Extracting multiple strings and combining to .csv in bash-CodePudding

I have a long list of ID's I need to parse. I want to extract three pieces of information and write to a 3 column CSV. Column 1 = the field between tr|XXXX|, column 3 = the field after the second | but before OS=.

Column 2 would be conditional. If there is 'GN=XXX' in the line, I'd like it to return XXX. If GN= isn't present, I'd like to write the first section of column 3 (i.e. up to the first space).

Input:

>tr|I1WXP1|I1WXP1_9EURY Methyl coenzyme M reductase subunit A (Fragment) OS=uncultured euryarchaeote OX=114243 GN=mcrA PE=4 SV=1
>tr|A0A059VAR9|A0A059VAR9_9EURY V-type ATP synthase beta chain (Fragment) OS=Halorubrum sp. Ga66 OX=1480727 GN=atpB PE=3 SV=1
>tr|Q51760|Q51760_9EURY Glutaredoxin-like protein OS=Pyrococcus furiosus OX=2261 PE=1 SV=1

Desired output:

I1WXP1,mcrA,I1WXP1_9EURY Methyl coenzyme M reductase subunit A (Fragment)
A0A059VAR9,atpB, A0A059VAR9_9EURY V-type ATP synthase beta chain (Fragment)
Q51760,Q51760_9EURY,Q51760_9EURY Glutaredoxin-like protein

I can get the first two with awk, for e.g.:

awk '{split($0,a,"|"); print a[2]

But I can't work out the conditional, or how to act on the 'GN=' pattern neatly.

So for example, extracting bold text:

tr|**I1WXP1**|**I1WXP1_9EURY Methyl coenzyme M reductase subunit A (Fragment)** OS=uncultured euryarchaeote OX=114243 GN=**mcrA** PE=4 SV=1

Becomes:

I1WXP1, mcrA, I1WXP1_9EURY Methyl coenzyme M reductase subunit A(Fragment)

CodePudding user response：

With your shown samples, please try following awk code. Written and tested with shown samples in GNU awk. It will generate comma separated values and you can output into a new file as per your wish.

awk -F'^>tr\\|| OS=' '
BEGIN{ OFS="," }
NF>=2{
  gsub(/\|/,OFS,$2)
  match($0,/GN=(\S )/,arr1)
  if(!arr1[1]){
    split($2,arr2,"[, ]")
  }
  printf("%s%s\n",$2,arr1[1]?OFS arr1[1]:OFS arr2[2]"")
}
'  Input_file