mjhjmtu

I want to merge two files based on the common data present in them as header.

Following is the example

File1

>Feature scaffold1
1 100 g
101 200 g
201 300 g
>Feature scaffold2
1 100 g
01 500 g
>Feature scaffold3
10 500 g
>Feature scaffold4
10 300 g

File 2

>Feature scaffold1
500 500 r
900 1000 r
>Feature scaffold2
200 300 r
>Feature scaffold3
100 200 r
>Feature scaffold4
500 600 r
>Feature scaffold5
1 1000 r

And here's the kind of output I want:

>Feature scaffold1
1 100 g
101 200 g
201 300 g
500 500 r
900 1000 r
>Feature scaffold2
1 100 g
01 500 g
200 300 r
>Feature scaffold3
10 500 g
100 200 r
>Feature scaffold4
10 300 g
500 600 r
>Feature scaffold5
1 1000 r

I have tried some awk and sed but clearly have not been successful, how can I do this?

Awk solution:

awk '/^>/ k=$1 FS $2 
 NR==FNR 
 if (!/^>/) a[k]=(a[k]!="")? a[k] ORS $0: $0; next
 
 k in a 
 print $0 ORS a[k]; delete a[k]; next 
 1' file1 file2

• 
  /^>/ k=$1 FS $2 - on encountering header line(i.e. >Feature ...) - compose a key k from the 1st $1 and 2nd $2 fields


• 
  NR==FNR ... - processing the 1st input file (file1):
  
  
  • 
    if (!/^>/) a[k]=(a[k]!="")? a[k] ORS $0: $0 - accumulate non-header lines into array a using current key k
    
  
  
  • 
    next - jump to next record
  
  


• 
  k in a - if current key based on file2 record is in array a(based on file1 records):
  
  
  • 
    print $0 ORS a[k] - print related records
  
  
  • 
    delete a[k] - delete processed item(s)
  
  

The output:

>Feature scaffold1
1 100 g
101 200 g
201 300 g
500 500 r
900 1000 r
>Feature scaffold2
1 100 g
01 500 g
200 300 r
>Feature scaffold3
10 500 g
100 200 r
>Feature scaffold4
10 300 g
500 600 r
>Feature scaffold5
1 1000 r

Another approach and to make it simpler.

grep -v '^scaffold' <(awk -v RS='>Feature ' 
 'NFs[$1]=s[$1]$0 ENDfor (x in s)print RS""s[x]' file[12])