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Parse file for fields and specific text

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# 15  
Old 09-18-2015
In this case, X is not a variable with a contents (which is zero as it's undefined), but a placeholder for the unknown number of spaces matched by the * regex.
Try
Code:
T2=substr ($0, RSTART+12, RLENGTH-13)

# 16  
Old 09-18-2015
That worked. Thank you Smilie.

This is the code:

Code:
awk '
        {match ($0, /gene_name [^ ]*/)
         T1=substr ($0, RSTART+11, RLENGTH-13)
         match ($0, /exon_number [^ ]*/)
         T2=substr ($0, RSTART+12, RLENGTH-13)
         print $1, $2, $3, T1":""exon""."T2
        }
' FS="\t" OFS="\t" /home/cmccabe/Desktop/NGS/bed/gencode.exons.bed > /home/cmccabe/Desktop/NGS/bed/parse_gencode.bed

I thought I understood but I think I am a bit off in my thinking, do you mind briefly explaining. Thank you very much.
# 17  
Old 09-18-2015
match finds the pattern consisting of a constant and a regex. substr extracts the substring starting from RSTART plus the length of the constant in the pattern, of length RLENGTH plus the constant plus eventual additional closing characters ( "; or ; ). Then fields 1 to 3 are printed, followed by the two substrings obtained as above.

---------- Post updated at 20:33 ---------- Previous update was at 20:31 ----------

Use ":exon." instead of ":""exon"".".
This User Gave Thanks to RudiC For This Post:
cmccabe
# 18  
Old 09-18-2015
Thank you very much for your help and explanation, I appreciate it Smilie.
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