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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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FASconCAT-G v1.05.6 #14

Open JGLAHE opened 1 year ago

JGLAHE commented 1 year ago

Hi Patrick,

I meant to deal with this ~2 years ago after the other minor changes but I got distracted by other projects.

Material changes to code marked with '#jgl#'

Please test this version and ensure it's cross compatible with the previous one.

There's also some unintuitive behaviour with the way the -g option works, especially if you have N|X, -,? characters in a locus file that has less that the total number of sequences in the supermatrix, whereby the residual sequences that get filled-in following concatenation can then have a distinctly different makeup to the almost-empty sequneces in the original locus file. -This can be fixed later

Something else to watch out for is pasting code into github issue reponses: the code in some of your response got severely munged, e.g. the parameter array references got replaced by your redacted email, etc.

Cheers

PatrickKueck commented 1 year ago

Dear ILLHHM (sorry don't know your real name),

 

first of all, thank you for not forgetting to check fcc again after such a long time. amazing!

Thank you also for your recent work and comments on fcc.

I am full of work today and the weather here today is nice and warm for the first time since a while, welcoming me to go to the park later.

So I would like to go through all your stuff next week if its ok for you. ;)

 

Again thank you.

 

Have a nice weekend!

 

Best

 

Patrick  

 

   

Gesendet: Mittwoch, 16. August 2023 um 18:35 Uhr Von: "lLLHMM" @.> An: "PatrickKueck/FASconCAT-G" @.> Cc: "Subscribed" @.***> Betreff: [PatrickKueck/FASconCAT-G] FASconCAT-G v1.05.6 (PR #14)

Hi Patrick,

I meant to deal with this ~2 years ago after the other minor changes but I got distracted by other projects.

Material changes to code marked with '#jgl#'

cleaned up some formatting
replaced tab characters with 4 whitespaces
script and perl versioning info added to paramters screen and preface as variables
implemented P Kuek change 22nd april to help option
screen clearing that works on macOS, linux and cygwin (check)
attempted to resolve multiple warning, or at least mark them in code, see '#jgl#'
identified info reporting issues [see desription lines in sub info_all], and added
additional columns to info report.
fixed "N PARSIMONY INFORMATIVE SITES" and "N CODING CHARACTERS" bug by switching the column headers.

Please test this version and ensure it's cross compatible with the previous one.

There's also some unintuitive behaviour with the way the -g option works, especially if you have N|X, -,? characters in a locus file that has less that the total number of sequences in the supermatrix, whereby the residual sequences that get filled-in following concatenation can then have a distinctly different makeup to the almost-empty sequneces in the original locus file. -This can be fixed later

Something else to watch out for is pasting code into github issue reponses: the code in some of your response got severely munged, e.g. the parameter array references got replaced by your redacted email, etc.

Cheers

You can view, comment on, or merge this pull request online at:

  https://github.com/PatrickKueck/FASconCAT-G/pull/14

Commit Summary

2af49b3 Delete FASconCAT-G_v1.05.1.pl
d009386 Add files via upload
31d5063 Update of additional alignment reporting and fixing of warnings

File Changes

(2 files)

D FASconCAT-G_v1.05.1.pl (5164)
A FASconCAT-G_v1.05.6.pl (5251)

Patch Links:

https://github.com/PatrickKueck/FASconCAT-G/pull/14.patch
https://github.com/PatrickKueck/FASconCAT-G/pull/14.diff

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>

JGLAHE commented 1 year ago

No worries take you time. Also disregard the bit about inconsistencies in N|X, -,? coding - it really doesn't matter