resulting trimmed alignment not printed to specified output file (-o) when also using -log

[jolienvanhooff]

Hi Jacob & team,

With interest I'm exploring the alignments processed by ClipKIT, including how each site is classified. For the latter, I appreciate the option to generate a log file with the option -log. However, it appears that using this option in combination with specifying an output file for the trimmed alignment itself (with the -o option) does prohibit the latter, since in this case the results are written to output file 'g' (and the classifications to 'g.log'). Possibly I'm submitting the wrong command (e.g. clipkit [alignment file] -m kpi-gappy -g 0.7 -o [trimmed alignment file] -log), in that case I'd like to figure that out.

Best regards, Jolien

[JLSteenwyk]

Hi Jolien,

Thank you for bringing this to our attention. We value and rely on user feedback to improve ClipKIT. I have recreated your issue and agree that ClipKIT isn't functioning properly with the command you provided. However, I am currently on vacation and will not be able to remedy this issue until mid-August. For the time being, it may be easiest to rename the output files in a loop.

Again, thank you for bringing this to our attention and for using ClipKIT!

best,

Jacob

[jolienvanhooff]

Dear Jacob,

Thanks for your fast provisional response. Indeed, for the moment I can easily find a workaround to gather and save (multiple) alignment and log files.

Enjoy your vacation!

Best regards, Jolien

[JLSteenwyk]

Thank you for your patience Jolien!

In addition to your workaround, I have also found that changing the order of arguments allows you to obtain a log file and specify the name of your output file. For example, I was able to use the following command clipkit <input file> -m kpi-gappy -g 0.7 -log -o <output file> and got the expected output.

I will investigate the issue further later.

Thank you again for using ClipKIT!

All the best,

Jacob

[JLSteenwyk]

Hi Jolien,

I realized what the issue is!

The issue stems from improper usage of the log argument (however, you were very close to being correct!!). When specifying the log argument in long form, please use --log instead of -log. If you wish to use the short form of the log argument, please use -l.

Thus, for your command, you would type in the following: clipkit <input_file> -m kpi-gappy -g 0.7 -o <output_file> --log which will result in the correct output and log files being made :)

Please let me know if you come across any other issues. Also, please let me know via email (https://jlsteenwyk.com/contact.html) or twitter (https://twitter.com/jlsteenwyk) if you have any suggestions to improve the user experience.

All the best,

Jacob L. Steenwyk

[jolienvanhooff]

Dear Jacob,

Oh, I see, I'm sorry for the confusion! I'll properly check the argument options in my future usage.

Thanks for solving it anyway!

Best, Jolien

Op wo 4 aug. 2021 om 17:27 schreef Jacob L. Steenwyk < @.***>:

Closed #15 https://github.com/JLSteenwyk/ClipKIT/issues/15.

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-- Jolien van Hooff @.*** +31 (0)6 48101844

[JLSteenwyk]

Hi Jolien,

Not a problem at all! I am so grateful that you use ClipKIT for your research needs.

Please do not hesitate to reach out again!

All the best,

Jacob L. Steenwyk