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Using awk to parse multiple conditions

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# 1  
Old 03-14-2015
Using awk to parse multiple conditions
There are 4 ways the user can input data and unfortunately the parse rules for each are slightly different. The first condition works great and the input file is attached for the second condition. Conditions 3 and 4 will follow I'm sure I will have trouble with them and need help as well. The code below parses condition 1 perfectly:

I apologize for the long post but just wanted to provide all the details. Thank you Smilie.

Code:
 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

Code:
 
1. c.79G>A
parse rules:
1 four zeros after the NC_  (not always the case) and the digits before the .
2 g. ###   g.###
3 letter before the >
4 letter after the >
Desired Output:  13     20763642     20763642     C     T

2. c.35delG
1 four zeros after the NC_  (not always the case) and the digits before the .
2 g. ###   g.###
3 letter before the del
4 "-" after the del
Desired Output:  13     20763686     20763686     C     -

3. c.575_576delCA 
4. .34_35delGGinsT

# 2  
Old 03-14-2015
Where does the C T or C - come from?
# 3  
Old 03-14-2015
The C T and comes from the ${id}_position.txt which is parsed by the awk in the post.

The C - also comes from the ${id}_position.txt which is parsed, however the del in the field being parsed: NC_000013.10:g.20763686delC is how the C then - (leterr after the del goes first, and a "-" is used in the second position). The attached file has this in it as well. Thank you Smilie.
# 4  
Old 03-16-2015
I don't know if something like the below would work. Also, how does awk know which parser to use?

Code:
 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])),a[5]}' OFS="\t" ${id}_position.txt > ${id}_parse.txt

There are two conditions the first has a > and the second has a del in in it:

Code:
 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

will parse the >, but not the del. So do I need some identifier for the correct parser to be used? Thank you Smilie.

Maybe:

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

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])),a[5]}' OFS="\t" ${id}_position.txt > ${id}_parse.txt

Last edited by cmccabe; 03-16-2015 at 03:25 PM..
# 5  
Old 03-16-2015
I tried the below code on the file attached.

Code:
 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])),a[-]}' OFS="\t" del_position.txt >del_parse.txt

awk: cmd. line:1: 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])),a[-]}
awk: cmd. line:1:                                                                                                            ^ syntax error
awk: cmd. line:1: error: invalid subscript expression

Desired Output:
13 20763686 20763686 C -


Thank you Smilie.
del_position.txt (204 Bytes) 
# 6  
Old 03-16-2015
couple of questions:
  1. what do you think this will do? split($2,a,"[_.del]")
  2. what do you think this will do? length(a[4]-1)
  3. what's the meaning of this? a[-]
Last edited by vgersh99; 03-16-2015 at 05:08 PM..
# 7  
Old 03-16-2015
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
2. length(a[4]-1) - capture all field 3 digits
3. a[-] - typo -[5] - put a "-" in field

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.
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