Remove line based on condition in awk


 
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# 1  
Old 08-25-2016
Remove line based on condition in awk

In the following tab-delimited input, I am checking $7 for the keyword intronic. If that keyword is found then $2 is split by the .[ in each line and if the string after the digits or the +/- is >10, then that line is deleted. This will always be the case for intronic. If $7 is exonic then nothing is done and the next line is processed.

For example, using the first line in input:
$7=intronic, so $2 or c.[433+79A>G]+[433+79A>G] is split using the .[ in bold, and the string after the digits after the + is >10, so that line is removed.

awk
Code:
awk -F'\t' -v OFS='\t' FNR==NR 'if ($7 ==/intronic/) ; {split($2,f2,"[[digits]");a[f2[1]];next} $2 in a' or ; {split($2,f3,"[[digits]");a[f3[1]];next} $2 in a' input

input
Code:
Index    Mutation Call    Start    End    Ref    Alt    Func.refGene    Gene.refGene    ExonicFunc.refGene    Sanger
1    c.[433+79A>G]+[433+79A>G]    40556922    40556922    T    C    intronic    PPT1        
2    c.[362+8C>T]+[=]    40557656    40557656    G    A    intronic    PPT1        
3    c.276-31delG    43396570    43396570    C    -    intronic    SLC2A1    
20    c.[5109C>T]+[=]    166245425    166245425    C    T    exonic    SCN2A    synonymous SNV    
21    c.[5139C>T]+[=]    166848646    166848646    G    A    exonic    SCN1A    synonymous SNV

desired output
Code:
Index    Mutation Call    Start    End    Ref    Alt    Func.refGene    Gene.refGene    ExonicFunc.refGene    Sanger
2    c.[362+8C>T]+[=]    40557656    40557656    G    A    intronic    PPT1         
20    c.[5109C>T]+[=]    166245425    166245425    C    T    exonic    SCN2A    synonymous SNV    
21    c.[5139C>T]+[=]    166848646    166848646    G    A    exonic    SCN1A    synonymous SNV


Last edited by cmccabe; 08-25-2016 at 04:39 PM.. Reason: fixed format
# 2  
Old 08-25-2016
Try this:

Code:
awk -F'\t' '
$7=="intronic" {
   v=$2
   sub(/.*\.\[[^+-]+[+-]/,"",v)
   if(v + 0 > 10) next
}
1' input

output:
Code:
Index   Mutation        Call    Start   End     Ref     Alt     Func.refGene    Gene.refGene    ExonicFunc.refGene      Sanger
2       c.[362+8C>T]+[=]        40557656        40557656        G       A       intronic        PPT1
3       c.276-31delG    43396570        43396570        C       -       intronic        SLC2A1
20      c.[5109C>T]+[=] 166245425       166245425       C       T       exonic  SCN2A   synonymous      SNV
21      c.[5139C>T]+[=] 166848646       166848646       G       A       exonic  SCN1A   synonymous      SNV

Edit: Line 3 is not deleted as it didn't contain .[ - your sampe output still has it deleted. is the .[ not important?

Last edited by Chubler_XL; 08-25-2016 at 05:05 PM..
This User Gave Thanks to Chubler_XL For This Post:
# 3  
Old 08-25-2016
So what is to be done with those lines that have neither intronic or exonic in them?
This User Gave Thanks to shamrock For This Post:
# 4  
Old 08-25-2016
It doesn't look like the .[ is important as long as all the +/- get removed if they meet the condition, but $7 could be intronic or UTR5 or UTR3, is this possible to include in one awk?
@Shamrock the exonic will be used in another awk, but I'm not quite sure of the details yet. Thank you Smilie.

Maybe
Code:
awk -F'\t' '
$7=="intronic || UTR3 || UTR5" {
   v=$2
   sub(/.*[^+-]+[+-]/,"",v)
   if(v + 0 > 10) next
}
1' input


Last edited by cmccabe; 08-25-2016 at 06:03 PM.. Reason: added details and awk
# 5  
Old 08-25-2016
Try:

Code:
awk -F'\t' '
$7 ~ "^(intronic|UTR3|UTR5)$" {
   v=$2
   sub(/^[^+-]+[+-]/,"",v)
   if(v + 0 > 10) next
}
1' input

This User Gave Thanks to Chubler_XL For This Post:
# 6  
Old 08-26-2016
Quote:
Originally Posted by Chubler_XL
Try:

Code:
awk -F'\t' '
$7 ~ "^(intronic|UTR3|UTR5)$" {
   v=$2
   sub(/^[^+-]+[+-]/,"",v)
   if(v + 0 > 10) next
}
1' input

Thank you Chubler_XL for nice code. Could you please help me here in one of my confusion. So when I print the value of variable na,ed v(which has 2nd field's value in it) as follows.
Code:
awk '                                                                                                                  
$7 ~ "^(intronic|UTR3|UTR5)$" {
   v=$2
   sub(/^[^+-]+[+-]/,"",v)
   print v;if(v + 0 > 10) next
}
1' Input_file

Output will be as follows then.
Code:
Index    Mutation Call    Start    End    Ref    Alt    Func.refGene    Gene.refGene    ExonicFunc.refGene    Sanger
79A>G]+[433+79A>G]   #### Value of variable v
8C>T]+[=]                     #### Value of variable v
2    c.[362+8C>T]+[=]    40557656    40557656    G    A    intronic    PPT1        
8C>T]+[=]
2    c.[362+8C>T]+[=]    40557656    40557656    G    A    UTR3    PPT1
31delG
20    c.[5109C>T]+[=]    166245425    166245425    C    T    exonic    SCN2A    synonymous SNV    
21    c.[5139C>T]+[=]    166848646    166848646    G    A    exonic    SCN1A    synonymous SNV

So in above as we could see value of variable v is 79A>G]+[433+79A>G], so I understood like by doing v+0 e are telling awk here to consider it as digit and then comparing it with 10 but doubt here is, it has alphabets as well as digits into it after 79A, so awk will still consider 79 only for comparison here? Could you please guide me here, will be grateful to you sir.


Hello cmccabe,

Could you please try following and let me know if this helps you too. Though my solution is based on I am trying to take exact digits between -/+ to </>here then later by adding 0 to it comparing it.
Code:
awk -F'\t' '($7 ~ /intronic||UTR3||UTR5/){v=$2;a=sub(/^[^+-]+\+/,X,v);if(a){sub(/([><]).*/,X,v)};if((v+0)>10){next}} 1'  Input_file

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
# 7  
Old 08-26-2016
Quote:
Originally Posted by RavinderSingh13
So in above as we could see value of variable v is 79A>G]+[433+79A>G], so I understood like by doing v+0 e are telling awk here to consider it as digit and then comparing it with 10 but doubt here is, it has alphabets as well as digits into it after 79A, so awk will still consider 79 only for comparison here? Could you please guide me here, will be grateful to you sir.
Yes, that is how awk works when converting strings value to numeric. It will continue until it comes to a character that makes the string non-numeric and just ignores the rest of the string. Try this code for some examples
Code:
awk '
function try(A) {
  print A "\t" A + 0
}
BEGIN {
  try("27.2A")
  try("3..1415")
  try(".23A27")
  try("009001A")
} '

These 2 Users Gave Thanks to Chubler_XL For This Post:
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