Question

感谢@Jose Ricardo Bustos M.使用file1和file2帮助导致以下内容：

但是，我似乎无法从BRCA2 file1中抓取BRCA 1, BRCA2来file2（第2行跳过标题）。我不确定这是因为BCRA2是,之后的第二个实例，还是$7是full gene sequence and full deletion/duplication analysis的问题，full gene sequence是部分匹配$7中的整行？谢谢你:)。

文件1

BRCA2
BCR
SCN1A
fbn1

file2的

Tier    explanation .   List code   gene    gene name   methodology disease
Tier 1  .   .   811 DMD dystrophin  deletion analysis and duplication analysis, if performed Publication Date: January 1, 2014  Duchenne/Becker muscular dystrophy
Tier 1  .   Jan-16  81  BRCA 1, BRCA2   breast cancer 1 and 2   full gene sequence and full deletion/duplication analysis   hereditary breast and ovarian cancer
Tier 1  .   Jan-16  70  ABL1    ABL1    gene analysis variants in the kinse domane  acquired imatinib tyrosine kinase inhibitor
Tier 1  .   .   806 BCR/ABL 1   t(9;22) major breakpoint, qualitative or quantitative   chronic myelogenous leukemia CML
Tier 1  .   Jan-16  85  FBN1    Fibrillin   full gene sequencing    heart disease
Tier 1  .   Jan-16  95  FBN1    fibrillin   del/dup heart disease

AWK

awk 'BEGIN{FS=OFS="\t"}  # define fs and output
{$0=toupper($0)}  # convert all `file1` to uppercase
{$5=toupper($5)} # convert '$5' in `file2` to uppercase
{$7=toupper($7)} # convert '$7' in `file2` to uppercase
FNR==NR{ # process each field in line of `file1`
if(NR>1 && ($7 ~ /FULL GENE SEQUENC/)) {  # skip header and check for full gene sequenc or full gene sequencing, using `regexp`
      gsub(" ","",$5)       #removing white space
      n=split($5,v,"/")
      d[v[1]] = $4          #from split, first element as key
  }
  next
}{print $1, ($1 in d?d[$1]:279)}' file2 file1 # print name then default if no match

BRCA2    279
BCR    279
SCN1A    279
FBN1    85

期望的输出

BRCA2    81  --- match in line 2 of $5 in file 2, BRCA 1, BRCA2 and $7 has full gene sequence
BCR    279
SCN1A    279
FBN1    85

Answer 1

问题在于代码中的以下部分，

gsub(" ","",$5)
n=split($5,v,"/")
d[v[1]] = $4

AFAIK，它正好适用于案例BCR/ABL 1，但当您将其用于BRCA 1, BRCA2时，它 NOT 会产生您期望的结果。删除BRCA 1, BRCA2上的空格将为BRCA1,BRCA2，并且/分割将产生相同的字符串BRCA1,BRCA2本身，因为去限制器是错误的。

所以你需要,和hash-it再次需要拆分字符串。像，

n=split($5,v,",")
for (i=1; i <= n; i++) {
  d[v[i]] = $4
}

现在，d与d[BRCA1]和d[BRCA2]进行了哈希处理。将上述内容与现有代码一起使用。

或者）删除代码

gsub(" ","",$5)
n=split($5,v,"/")
d[v[1]] = $4

完全和做，

gsub(" ","",$5)
n=split($5,v,"\\||,") 
for (i=1; i <= n; i++) {
  d[v[i]] = $4
}

表示在$5或|上拆分,并循环其内容并将其散列到数组d。

awk没有为使用多个条件的1个条件打印正确的值

1 个答案: