continuuos intervals

mesana has asked for the wisdom of the Perl Monks concerning the following question:

Hi!! this is my input file:

gene    chrom   start   end
NRAS    chr1    115247085       115250671
NRAS    chr1    115250775       115250813
NRAS    chr1    115251152       115251275
NRAS    chr1    115252190       115252349
NRAS    chr1    115256421       115256599
NRAS    chr1    115258671       115258798
NRAS    chr1    115259279       115259515
TNNT2   chr1    201328142       201328383
TNNT2   chr1    201328751       201328791
TNNT2   chr1    201330407       201330497
TNNT2   chr1    201331041       201331155
TNNT2   chr1    201331238       201331243
TNNT2   chr1    201332423       201332534
TNNT2   chr1    201333426       201333503
TNNT2   chr1    201334319       201334435
TNNT2   chr1    201334738       201334798
TNNT2   chr1    201335966       201335999
[download]

I need to generate a file with intervals of 200, considering that if the interval does not finish exactly in the second column, it should end in the second row. The same for each genes(name in the first column). for example...

NRAS chr1    115247085       115247285
NRAS chr1    115247287       115247487
NRAS chr1    115247489       115247689...
...
NRAS chr1    115250400       115250600
(for example...
NRAS chr1    115250602      115250906
NRAS chr1    115250908  115251108
[download]

anyone has any idea?

thank u a lot

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Re: continuuos intervals by perldigious (Priest) on Aug 31, 2016 at 13:23 UTC
Hi mesana, Welcome to the monastery. What you are asking would probably be pretty trivial and simple to implement in Perl, but the desired output pattern you describe isn't quite clear to me. Your output begins at the first input "start" value, 115247085, and then adds 200 to get your first output "end" value, 115247285. But then for some reason you add 2 to this to get your output's next "start" value, 115247287. This pattern continues, but 115250400 less 115247489 is not divisible by 202, so the pattern seemingly broke down there. You pick the pattern up again, but at 115250602 inexplicably add 304 to get 115250906. Then your original pattern of adding 2 and then adding 200 continues. I'm also not clear on why you would stop at the value 115251108, but perhaps that was just an arbitrary stopping point. Do you see why we might be confused? :-) If you explain that a little more clearly the monks here can probably help you out. Update: Fixed some number errors of my own. I love it when things get difficult; after all, difficult pays the mortgage. - Dr. Keith Whites I hate it when things get difficult, so I'll just sell my house and rent cheap instead. - perldigious	[reply]
Re: continuuos intervals by GotToBTru (Prior) on Aug 31, 2016 at 12:13 UTC
In your example output, I get how the first interval is 115247085 to 115247285 .. but I wonder what happened to 115247286, and I can't figure out how you decided where any of the following intervals started. But God demonstrates His own love toward us, in that while we were yet sinners, Christ died for us. Romans 5:8 (NASB)	[reply]
Re: continuuos intervals by Anonymous Monk on Aug 31, 2016 at 11:23 UTC
Sure, first read file, then match or split, then print. Simple perlintro stuff	[reply]
Re: continuuos intervals by mesana (Initiate) on Aug 31, 2016 at 14:06 UTC
thank you a lot,you are right!it is not so clear my explanation! so...the input file is composed by intervals of different lenght of piece of genes (the name is in the first column).I have to split these intervals in smaller intervals of 200, considering to "complete the gap" among the intervals. At the same time, the intervals have to be of 200 but the next start has to be 200+2. To make it easier.. this is an easier input file. The intervals I have to create is 10 input.txt gene1 chr1 10 25 gene1 chr1 46 99 gene1 chr1 103 190 gene2 chr4 50 63 gene2 chr4 90 110 output.txt gene1 chr1 10 20 gene1 chr1 22 53 gene1 chr1 55 65 gene1 chr1 67 77 gene1 chr1 79 89 gene1 chr1 91 99 gene2 chr4 50 60 gene2 chr4 62 99 gene2 chr4 101 110	[reply]
Re^2: continuuos intervals by perldigious (Priest) on Aug 31, 2016 at 14:40 UTC
Hi mesana, just a few helpful new PerlMonks user tips. Please put separate `<p>` and `<code>` tags around your input and output data like you did in your original post. This helps the monks here quickly copy and paste your data if necessary. Please reply directly to a node you are responding to by clicking the individual "reply" button on that node. This helps keeps conversations organized and understandable. You can similarly "edit" any of your own nodes if you need to make fixes and updates, but it's considered courteous to include "UPDATE" or "EDIT" text when you do so explaining what you changed. If you intend to delete large portions this way, it's also nice to use `<del>` tags around the deleted portions instead so it appears ~~like this~~. This also helps future readers in case you get responses discussing things you have deleted. A quick and helpful PerlMonks tutorial for other basic things can be found in How do I post a question effectively? I love it when things get difficult; after all, difficult pays the mortgage. - Dr. Keith Whites I hate it when things get difficult, so I'll just sell my house and rent cheap instead. - perldigious	[reply] [d/l] [select]