I am trying to use awk to update the below tab-delimitedfile based on 5 different rules/conditions. The final output is also tab-delimited and each line in the file will meet one of the conditions. My attemp is below as well though I am not very confident in it. Thank you .
Condition 1: The field Classification has a default value of "VUS" for all lines in file
Condition 2: The CLINSIG field updates Classification with the value in it if it hasa lenghth < 12, else it isConflicting is the result
- since it is possible for this field to have multiple strings in it I used the greatest single value "Likely Benign" and if the value in the field exceeds 12 characters
then "Conflicting" is the result, the multiple values are also separated by | symbol
Condition 3: If the Func.IDP.refGene = UTR then the value of Classification is Likely Benign,
unleess CLINSIG had a value already
Condition 4: If the PopFreqMax> .01 then If the Classification is Likely Benign else it is VUS,
unleess CLINSIG had a value already
Condition 5: If Func.IDP.refGene = spicing AND GeneDetail.IDP.refGene has +/- > 10
then the value of Classification is Likely Benign, unleess CLINSIG had a value already
Thank you .
file
Code:
R_Index Chr Start End Ref Alt Func.IDP.refGene GeneDetail.IDP.refGene AAChange.IDP.refGene PopFreqMax CLINSIG CLNDBN Classification Quality
1 chr1 40562993 40562993 T C UTR5 NM_000310.3:c.-83A>G . 0.9 . . . 15
2 chr5 125887685 125887685 C T splicing NM_001201377.1:exon14:c.1233+28G>A . 0.82 . . . 10
3 chr16 2105400 2105400 C T splicing NM_000548.4:exon6:c.482-3C>T . 0.21 not provided|not provided|not provided|not provided|other|Benign TSC . 25
4 chr16 2110805 2110805 G A exonic . TSC2:NM_000548.4:exon11:c.1110G>A:p.Q370Q .004 Pathogenic TSC . 40
Descri[tion of fields
Code:
awk 'NR==1{for(i=1;i<=NF;i++){print "Number of field in terms of NF is--> NF-" NF-i", value is-->" $i}}' file
Number of field in terms of NF is--> NF-13, value is-->R_Index
Number of field in terms of NF is--> NF-12, value is-->Chr
Number of field in terms of NF is--> NF-11, value is-->Start
Number of field in terms of NF is--> NF-10, value is-->End
Number of field in terms of NF is--> NF-9, value is-->Ref
Number of field in terms of NF is--> NF-8, value is-->Alt
Number of field in terms of NF is--> NF-7, value is-->Func.IDP.refGene
Number of field in terms of NF is--> NF-6, value is-->GeneDetail.IDP.refGene
Number of field in terms of NF is--> NF-5, value is-->AAChange.IDP.refGene
Number of field in terms of NF is--> NF-4, value is-->PopFreqMax
Number of field in terms of NF is--> NF-3, value is-->CLINSIG
Number of field in terms of NF is--> NF-2, value is-->CLNDBN
Number of field in terms of NF is--> NF-1, value is-->Classification
Number of field in terms of NF is--> NF-0, value is-->Quality
i have a file in unix in which the records are like this
aaa 123 233
aaa 234 222
aaa 242 222
bbb 122 111
bbb 122 123
ccc 124 222
In the output i want only the below records
aaa
ccc
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