I have an input file (more than 20K records) as following. The information I'm interested to manipulate are at column 10, 11 and 13.
Column 13: It's item name, item name may appear more than once in the table.
Column 10: A string of "start position" seperated by comma.
Column 11: A string of "end position" seperated by comma.
I'm would like to find overlapping regions for each item.
Output:
Code:
Item Start End
B1 90098643,90152028,90178260 90098890,90152170,90185093
B2 76540388,76779489,76877692 76540569,76779684,76878102
By literally, overlapping regions of B1 are (90098643-90098890,90152028-90152170,90178260-90185093)
The following is my script,
Code:
{a[$13]++
start[$13]=start[$13] "" $10
end[$13]=end[$13] "" $11
}
END {
for (i in a){
split(start[i],split_start,",")
split(end[i],split_end,",")
mylen=length(split_start)
for (k=1;k<mylen;k++){
if (split_start[k]"+"split_end[k] in mypair) continue
else {
mypair[split_start[k]"+"split_end[k]]++
if (k==1) mystring=split_start[k]"+"split_end[k]
else mystring=mystring","split_start[k]"+"split_end[k]
}
}
split(mystring,mylist,",")
asort(mylist)
count=length(mylist)
#---------finding overlapping regions
ind=0
for (z=1;z<=count;z++){
split(mylist[z],item,"+")
if (z==1){
ind+=1
unionlist[ind]=mylist[z]
}else{
split(unionlist[ind],old,"+")
aa=old[1]
bb=old[2]
cc=item[1]
dd=item[2]
if (cc>bb){
ind+=1
unionlist[ind]=cc"+"dd
}else if (cc>=aa && cc<bb){
if (dd>bb){ unionlist[ind]=aa"+"dd}
else {unionlist[ind]=aa"+"bb}
}
}
}
for (j=1;j<=ind;j++) mystring3=mystring3","unionlist[j]
print i,length(unionlist),mystring3
delete mypair
delete unionlist
delete mylist
mystring3=""
}}
From the above script, you would see I store string of regions in this format, (90098643+90098890,90152028+90152170,90178260+90185093).
I want to sort them in ascending order so that it will ease the finding of overlapping region. The function asort() is not appropriate in the following case,
Code:
33+54
11+34
22+33
222+456
The output sorted region would be,
Code:
11+34
22+33
222+456
33+54
The order is incorrect as 222+456 should have positioned at last.
I'm sure that the part finding overlapping region is correct, I tested it with another programming language. Now the only problem I have is the sorting part.
Does anyone could suggest me to sort a 2 dimentional array?
Thanks,
phoebe
Last edited by Franklin52; 08-09-2010 at 04:06 PM..
Reason: Please use code tags
---------- Post updated at 03:04 PM ---------- Previous update was at 03:02 PM ----------
Quote:
Originally Posted by frans
a simple
Code:
sort -n file
does the job too
No, it does not. It may give you the correct result with this particular dataset and your particular sort implementation, but it is definitely not a correct solution.
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