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Using awk to parse multiple conditions

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# 8  
Old 03-16-2015
Quote:
Originally Posted by cmccabe
Here is what I am trying to do and my attempt. Thanks you Smilie.

If ">" in field then use first code, but if "del" in the field then use second code.
Example:
NC_000013.10:g.20763642C>T - uses code 1
NC_000013.10:g.20763686delC - uses code 2

1. split($2,a,"[_.del]") - split on the _ . del
no, this will split $2 by EITHER '_', or '.' or 'd' or 'e' or 'l' (single characters)
Quote:
Originally Posted by cmccabe
2. length(a[4]-1) - capture all field 3 digits
Field 3? feels like you're doing a[4]? Where's "field 3" come into play?
if field 4 of an array 'a' has a value of 15, what do you think the following should return? length(a[4]-1) [icode]
Quote:
Originally Posted by cmccabe
3. a[-] - typo -[5] - put a "-" in field
Hmm.... I don't understand what's being said here....
Thank you
Quote:
Originally Posted by cmccabe
Code:
 echo '>' | awk 'NR==2 {split($2,a,"[_.>]");b=substr(a[4],1,length(a[4]-1));print a[2]+0,b,b,substr(a[4],length(a[4])),a[5]}' OFS="\t" ${id}_position.txt > ${id}_parse.txt   # SNP

echo 'del' | awk 'NR==2 {split($2,a,"[_.>]");b=substr(a[4],1,length(a[4]-1));print a[2]+0,b,b,substr(a[4],length(a[4])),-[5]}' OFS="\t" ${id}_position.txt >${id}_parse.txt   # Deletion

Thank you Smilie.
# 9  
Old 03-17-2015
Would the below work?

Code:
 
echo '>' | awk 'NR==2 {split($2,a,"[_.>]");b=substr(a[4],1,length(a[4]-1));print a[2]+0,b,b,substr(a[4],length(a[4])),a[5]}' OFS="\t" ${id}_position.txt > ${id}_parse.txt   # SNP

echo 'del' | awk 'NR==2 {split($2,a,"[_.'del']");b=substr(a[4],1,length(a[4]-1));print a[2]+0,b,b,substr(a[4],length(a[4])),-[5]}' OFS="\t" ${id}_position.txt >${id}_parse.txt   # Deletion

1. split on the > or del

2. return all digits after g. (regardless of length) so if it was 15 or 1025 all the #'s are returned

3. depending what is split on (the > or del), defines the parser to use.
So, if there is a ">" in the split then the first code is used
if there is "del" in the split then the second code is used. Thank you Smilie.

---------- Post updated 03-17-15 at 09:00 AM ---------- Previous update was 03-16-15 at 04:08 PM ----------

Does this make sense or is there a better way to do this? Thank you Smilie.
# 10  
Old 03-18-2015
I'd like to ask moderators to close this thread.
Thank you.
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