I need to write a script that reads through an input .txt file and replaces the end value with the end value of the next line for lines that have distance <=4000. The first label line is not actually in the input. In the below example, 3217 is the distance from the end of the first line to the start of the second line. 14021 is the distance from the previous line (not included) to the start of the first line. So once the script finds a distance <=4000, it needs to replace the end of the previous line with the end of the current line.
Any help would be greatly appreciated! Thanks!
INPUT:
chrm start end block length distance
Desired OUTPUT:
chr7 27398704 27402466
If I understand correctly the output should be:
chr7 27398704 27402466
chr7 27412536 27416424
Am I missing something?
No, actually I meant to put the original
because the next distance is <=4000 as well, so those two would get merged as well. See, when you have several distances<=4000 consecutively, you continue to merge them, until the distance is no longer <=4000.
Could you post a bigger input sample with the desired input?
Sure! This may take me a little while since I'm doing it manually, but it should be up in about 15 minutes. Thanks for your interest!
INPUT: Use distance <=1000 to merge
chr7 27104483 27104633 ENm010Block71 150 0
OUPUT:
chr7 27104483 27105154
Hm,
awk 'END { print _, __ }
1 == NR || $NF >= 1000 {
if (c) print _, __
_ = $1 FS $2
c = 1
}
{ __ = $3 }' file
I get this output:
chr7 27104483 27105154
chr7 27106872 27110789
chr7 27111956 27112830
chr7 27114388 27125180
chr7 27126966 27131260
chr7 27135440 27137796
Do you realy want to treat the last line as in the example output?
It makes the code a bit ugly:
awk 'END { print _, ___ RS ____ }
1 == NR || $NF >= 1000 {
if (c) print _, __
_ = $1 FS $2
c = 1
}
{ ___ = __
__ = $3
____ = $1 FS $2 FS $3 }
' file
You may need to check if the last line has $NF >= 1000,
And ..., don't blame me for choosing such variable names,
I'm a begginer awk user and not sure how to use nawk. Is there a way to make the first code work for awk?
Yes. This is Old-AWK compatible:
awk '1 == NR || $NF >= 1000 {
if (c) print _, __
_ = $1 FS $2
c = 1
}
{ __ = $3 }
END {
print _, __
} ' file
To run the original code under the New AWK just invoke the correct interpreter:
nawk 'END { print _, __ }
1 == NR || $NF >= 1000 {
if (c) print _, __
_ = $1 FS $2
c = 1
}
{ __ = $3 }' file
It WORKED! Thanks so much!! The way you had it was perfect, for some reason, it just had problems when I cut and paste it, and use dos2unix. But in the end, it worked. Thank you!
It worked! I was having copy and pasting problems..
awknerd:
The first code for awk is still not working for me. Are there supposed to be commas after the first print command? I am using
awk '1 == NR || $NF >= 1000 { if (c) print _, __, _ = $1, FS, $2; c = 1 } { __ = $3 } END { print _, __ } ' file
If you're going to put it all on one line, try it like this:
awk '1 == NR || $NF >= 1000 { if (c) print _, __; _ = $1 FS $2; c = 1 } { __ = $3 } END { print _, __ } ' file
Thanks. I didn't realize that copying and pasting onto a WordPad document then saving it as .txt, then doing dos2unix file.txt didn't work. So I tried pasting it just to notepad, doing dos2unix on it, and it worked. Lesson learned!
