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biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
http://bioepic.readthedocs.io
MIT License
31 stars 6 forks source link

custom chromosomes with . in name #54

Closed saycheeeeese closed 7 years ago

saycheeeeese commented 7 years ago

Hi,

My chromosome names unfortunately contain full stops (chr1_v2.1, chr_v2.1 etc). When I use --chromsizes option and a file containing chromosome names and length I get an error. When I remove the full stops this is resolved, but the chromosome names are incorrect now.

In the Genome.py script:

chromosome_lengths = [l.split() for l in open(chromsizes).readlines()]

appears not just to be splitting with white space, the full stops are causing a problem here for some reason. Any chance of a solution?

Thanks!

endrebak commented 7 years ago

Please post the output of

cat -et chromsizes

and the error message you get running epic.

endrebak commented 7 years ago

According to the error message you emailed epic is not able to find your chromsizes file :)

Are you sure you called it Tbrucei_hybrid_chromsizes? Perhaps there should be a dot at the end of the hybrid, not an underscore?

Thanks for trying epic and reporting this btw.

saycheeeeese commented 7 years ago

Ahaha I know sorry it was the wrong error message (I ran it again in the wrong directory by mistake), hence why I deleted the post. I somehow fixed the problem however and am re running epic now.
For some reason deleting the dots and then adding them back in and re-saving the file (done in sublime) produced a format epic could use. If I ever work out why that made a difference I'll let you know!

endrebak commented 7 years ago

Your file probably contained whitespace you could not see. The cat -et command makes whitespace explicit. Anyways, the important thing is that you got it working! I'm glad to hear.

On Wed, May 24, 2017 at 3:47 PM, saycheeeeese notifications@github.com wrote:

Ahaha I know sorry it was the wrong error message (I ran it again in the wrong directory by mistake), hence why I deleted the post. I somehow fixed the problem however and am re running epic now. For some reason deleting the dots and then adding them back in and re-saving the file (done in sublime) produced a format epic could use. If I ever work out why that made a difference I'll let you know!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/biocore-ntnu/epic/issues/54#issuecomment-303728933, or mute the thread https://github.com/notifications/unsubscribe-auth/AQ9I0tTTCe_4zCe5-1xGTadiZeYFJQHsks5r9DUKgaJpZM4NkVM5 .

endrebak commented 7 years ago

Feel free to reopen if the problem persists.