   -6.6600,    35
10V1,   lig12,  1,  0.922741,   -9.3600,    19
1000,   lig868, 1,  0.933209,   -5.6100,    42
1000,   lig278, 1,  0.933689,   -5.7600,    40
10V1,   lig12,  8,  0.934144,   -7.4600,    24
10V2,   lig800, 5,  0.94576,    -5.9100,    35
1000,   lig619, 3,  0.946354,   -7.6100,    20
10V1,   lig40,  2,  0.949955,   -5.9000,    34
1000,   lig211, 1,  0.960048,   -5.2800,    39
10V1,   lig800, 5,  0.964194,   -5.9200,    30
10V1,   lig868, 2,  0.966243,   -6.9100,    20
1000,   lig40,  2,  0.971051,   -4.9900,    40
10V1,   lig12,  2,  0.972575,   -8.3000,    10
10V1,   lig619, 6,  0.979168,   -8.1600,    9
10V1,   lig619, 4,  0.986202,   -8.7800,    5
1000,   lig868, 3,  0.986384,   -5.5000,    29
1000,   lig12,  3,  0.988506,   -6.7100,    16
10V1,   lig800, 2,  0.989599,   -6.2400,    20
10V1,   lig619, 1,  0.989725,   -9.2900,    3
10V1,   lig12,  7,  0.991535,   -7.5800,    9
1000,   lig800, 16, 0.995574,   -4.5300,    40
1000,   lig800, 1,  0.999935,   -5.7900,    22
1000,   lig619, 1,  1.00876,    -7.9000,    3
1000,   lig619, 2,  1.02254,    -7.6400,    1
1000,   lig12,  1,  1.02723,    -6.8600,    5
1000,   lig12,  2,  1.03273,    -6.8100,    4
1000,   lig211, 2,  1.03722,    -5.2000,    19
1000,   lig211, 3,  1.03738,    -5.0400,    21
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