Hi I have 2 files; usually the end position in the file1 is the start position in the file2 and the end position in file2 will be the start position in file1 (flanks)
Read file1 into an indexed array pair, then read file2 into variables and walk through the array pair looking for the relationships, and when you find a hit, echo out the desired variables. Maybe I have that backwards, but that is the flavor.
If there is a size problem, sorting the files if not always sorted and some sort of merge would be faster, but that is a bit hard in shell. Also, you may need multiple lines of reference to solve a line of query, so you are back keeping at least a local array, or seeking back before the next query line.
Sticking the data in an RDBMS, or using a JDBC or similar text file as table SQL tool makes it a trivial SQL query.
Code:
Select a.Id, a.start. a.end, b1.name, b2.name
from
file1 a
join file2 b1
on a.start between b1.start and b1.end
join file2 b2
on a.end between b2.start and b2.end
order by 1,2,3
I have a positions file with markers in col1 and position defined by chromosome and location in col2 and col3
m1 ch1 1
m2 ch1 5
m3 ch1 50
m4 ch2 567
m5 ch2 4567
m6 ch2 7766
m7 ch2 554433
m8 ch3 76
m9 ch3 456
m10 ch3 2315
Given a set of query marker, I would like to know what are the... (1 Reply)
Hi all,
I have a file like this I want to extract only those regions which are big and continous
chr1 3280000 3440000
chr1 3440000 3920000
chr1 3600000 3920000 # region coming within the 3440000 3920000. so i don't want it to be printed in output
chr1 3920000 4800000
chr1 ... (2 Replies)
Hello, here I am posting my query again with modified data input files.
see my query is :
i have two input files file1 and file2.
file1 is smalldata.fasta
>gi|546671471|gb|AWWX01449637.1| Bubalus bubalis breed Mediterranean WGS:AWWX01:contig449636, whole genome shotgun sequence... (20 Replies)
HI,
I have a Complete genome fasta file and I have list of sub sequence regions
in the format as :
4353..5633
6795..9354
1034..14456
I want a script which can mask these region in a single complete genome fasta file with the alphabet N
kindly help (2 Replies)
I have 2 files; file 1 having smaller positions that overlap with the positions with positions in file2.
file1
aaa 20 22 apple
aaa 18 25 banana
aaa 12 30 grapes
aaa 22 25 melon
file2
aaa 18 26 cdded
aaa 10 35 abcde
I want to get something like this
output
aaa 18 26 cdded banana... (4 Replies)
Discussion started by: anurupa777
4 Replies
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The forums have been seeing a sharp increase in spam bots, forum robots, and malicious registrations from certain countries. If you have been directed to this thread due to a "No Permission Error" when trying to register please post in this thread and request permission to register, including... (1 Reply)
Hi, I have a file1 of many long sequences, each preceded by a unique header line. file2 is 3-columns list: headers name, start position, end position. I'd like to extract the sequence region of file1 specified in file2.
Based on a post elsewhere, I found the code:
awk... (2 Replies)
Hi all,
I have difficulty to solve the followign problem.
mydata:
StartPoint EndPoint
22 55
2222 2230
33 66
44 58
222 240
11 25
22 60
33 45
The union of above... (2 Replies)
Anyone help ! From where can I download a free version of FreeBSD ?
I am trying to teach myself this OS, have all the documentation needed, but am short the OS itself.
If anyone can send me a link, I would be most appreciative ! (3 Replies)
