awk to supress error message with custom text


 
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# 1  
Old 03-09-2017
awk to supress error message with custom text

After a bash function is run the below file is produced:

out_name.txt tab-delimeted
Code:
Input    Errors and warnings    AccNo    Genesymbol    Variant    Reference Sequence Start Descr.    Coding DNA Descr.    Protein Descr.    GeneSymbol Coding DNA Descr.    GeneSymbol Protein Descr.    Genomic Reference    Coding Reference    Protein Reference    Affected Transcripts    Affected Proteins    Restriction Sites Created    Restriction Sites Deleted
NM_003924.3:c.242-1G>A    (variantchecker): Intronic position given for a non-genomic reference sequence.    
NM_003924.3:c.*18_*19delGCinsAA        NM_003924.3    PHOX2B_v001    c.*18_*19delGCinsAA    n.1323_1324delinsAA    c.*18_*19delinsAA    p.(=)    PHOX2B_v001:c.*18_*19delinsAA    PHOX2B_v001:p.(=)        NM_003924.3    NP_003915.2    NM_003924.3(PHOX2B_v001):c.*18_*19delinsAA    NM_003924.3(PHOX2B_i001):p.(=)    HpyAV        
NM_003924.3:c.013G>T        NM_003924.3    PHOX2B_v001    c.013G>T    n.373G>T    c.13G>T    p.(Glu5*)    PHOX2B_v001:c.13G>T    PHOX2B_v001:p.(Glu5*)        NM_003924.3    NP_003915.2    NM_003924.3(PHOX2B_v001):c.13G>T    NM_003924.3(PHOX2B_i001):p.(Glu5*)

I am trying to add a condition that will suppress the warning message produced if $2 is
(variantchecker): Intronic position given for a non-genomic reference sequence.,
In addition, that the $1 string "is an intronic variant" is displayed instead of the waring. My 2nd attempt to incorporate these changes is below,
which executes but nothing results. Thank you Smilie.

desired result
Code:
NM_003924.3:c.242-1G>A is an intronic variant

awk
Code:
while read LINE; do
    awk -F'\t' '$2 == "variantchecker): Intronic position given for a non-genomic reference sequence." {print $1 && "is an intronic variant"}' 2>/dev/null
done < out_name.txt


Last edited by cmccabe; 03-09-2017 at 01:11 PM.. Reason: fixed format
# 2  
Old 03-09-2017
Code:
print $1 && "is an intronic variant" | "cat 1>&2"

This User Gave Thanks to vgersh99 For This Post:
# 3  
Old 03-09-2017
Hello cmccabe,

String variantchecker): Intronic position given for a non-genomic reference sequence. will NOT be considered as a 2nd field because you have set the field separator as default which will be space and in above string we have many spaces, so condition with $2=="above_string" will NOT be TRUE.
Could you please try following and let me know if this helps.
Code:
awk '/variantchecker): Intronic position given for a non-genomic reference sequence./{print $1 " is an intronic variant."}'   Input_file

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
# 4  
Old 03-13-2017
Thank you both very much Smilie.
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