DNAconvert

Convert between different file formats containing genetic information.

Installation

Install the latest version directly using pip (requires Python 3.8.6 or later):

pip install git+https://github.com/iTaxoTools/DNAconvert.git#egg=DNAconvert

Executables

Download and run the standalone executables without installing Python.

Usage

usage: DNAconvert [-h] [--cmd] [--allow_empty_sequences]
                  [--automatic_renaming] [--preserve_spaces]
                  [--informat INFORMAT] [--outformat OUTFORMAT]
                  [infile] [outfile]

Converts between file formats with genetic information. Uses graphical
interface by default.

positional arguments:
  infile                the input file
  outfile               the output file

optional arguments:
  -h, --help            show this help message and exit
  --cmd                 activates the command-line interface
  --allow_empty_sequences
                        set this to keep the empty sequences in the output
                        file
  --automatic_renaming  enables automatic renaming of sequences (to avoid
                        duplicate sequence names in Phylip and Nexus files)
  --preserve_spaces     preserve spaces in sequences
  --informat INFORMAT   format of the input file
  --outformat OUTFORMAT
                        format of the output file

Batch processing

If infile is a directory, all files in it will be converted. In this case informat and outformat arguments are required.

Specifying names of the output files:

• outfile contains a '#' character: '#' will be replaced with the base names of input files.
• outfile is a directory: the output files will be written in it, with the same names as input files.

Supported formats

• tab: Internal tab format
• tab_noheaders: Internal tab format without headers
• fasta: FASTA format
• fasta_nogaps: Output-only FASTA format with gaps removed
• relaxed_phylip: relaxed Phylip format
• fasta_hapview: FASTA format for Haplotype Viewer
• phylip: Phylip format
• fastq: FASTQ format
• fasta_gbexport: FASTA format for export into Genbank repository
• nexus: NEXUS format
• nexml: DnaCharacterMatrix in NeXML format
• genbank: Genbank flat file format
• mold_fasta: FASTA format with sequence name matching requirements for the tool MolD
• ali_fasta: Ali variant of the FASTA format

Recognised extension

If format is not provided, the program can infer it from the file extension

Currently recognised:

• .tab, .txt, .tsv: Internal tab format
• .fas, .fasta, .fna: FASTA format
• .rel.phy: relaxed Phylip format
• .hapv.fas: FASTA format for Haplotype Viewer
• .phy: Phylip format
• .fastq, .fq: FASTQ format
• .fastq.gz, .fq.gz: FASTQ format compressed with Gzip
• .gb.fas: FASTA format for export into Genbank repository
• .nex: NEXUS format
• .xml: NeXML format
• .gb: Genbank flat file format
• .ali: FASTA Ali format

Files with extension .gz are uncompressed automatically

Adding new formats

Link to documentation

Options

DNAconvert uses two parsers for NEXUS format: internal (default) and the one from python-nexus package.

In the file DNAconvert/config.json (found in %APPDATA%\iTaxoTools or in $XDG_CONFIG_HOME$/) the key-value pair

"nexus_parser" : "(method)""

determines the parser. (method) is either internal or python-nexus.

Generating an executable

Scripts for building Windows and macOS executables are included in the tools folder. Executables are also built automatically using GitHub actions.

Dependencies

Automatically installed when using pip:

• python-nexus
• dendropy