awk to update file with numerical difference if condition is met
In the file1 below if $9 and $12 are . (dot) then the value in $8 of file1 is used as a key (exact match) to lookup in each $2 of file2, when a match is found then the value of $4
in file1 is used to look for a range match within +/- 50 using the values in $4 and after in file2. The number of fields can be variable but will always start at $4.
For example, ISG15 has 2 fields in it with coordinates starting at $4 and ending at $5. CR2 has 19 coordinates in it starting at $4 ending at $22. The value in $1 of file2
tells you how many coordinates there are but the start or first will always be in $4.
There will only be one range match but if the number is closer to the first value before the - (hyphen) in it the $9 of file1 is updated from a . to the numerical difference between the two numbers with a - (minus) in front. If the number is closer to the second value after the - (hyphen) in it the $9 of file1 is updated from a . (dot) to the numerical difference between the two numbers with a + (plus) in front. However is the calculated difference is greater than 50, then >50 is printed in $9 of file1.
If $9 or $12 of file1 have a value other then . (dot) in them then that line is skipped (nothing happens) and the next line is processed. In file1 lines 2 and 3 are skipped. The awk below will identify these lines and print them, but I am not sure how to do the rest and need some expert help. Thank you .
file1 tab-delimited
Code:
R_Index Chr Start End Ref Alt Func.IDP.refGene Gene.IDP.refGene GeneDetail.IDP.refGene Inheritence ExonicFunc.IDP.refGene AAChange.IDP.refGene
1 chr1 948846 948846 - A upstream ISG15 . . . .
2 chr1 948870 948870 C G UTR5 ISG15 NM_005101.3:c.-84C>G . .
3 chr1 949608 949608 G A exonic ISG15 . . nonsynonymous SNV ISG15:NM_005101.3:exon2:c.248G>A:p.S83N
4 chr1 949925 949925 C T downstream ISG15 . . . .
5 chr1 207646923 207646923 G A intronic CR2 . . . .
6 chr2 3653844 3653844 T C intronic COLEC11 . . . .
7 chr1 154562623 154562625 CCG - intronic ADAR . . . .
8 chr1 948840 948840 - C upstream ISG15 . . . .
R_Index Chr Start End Ref Alt Func.IDP.refGene Gene.IDP.refGene GeneDetail.IDP.refGene Inheritence ExonicFunc.IDP.refGene AAChange.IDP.refGene
1 chr1 948846 948846 - A upstream ISG15 0 . . .
2 chr1 948870 948870 C G UTR5 ISG15 NM_005101.3:c.-84C>G . . .
3 chr1 949608 949608 G A exonic ISG15 . . nonsynonymous SNV ISG15:NM_005101.3:exon2:c.248G>A:p.S83N
4 chr1 949925 949925 C T downstream ISG15 +6 . . .
5 chr1 207646923 207646923 G A intronic CR2 >50 . . .
6 chr2 3653844 3653844 T C intronic COLEC11 >50 . . .
7 chr1 154562623 154562625 CCG - intronic ADAR >50 . . .
8 chr1 948840 948840 - C upstream ISG15 -6 . . .
Description of updated file1
Code:
line1:file1 $9 updated to 0 because ISG15 is matched to line 1, $2 of file2 and the value in $4 of file1, 948846 is a exact match to the first cordinate in $4 before the -
line2:not updated, skipped because $9 or $12 in file1 have a value other then . in them
line3:not updated, skipped because $9 or $12 in file1 have a value other then . in them
line4:file1 $9 updated to +6 because ISG15 is matched to line 1, $2 of file2 and the value in $4 of file1, 949925 is a range match to the second coordinate in $5 after the -
line5:file1 $9 updated to >50 because CR2 is matched to line 2, $2 of file2 and the value in $4 of file1, 207646923 is a range match to the first coordinate in $14 before the - but the difference of 222 is > 50
line6:file1 $9 updated to >50 because COLEC11 is matched to line 3, $2 of file2 and the value in $4 of file1, 3653844 is a range match to the second coordinate in $2 after the - but the difference of 1784 is > 50
line7:file1 $9 updated to >50 because ADAR is matched to line 4, $2 of file2 and the value in $4 of file1, 154562625 is a range match to the second coordinate in $12 after the - but the difference of112 is > 50
line8: file1 $9 updated to -6 because ISG15 is matched to line 1, $2 of file2 and the value in $4 of file1, 948840 is a range match to the first coordinate in $4 before the -
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