Btukfyl

The below awk will produce the tab-delimeted file1 with the difference between $3-$2 calulated for each line and printed in $6. Before the awk is executed only 5 fields exist.

What I am having trouble with updated each $2 value in file2 with the $7 value of file1 if the $1 value of file2 matches the $5 of file1 and $6 in file1 is not intron. If the value of $5 is intron then then the value of $7 in file1 is zero. So for example line 1 in file1 is intron so that is equvilant to zero or skipped (those lines are not needed in the calculation).

It is possible that a $1 value in file2 may not exist in file1 and in this case the value of $2 in file2 is zero. Line3 infile2 is an example and is set to zero because it does not exist in file1. Thank you:).

Awk w/ output

awk '

  FNR==NR{                 # process same line

     b[$4]=$3-$2;

     next  # process next line

}

{

 a[$5]+=($3-$2)

}

{

  split($1, b, " "); print b[0], a[b[0]]

}' OFS="t" file1 file2

Output

-2135

-2135

-2222

-2351

-2351

-2414

File1 tab-delimited

chr5    86667863    86667879    RASA1   intron  16

chr5    86669977    86669995    RASA1   splicing    18

chr5    86670703    86670805    RASA1   exon    102

chr5    86679453    86679547    RASA1   intron  94

chr5    86679571    86679673    RASA1   exon    102

chr19   15088950    15088961    NOTCH2  intron  50

chr19   15288950    15288961    NOTCH3  intron  11

chr19   15308240    15308275    NOTCH3  exon    35

File2 space delimited

RASA1 2135

NOTCH2 0

GIMAP8 87

NOTCH3 129

FOXF2 0

PRB3 63

Desired out after file2 is updated

RASA1 222  `(102+102+18)`

NOTCH2 0

GIMAP8 0

NOTCH3 35  `(35)`

FOXF2 0

PRB3 0

Maybe adding a | after the first awk with:

awk 'FNR==NR { a[$1]=$7; next } { if(a[$5]){$1=a[$5] }; print }'

To update file2

Could you please try following. It will provide you sequence of output in same order of Input_file's order.

awk '

FNR==NR{

  if(!b[$1]++){

     c[++count]=$1

  }

  a[$1]

  next

}

($4 in a) && $5!="intron"{

  a[$4]+=$NF

}

END{

  for(i=1;i<=count;i++){

    print c[i],a[c[i]]?a[c[i]]:0

  }

}'  Input_file2   Input_file1 

Since your Input_file1 is NOT TAB delimited as per your claim, so in case it is then edit Input_file2 Input_file1 -----> Input_file2 FS="t" Input_file1. To get output as TAB delimited either append above code's output to | column -t command or set OFS="t" near to FS="t" too.

Output will be as follows.

RASA1 222

NOTCH2 0

GIMAP8 0

NOTCH3 35

FOXF2 0

PRB3 0

if I understood it correctly, this should do what you expect

$ awk 'FNR==NR && $5!="intron" {a[$4]+=$3-$2; next}

       {$2=($1 in a)?a[$1]:0}1' file1 file2 > file2.updated