I have a variation table (variation.txt) which is a very big file. The first column in the chromosome number and the second column is the position of the variation. I have a second file annotation.txt which has a list of 37,000 genes (1st column), their chromosome number(2nd column), their start and end coordinates (3rd and 4th column), followed by some details
I have to assign the variations (based on chromosome number and its position) to the genes. First, it should look for the **matching chromosome number** in both files, and if that matches, the coordinate of the variation should be within (including) start and end position of the gene. I have made an attempt to print the entries of variation table. I want to append the gene IDs also from annotation table in the first column of the output. How do I do that ?
variation.txt
Code:
SL3.0ch02 702679 C A - - - - - - - -
SL3.0ch01 711131 A G - - - - - - - -
SL3.0ch00 715124 G A - - - - - - - -
SL3.0ch00 719289 C T - - - - - - - -
SL3.0ch00 720926 A C - - - - - - - -
SL3.0ch00 723860 A C Solyc00g005060.1 CDS NONSYNONYMOUS W/G 52 0 novel DELETERIOUS (*WARNING! Low confidence)
SL3.0ch00 723867 A C Solyc00g005060.1 CDS SYNONYMOUS G/G 49 1 novel TOLERATED
SL3.0ch00 723903 T C Solyc00g005060.1 CDS SYNONYMOUS G/G 37 1 novel TOLERATED
Solyc00g005060.1.1 SL3.0ch02 702679 C A - - - - - - - -
made it into the desired ouput - there is no connection between Solyc00g005060.1.1 and SL3.0ch02 in your annotation file, but it exists for the Solyc00g005000.3.1 and SL3.0ch02 pair. And, why isn't Solyc00g005050.3.1 / SL3.0ch00 mentioned? Shouldn't that match the third variation line?
Howsoever, pls try and report back
Code:
awk '
NR==FNR {a[$2 FS $3 FS $4] = $1
next
}
{for (i in a) if (split (i,t) && $2>=t[2] && $2<=t[3]) print a[i], $0
}
' annotation.txt variation.txt
Solyc00g005000.3.1 SL3.0ch02 702679 C A - - - - - - - -
Solyc00g005040.3.1 SL3.0ch00 715124 G A - - - - - - - -
Solyc00g005060.1.1 SL3.0ch00 723860 A C Solyc00g005060.1 CDS NONSYNONYMOUS W/G 52 0 novel DELETERIOUS (*WARNING! Low confidence)
Solyc00g005080.2.1 SL3.0ch00 723860 A C Solyc00g005060.1 CDS NONSYNONYMOUS W/G 52 0 novel DELETERIOUS (*WARNING! Low confidence)
Solyc00g005060.1.1 SL3.0ch00 723867 A C Solyc00g005060.1 CDS SYNONYMOUS G/G 49 1 novel TOLERATED
Solyc00g005080.2.1 SL3.0ch00 723867 A C Solyc00g005060.1 CDS SYNONYMOUS G/G 49 1 novel TOLERATED
Solyc00g005060.1.1 SL3.0ch00 723903 T C Solyc00g005060.1 CDS SYNONYMOUS G/G 37 1 novel TOLERATED
Its results match the desired output except for the two mentioned lines plus, mayhap, the field separators (which weren't specified, btw).
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