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Parse file for fields and specific text

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# 8  
Old 09-17-2015
That code works great.
If I was trying to get the output to look like:
Code:
 chr1    11868    12227    DDX11L1:1 
chr1    12009    12057    DDX11L1:1 
chr1    12178    12227    DDX11L1:2

Basically, just gene:exon in field 4

Code:
 
cmccabe@DTV-A5211QLM:~/Desktop/NGS$ awk '
>         {match ($0, /gene_name [^ ]*/)
>          T1=substr ($0, RSTART+11, RLENGTH-13)
>          match ($0, /exon_number [^ ]*/)
>          T2=substr ($0, RSTART+11, RLENGTH-12)
>          print $1, $2, $3, T1:T2
>         }
> ' FS="\t" OFS="\t" /home/cmccabe/Desktop/NGS/bed/gencode.exons.bed > /home/cmccabe/Desktop/NGS/bed/parse2_gencode.bed

awk: line 6: syntax error at or near :
[/CODE] Thank you Smilie
Last edited by cmccabe; 09-17-2015 at 02:01 PM.. Reason: fixed formatting
# 9  
Old 09-17-2015
T1:T2 is not valid awk syntax. Did you mean T1":"T2 ?
This User Gave Thanks to Corona688 For This Post:
cmccabe
# 10  
Old 09-17-2015
Use quotes: T1":"T2
This User Gave Thanks to RudiC For This Post:
cmccabe
# 11  
Old 09-17-2015
Thank you. I modified (very little) the awk to the below:

Code:
cmccabe@DTV-A5211QLM:~/Desktop/bed$ awk '
>         {match ($0, /gene_name [^ ]*/)
>          T1=substr ($0, RSTART+11, RLENGTH-13)
>          match ($0, /exon_number [^ ]*/)
>          T2=substr ($0, RSTART+11, RLENGTH-12)
>          print $1, $2, $3, T1":""exon"T2
>         }
> ' FS="\t" OFS="\t" /home/cmccabe/Desktop/NGS/bed/gencode.exons.bed > /home/cmccabe/Desktop/NGS/bed/parse2_gencode.bed

There appears to be a space between exon and 1 that may cause an issue later on. I'm not sure why the space is there or how to remove it? Thank you.

parse2.txt
Code:
chr1    11868    12227    DDX11L1:exon 1
chr1    11871    12227    DDX11L1:exon 1
chr1    11873    12227    DDX11L1:exon 1

# 12  
Old 09-17-2015
I suspect the space is actually part of T2.

This regex /exon_number [^ ]*/ I think should be /exon_number *[^ ]*/ in case there's multi spaces
# 13  
Old 09-17-2015
You'd need to count the spaces, then, as they would increase the RSTART+X value.
# 14  
Old 09-18-2015
The RSTART+X removed the space but now the output looks like:

Code:
chr1    11868    12227    DDX11L1:exonex
chr1    11871    12227    DDX11L1:exonex
chr1    11873    12227    DDX11L1:exonex

chould be:

Code:
chr1    11868    12227    DDX11L1:exon1
chr1    11871    12227    DDX11L1:exon1
chr1    11873    12227    DDX11L1:exon1

Thank you Smilie.
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