v3.0.0

Version 3.0.0 - Released on December 20, 2023

Note: To get the newest version of seqconverter, use pip to install from PyPi. Releases are mostly used to keep track of important changes to interface.

This release significantly updates the user interface, focusing on making option names more consistent and logical. Additionally some new functionality has been added, and a few bugs fixed.

The tables below give an overview of old and new option names for those options that have changed, divided into the 7 argument groups used when printing the command line help.

Overview of changes in user-interface

Input/Output

Old Option	New Option	Comments
seqconverter [...] SEQFILE	-i SEQFILE	Input file was originally positional argument, but is now specified with -i
-I FORMAT	--informat FORMAT	Default is to autodetect, so can often be omitted
-O FORMAT	--outformat FORMAT	Default output format is fasta, so can be omitted in that case Removed nexusgap as possible output format - rarely used, and will create new options for gapencoding instead

Selecting subset of sequences

Old Option	New Option	Comments
--subsample N	--sampleseq N
--select "REGEXP"	--keepreg "REGEXP"
--discard "REGEXP"	--remreg "REGEXP"
--subset NAMEFILE	--keepname NAMEFILE
--remseqs NAMEFILE	--remname NAMEFILE
--filterpos VARIANT[,VARIANT,...]	--keepvar VARIANT [...]
--filterdupseq	--remdupseq	In v3.0.0: no longer prints names of removed sequences on stderr
--filterdupname	--remdupname

Selecting subset of positions in sequences

Old Option	New Option	Comments
	--samplecols N	New in 3.0.0: Randomly select N columns from alignment
--subseq START.STOP	--keepcols INDEX_OR_RANGE [...]	Example: --keepcols 10 15 22-40 57
--remcols INDEX-LIST	--remcols INDEX_OR_RANGE [...]	Example: --remcols 10 15 22-40 57
--remgapcols --remallgapcols --remfracgapcols FRAC	--remgapcols [FRAC]	Covers all variants. If FRAC not given: remove column if any gaps. If FRAC given: remove column if >= FRAC fraction gaps
--remambigcols	--remambigcols [FRAC]	Now works like the new --remgapcols [FRAC] command. If FRAC not given: remove column if any ambiguity symbols. If FRAC given: remove column if >= FRAC fraction ambiguity symbols
--remendgapcols FRAC	--remendgapcols [FRAC]	Now works the same way as two options above
--remhmminsertcols		Remove option which is rarely used. User can directly use sequencelib if function needed.

Renaming sequences

Old Option name	New Option Name	Comments
--renamenumber	--renamenum
--appendnumber		Removed rarely used option
--renameregexp "REGEXP"	--renamereg "OLD_REGEX" "NEW_STRING"	Shortened name. In new version user can provide replacement string (old version always deleted regex)
--regdupfix		Removed: now fails with error message indicating duplicate created
--savenames FILE	--saverename NAMEFILE
--restorenames FILE	--renamefile NAMEFILE

Combining multiple sequence files

Old Option name	New Option Name	Comments
--overlap --minoverlap N	--overlap [MIN]	Optional value MIN can now be given directly to --overlap
--mbpartblock	--mb

DNA manipulations

Old Option name	New Option Name	Comments
--translate	--translate READING_FRAME	User can now specify in which reading frame to perform translation

Summaries

Old Option name	New Option Name	Comments
--seqcom	--comseq

Bug fixes

• Fixed bug where automatic fileformat detection did not work when input was on stdin
• Fixed bug where --overlap did not work
• Fixed bug where --paste did not work