Question

我有一个包含以下字段的文件（以及右边的示例值）：

hg18.ensGene.bin 0
hg18.ensGene.name ENST00000371026
hg18.ensGene.chrom chr1
hg18.ensGene.strand -
hg18.ensGene.txStart 67051161
hg18.ensGene.txEnd 67163158
hg18.ensGene.exonStarts 67051161,67060631,67065090,67066082,67071855,67072261,67073896,67075980,67078739,67085754,67100417,67109640,67113051,67129424,67131499,67143471,67162932,
hg18.ensGene.exonEnds 67052451,67060788,67065317,67066181,67071977,67072419,67074048,67076067,67078942,67085949,67100573,67109780,67113208,67129537,67131684,67143646,67163158,
hg18.ensGene.name2 ENSG00000152763
hg18.ensGene.exonFrames 0,2,0,0,1,2,0,0,1,1,1,2,1,2,0,2,0,

这是文件的缩短版本：

0 ENST00000371026 chr1 - 67051161 67163158 67051161,67060631,67065090,67066082,67071855,67072261,67073896,67075980,67078739,67085754,67100417,67109640,67113051,67129424,67131499,67143471,67162932, 67052451,67060788,67065317,67066181,67071977,67072419,67074048,67076067,67078942,67085949,67100573,67109780,67113208,67129537,67131684,67143646,67163158, ENSG00000152763 0,2,0,0,1,2,0,0,1,1,1,2,1,2,0,2,0, uc009waw.1,uc009wax.1,uc001dcx.1,
0 ENST00000371023 chr1 - 67075869 67163055 67075869,67078739,67085754,67100417,67109640,67113051,67129424,67131499,67143471,67162932, 67076067,67078942,67085949,67100573,67109780,67113208,67129537,67131684,67143646,67163055, ENSG00000152763 0,1,1,1,2,1,2,0,2,0, uc001dcy.1
0 ENST00000395250 chr1 - 67075991 67163158 67075991,67076022,67078739,67085754,67100417,67109640,67113051,67129424,67131499,67143471,67162932, 67076018,67076067,67078942,67085949,67100573,67109780,67113208,67129537,67131684,67143646,67163158, ENSG00000152763 0,0,1,1,1,2,0,-1,-1,-1,-1, n/a

我需要总结外显子开始和结束的差异，例如：

hg18.ensGene.exonStarts    67051161,67060631,67065090,67066082,67071855,67072261,67073896,67075980,67078739,67085754,67100417,67109640,67113051,67129424,67131499,67143471,67162932,
hg18.ensGene.exonEnds    67052451,67060788,67065317,67066181,67071977,67072419,67074048,67076067,67078942,67085949,67100573,67109780,67113208,67129537,67131684,67143646,67163158,

差：

1290,157,227,99,122,158,152,87,203,195,156,140,157,113,185,175,226

总和（hg18.ensGene.exonLenSum）：

我希望输出包含以下字段：

hg18.ensGene.name
hg18.ensGene.name2
hg18.ensGene.exonLenSum

如：

ENST00000371026 ENST00000371023 3842

我想用输入文件中所有行的一个awk脚本来完成此操作。我怎样才能做到这一点？这对于计算外显子长度非常有用，例如RPMK（每百万映射读数读取每千克碱基外显子模型）计算。

Answer 1

so ross$ awk -f gene.awk gene.dat
ENST00000371026 ENSG00000152763 3842
ENST00000371023 ENSG00000152763 1645
ENST00000395250 ENSG00000152763 1622
so ross$ cat gene.awk
/./ {
  name = $2
  name2 = $9
  s = $7
  e = $8
  sc = split(s, sa, ",")
  ec = split(e, ea, ",")
  if (sc != ec) {
    print "starts != ends ", name, name2, sc, ec
  }
  diffsum = 0
  for(i = 1; i <= sc; ++i) {
    diffsum += ea[i] - sa[i]
  }
  print name, name2, diffsum
}

Answer 2

使用UCSC mysql匿名服务器：

mysql -N -h  genome-mysql.cse.ucsc.edu -A -u genome -D hg18 -e 'select name,name2,exonStarts,exonEnds from ensGene' |\
awk -F '    ' '{n=split($3,a1,"[,]"); split($4,a2,"[,]"); size=0; for(i=1;i<=n;++i) {size+=int(a2[i]-a1[i]);} printf("%s\t%s\t%d\n",$1,$2,size); }'

结果：

ENST00000404059 ENSG00000219789 632
ENST00000326632 ENSG00000146556 1583
ENST00000408384 ENSG00000221311 138
ENST00000409575 ENSG00000222003 1187
ENST00000409981 ENSG00000222027 1187
ENST00000359752 ENSG00000197490 126
ENST00000379479 ENSG00000205292 873
ENST00000326183 ENSG00000177693 918
ENST00000407826 ENSG00000219467 2820
ENST00000405199 ENSG00000220902 1231
(...)

使用awk从两个列值创建两个数组，查找差异和总和差异以及输出数据

2 个答案: