Geroge Geroge - 7 months ago 34
Python Question

Parsing data in awk

I have a genetics data like this:

MUT1 G_->_A_(het) 44%_(96)___[45%_(49)_/_43%_(47)] rs1799967_(Gene_file;_1000Genomes;_ClinVarVCF;_dbSNP,MutDB) c.4956G>A 1
MUT1 A_->_G_(homo) 99%_(297)___[99%_(151)_/_99%_(146)] rs206075_(Gene_file;_1000Genomes;_ClinVarVCF;_dbSNP) c.4563A>G 1
MUT1 G_->_C_(homo) 100%_(259)___[100%_(132)_/_100%_(127)] COSM4147689_(COSMIC),_COSM4147690_(COSMIC),_rs206076_(Gene_file;_1000Genomes;_ClinVar;_ClinVarVCF;_dbSNP) c.6513G>C 2
MUT1 A_->_C_(het) 41%_(103)___[42%_(53)_/_40%_(50)] COSM3753646_(COSMIC),_COSM147663_(COSMIC),_rs144848_(Gene_file;_1000Genomes;_ClinVarVCF;_dbSNP,MutDB) c.1114A>C 5

What I need to parse this data and extract only some kind of fields.

Require output is:

MUT1 het 44% rs1799967 c.4956G>A 1
MUT1 homo 99% rs206075c.4563A>G 1
MUT1 homo 100% rs206076 c.6513G>C 2
MUT1 het 41% rs144848 c.1114A>C 5

So output shoould be - all first column, from second column only het or hom, third column is only %, fifth column should be extracted only rs_number - this have always different position and last column.

note: I know, that info about homo/het is always in last filed of second column. And % is always on first field in third column.

My solution is:

awk -v OFS="\t" '{print $1,$5,$6,$9,$10,$11}' zkouska.csv | awk -v OFS="\t" 'NR>1{split($2,arr2,"_"); split($3,arr3,"_"); print $1,arr2[4],arr3[1],$4,$5,$6}'

But output is :

BRCA1 (het) 44% rs1799967_(Gene_file;_1000Genomes;_ClinVarVCF;_dbSNP,MutDB) c.4956G>A 1
BRCA1 (homo) 99% rs206075_(Gene_file;_1000Genomes;_ClinVarVCF;_dbSNP) c.4563A>G 1
BRCA1 (homo) 100% COSM4147689_(COSMIC),_COSM4147690_(COSMIC),_rs206076_(Gene_file;_1000Genomes;_ClinVar;_ClinVarVCF;_dbSNP) c.6513G>C 2
BRCA1 (het) 41% COSM3753646_(COSMIC),_COSM147663_(COSMIC),_rs144848_(Gene_file;_1000Genomes;_ClinVarVCF;_dbSNP,MutDB) c.1114A>C 5
BRCA1 (homo) 100% COSM148277_(COSMIC),_COSM3755561_(COSMIC),_rs16942_(Gene_file;_1000Genomes;_ClinVarVCF;_dbSNP) c.3548A>G 5

Still have problem to extract rs from fifth column. Erase quotes in second field. Inpout and output should be TAB separate. Solution could no be only in awk.


Using a combination of gsub and match might be the way to go, here is a portable example:


  gsub(/^[^(]+\(|\)/, "", $2)
  gsub(/_.*/, "", $3)
  match($4, /rs[0-9]+/)
  print $1, $2, $3, substr($4, RSTART, RLENGTH), $5, $6

Run it like this:

awk -f parse.awk OFS='\t' < infile


MUT1    het     44%     rs1799967   c.4956G>A   1
MUT1    homo    99%     rs206075    c.4563A>G   1
MUT1    homo    100%    rs206076    c.6513G>C   2
MUT1    het     41%     rs144848    c.1114A>C   5