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PatrickKueck / FASconCAT-G

FASconCAT-G offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options include sequence renaming, file format conversion, sequence translation, consensus generation of predefined sequence blocks, and RY coding as well as site exclusions in nucleotide sequences. FASconCAT-G implemented process options can be invoked in any combination and performed during a single process run. FASconCAT-G can also read in and handle different file formats (FASTA, CLUSTAL, and PHYLIP) in a single run.
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Pull request: issues with character encoding and comment formatting #8

Closed JGLAHE closed 1 year ago

JGLAHE commented 2 years ago

Hi Patrick,

I've found that commend option (-g) is assigned to both 'Replace missing sequences with' and 'Preface', and these are also linked to both (-g) and (-x) in the comments.

I've resolved this command conflict by setting 'Replace missing sequences with' to (-g) and 'Preface' to (-x); I've also made some minor character corrections in comments.

However, I haven't made the pull request because I'm having trouble with the encoding of your name, and with inconsistencies in the comment formating when I upload the .pl file to my forked repo (https://github.com/JGLAHE/FASconCAT-G)].

Would you be able to assist me with this?

Best regards,

James

PatrickKueck commented 2 years ago

Hi James.

First, thank you for fixing the -g bug. Since I got a pull request from you, I think you could solve the pull request problem? I have a question to you too. This is also my first pull request. I would like to transfer your changed file into my repository, but I don't know how to merge your changes with my .pl code. There should be an other solution than downloading and re-uploading the new FcC-G perl file from your repository to mine.

Can you help me with this?

Best wishes

Patrick

JGLAHE commented 2 years ago

Hi Patrick,

Unfortunately, I've never made a pull request either, or done anything with git/github other that post comments, so I'm flying blind too, but I'll make the pull request again: this should allow you to accept it and then apply for my commit permission (which I'll look out for), and then once I've granted that, you should be able make the commit. I'm still not sure where 'push' part comes in, but the commit part seems like it'll do the merging...

I have a deadline tomorrw on some work so I'm unable to fix the issues with the comment misalignments and the ü encoding issue, but those are mainly cosmetic. I didn't set out to translate parts of your comments; because my VSCode rendered ü into something similar to <?>, it didn't initially connect that those words were actually in German - my appologies for that.

I will look out for the commit approval request, but I may not be able to deal with it immediately, at least not until tomorrow afternoon (say ~early Friday morning your time).

Cheers,

James

PatrickKueck commented 2 years ago

Hi James.

Again, thank you for your great help! I merged and confirmed your pull request. Either I missed that link button the last time or it wasn't there. I am sorry for my confusion. Keep fingers crossed that we two 'half blinds' can manage your pull request :)

Would you mind to do further conversation via email (maybe you have some ideas about how FcC-G can be improved in the future as well)? In case you like the idea, my email is p.kueck[at]leibniz-zfmk.de but I am also fine if you think otherwise.

However, looking forward to read from you

Cheers

Patrick