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Remove line based on condition in awk

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# 8  
Old 08-26-2016
Note that some alphabetic characters are interpreted as parts of numeric values when awk converts a string to a number. The standards require that exponential notation be recognized (e.g., 1.05E-3) and allows but does not require awk to recognize hexadecimal constants of the forms 0xhexdigits and 0Xhexdigits. And, the standards allow, but do not currently require that the strings inf and infinity (case-insensitive on both) be treated as an infinity and that the string NaN (also case-insensitive) be treated as not-a-number.
This User Gave Thanks to Don Cragun For This Post:
cmccabe
# 9  
Old 08-26-2016
@RavinderSingh13 here is the result of the awk. Thank you all for your help Smilie.

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

output
Code:
Index    Mutation Call    Start    End    Ref    Alt    Func.refGene    Gene.refGene    ExonicFunc.refGene    Sanger
3    c.276-31delG    43396570    43396570    C    -    intronic    SLC2A1        
4    c.[13-22T>C]+[13-22T>C]    160090674    160090674    T    C    intronic    ATP1A2        
5    c.13-11_13-8delTCCT    160090685    160090688    TCCT    -    intronic    ATP1A2        
12    c.[268-28A>G]+[268-28A>G]    166153499    166153499    A    G    intronic    SCN2A        
13    c.[1035-3T>C]+[1035-3T>C]    166170127    166170127    T    C    intronic    SCN2A        
15    c.[1672-16C>T]+[1672-16C>T]    166179650    166179650    C    T    intronic    SCN2A        
16    c.[2994C>T]+[=]    166210776    166210776    C    T    exonic    SCN2A    synonymous SNV    
17    c.[3400-71C>T]+[3400-71C>T]    166221582    166221582    C    T    intronic    SCN2A        
18    c.4552-40delT    166243216    166243216    T    -    intronic    SCN2A        
19    c.[4914T>A]+[4914T>A]    166245230    166245230    T    A    exonic    SCN2A    synonymous SNV    
20    c.[5109C>T]+[=]    166245425    166245425    C    T    exonic    SCN2A    synonymous SNV    
21    c.[5139C>T]+[=]    166848646    166848646    G    A    exonic    SCN1A    synonymous SNV    
22    c.3152_3153insAACCACT    166892841    166892841    -    AGTGGTT    exonic    SCN1A    frameshift insertion    TP
23    c.2044-5delT    166898947    166898947    A    -    intronic    SCN1A        
24    c.[1663-47T>G]+[1663-47T>G]    166900606    166900606    A    C    intronic    SCN1A        
25    c.1530_1531insA    166901684    166901684    -    T    exonic    SCN1A    frameshift insertion    FP
26    c.[-44C>T]+[=]    66094008    66094008    C    T    UTR5    KCTD7
27    c.[*68A>G]+[=]    125880589    125880589    T    C    UTR3    ALDH7A1

@Chubler_XL

The awk is missing the last line (Index 27) presumably because of the *. Would adding \*\ capture that condition? Thank you Smilie.

Adding to the range was what I needed to do sub(/^[^*+-]+[*+-]/,"",v)
Last edited by cmccabe; 08-26-2016 at 10:53 AM.. Reason: added details, updated awk
# 10  
Old 08-26-2016
Try also
Code:
awk '$7 ~/intronic|UTR(3|5)/{match ($2, /[+-][0-9]*/); if (10 < 0+substr($2, RSTART+1, RLENGTH-1)) next}1' file

These 2 Users Gave Thanks to RudiC For This Post:
Chubler_XL cmccabe
# 11  
Old 08-26-2016
works great @RudiC... thank you Smilie.
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