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如何从第二列中减去所有相邻行并保留第一列

tag-icon • tag-icon awk command-line bioinformatics
如何从第二列中减去所有相邻行并保留第一列

我正在通过以下命令创建一个文件：

awk '{print $2 " "$7" "$8}' REACTOME_EXTENSION_OF_TELOMERES.xls |  awk '$8!="No"  {print $1 " " $2}' | awk 'NR>1' | awk 'BEGIN { OFS=", "; print "Name" " " "0" };{ print $0 " " "" }'

输出是这样的：

    Name 0
WRAP53 0.08495288 
NHP2 0.17606254 
POLA1 0.25320756 
POLD3 0.32372433 
PRIM1 0.38140765 
RFC5 0.44302294 
POLD1 0.497649 
...

我需要一个命令来减去第二列中的每个相邻行并给出以下结果：

WRAP53 0.0849529 
NHP2 0.0911097 
POLA1 0.077145 
POLD3 0.0705168 
PRIM1 0.0576833 
RFC5 0.0616153 
POLD1 0.0546261 
...

当我只保留第二列时，我知道该怎么做，它会是这样的：

awk '{print $2 " "$7" "$8}' REACTOME_EXTENSION_OF_TELOMERES.xls |  awk '$8!="No"  {print $1 " " $2}' | awk 'NR>1' | awk 'BEGIN { OFS=", "; print "Name" " " "0" };{ print $0 " " "" }' | awk '{print $NF}' | awk 'NR-1{print $0-p}{p=$0}'

但是如何才能保留如上所示的第一列呢？

REACTOME_EXTENSION_OF_TELOMERES.xls 文件如下所示：

NAME    PROBE   GENE SYMBOL     GENE_TITLE      RANK IN GENE LIST       RANK METRIC SCORE       RUNNING ES      CORE ENRICHMENT
row_0   WRAP53  null    null    163     1.5818238258361816      0.08495288      Yes
row_1   NHP2    null    null    201     1.5055444240570068      0.17606254      Yes
row_2   POLA1   null    null    283     1.3435969352722168      0.25320756      Yes
row_3   POLD3   null    null    367     1.240567684173584       0.32372433      Yes
row_4   PRIM1   null    null    501     1.1049883365631104      0.38140765      Yes
row_5   RFC5    null    null    557     1.0596935749053955      0.44302294      Yes
row_6   POLD1   null    null    653     1.0035457611083984      0.497649        Yes

如果我可以将整个命令的输出写入：REACTOME_EXTENSION_OF_TELOMERES.y，那就太好了

答案1

您的整个 awk 管道可以替换为

awk 'NR > 1 && $8 != "No" {print $2, $7 - prev} {prev = $7}' REACTOME_EXTENSION_OF_TELOMERES.xls

哪个输出

WRAP53 0.0849529
NHP2 0.0911097
POLA1 0.077145
POLD3 0.0705168
PRIM1 0.0576833
RFC5 0.0616153
POLD1 0.0546261

答案2

$ awk 'BEGIN { OFS=FS } $8 == "No" { next } { tmp = $7 } NR > 2 { $7 -= prev } { prev = tmp; print }' inputfile
NAME    PROBE   GENE SYMBOL     GENE_TITLE      RANK IN GENE LIST       RANK METRIC SCORE       RUNNING ES      CORE ENRICHMENT
row_0   WRAP53  null    null    163     1.5818238258361816      0.08495288      Yes
row_1   NHP2    null    null    201     1.5055444240570068      0.0911097       Yes
row_2   POLA1   null    null    283     1.3435969352722168      0.077145        Yes
row_3   POLD3   null    null    367     1.240567684173584       0.0705168       Yes
row_4   PRIM1   null    null    501     1.1049883365631104      0.0576833       Yes
row_5   RFC5    null    null    557     1.0596935749053955      0.0616153       Yes
row_6   POLD1   null    null    653     1.0035457611083984      0.0546261       Yes

该awk程序带有注释：

# Set output delimiter to input delimiter (tab, set with -F)
BEGIN { OFS = FS }

# Skip lines whose 8th column is "No"
$8 == "No" { next }  # or { exit } if "No"-lines are sorted at the end.

# Save the original value in column 7.
{ tmp = $7 }

# For any row past both the header and the first data line,
# decrease column 7 by the previous row's column 7 value.
NR > 2 { $7 -= prev }

# Remember the current row's original column 7 value
# in prev and print the (possibly) modified row.
{
    prev = tmp
    print
}

将输出重定向到新文件名来存储它：

awk '...as above...' inputfile >outputfile

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