finding overlapping genes

I need a list of lines that do not have any overlap, and a list of lines that have overlap. We can have any number of genes in each line (separated by comma)! I like to do it in awk, but I'm not very familiar with all the commands.

L1 ycjM,ycjN,ycjO,ycjP,ycjQ,ycjR,ycjS,ycjT,ycjU,ycjV,ymjB

L2 ydaS,ydaT, ydaU,ydaV,ydaW,rzpR

L3 ompn

L4 ycjX,ycjF

L5 ycjX,ycjF,tyrR

.................

Non-overlapping lines: L1 L2 L3

Overlapping lines: L4 L5

awk overlap

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updated 8.0 years ago by Biostar

• written 9.7 years ago by Fatima

1 answer

One way to do this in awk is with associative arrays.

Associative arrays are data structures that store key-value pairs. They are also known as hash tables in Perl, or dictionaries in Python.

You could keep a pair of arrays: one to store the line number of an element, and another to flag whether or not that element is was found on a previous line.

Perhaps you can modify the logic here to get the result you want:

$ awk -F',' 'BEGIN { n = 1; }{ for (i = 1; i <= NF; i++) { if ($i in ht) { print "non-unique element "$i" on line "ht[$i]" also found on line "NR; for (j in f) { if (f[j] == $i) f[j] = 0; } } else { ht[$i] = NR; f[n] = $i; n++; } } } END { for (i = 1; i < n; i++) { if (f[i] != 0) { print "unique element "f[i]" found on line "ht[f[i]]; } } }' genes.txt
non-unique element ycjX on line 4 also found on line 5
non-unique element ycjF on line 4 also found on line 5
unique element ycjM found on line 1
unique element ycjN found on line 1
unique element ycjO found on line 1
unique element ycjP found on line 1
unique element ycjQ found on line 1
unique element ycjR found on line 1
unique element ycjS found on line 1
unique element ycjT found on line 1
unique element ycjU found on line 1
unique element ycjV found on line 1
unique element ymjB found on line 1
unique element ydaS found on line 2
unique element ydaT found on line 2
unique element ydaU found on line 2
unique element ydaV found on line 2
unique element ydaW found on line 2
unique element rzpR found on line 2
unique element ompn found on line 3
unique element tyrR found on line 5

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written 9.7 years ago by Alex Reynolds

Thank you :)

I modified it to this code, and it worked :)

awk -F '[,  \t]' 'BEGIN { n = 1; }{ for (**i = 2**; i <= NF; i++) { if ($i in ht) { print "non-unique element "$i" was found on "ht[$i]" and **"$1"** "; for (j in f) { if (f[j] == $i) f[j] = 0; } } else { ht[$i] = $1 ; f[n] = $i; n++; } } } END { for **(i = 2**; i < n; i++) { if (f[i] != 0) { print "unique element "f[i]" found on line "ht[f[i]]; } } }' |\

How can I tell it to consider tab comma and space as separators? : '[, \t]' I guess this one doesn't consider white space.

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written 9.7 years ago by Fatima

Perhaps use tr or sed to strip out tabs and spaces, e.g.:

$ sed 's/[\t| ]//g' genes.txt | awk -F',' ...

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written 9.7 years ago by Alex Reynolds