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alanlhutchison / empirical-JTK_CYCLE-with-asymmetry

This repository contains the code described in Hutchison, Maienschein-Cline, and Chiang et al. (2015) Improved statistical methods enable greater sensitivity in rhythm detection for genome-wide data. PLoS Comput Biol 11(3): e1004094. doi:10.1371/journal.pcbi.1004094
MIT License
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Waveform files missing? #1

Open mathiasbockwoldt opened 9 years ago

mathiasbockwoldt commented 9 years ago

I just tried to get the extended JTK_cycle started. Unfortunately, the help texts don't help me enough to start the script. I can find asymmetries and periods in ref_files/ and guess what they are used to, but I could no find any waveform files or a hint on how to create such files. The waveforms default value (trough) led to a file-not-found error:

Traceback (most recent call last):
  File "./jtk7.py", line 551, in <module>
    main(args)
  File "./jtk7.py", line 48, in main
    waveforms = read_in_list(fn_waveform)
  File "./jtk7.py", line 111, in read_in_list
    with open(fn,'r') as f:
IOError: [Errno 2] No such file or directory: 'trough'

The same error occurs for any of the suggested included files (cosine (dflt), rampup, rampdown, impulse, step, trough). By the way, according to the help text (./jtk7.py -h), the default value is "cosine", although it is in fact "trough".

How do I include an appropriate waveform file?

alanlhutchison commented 9 years ago

Hi Mathias,

You are right on both counts! I have added a reference waveform file, which just has the name of the waveform in it (the idea is if you wanted to do both cosine and trough in the same analysis, you could include each on a separate line in the same file). I have also changed the default behavior to cosine as it says in the documentation. Thank you for pointing these both out to me!

Please let me know if you have any more questions or comments.

Alan

laloumdav commented 6 years ago

Hello!

Acrtually I did not succeed in using several waveforms in the same analysis as it is notified (waveform_file : "Should be a file with waveforms you wish to search for listed in a single column separated by newlines"). Appart from cosine and trough waveforms, other waveforms are not working, since it is specified we could use other waveform choices as :["waveform_cosine.txt","waveform_rampup.txt","waveform_rampdown.txt","waveform_step.txt","waveform_impulse.txt","waveform_trough.txt"]

Did I miss something ? Waiting for your help

David