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author itaxotools
date Sun, 29 Jan 2023 16:32:28 +0000
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1 # DNAconvert
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2 Convert between different file formats containing genetic information.
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3
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4 ## Installation
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5 Install the latest version directly using pip (requires Python 3.8 or later):
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6 ```
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7 pip install git+https://github.com/iTaxoTools/DNAconvert.git#egg=DNAconvert
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8 ```
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9
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10 ## Executables
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11 Download and run the standalone executables without installing Python.</br>
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12 [See the latest release here.](https://github.com/iTaxoTools/DNAconvert/releases/latest)
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13
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14 ## Usage
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15 usage: DNAconvert [-h] [--cmd] [--allow_empty_sequences]
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16 [--informat INFORMAT] [--outformat OUTFORMAT]
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17 [infile] [outfile]
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18 DNAconvert
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19
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20 positional arguments:
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21 infile the input file
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22 outfile the output file
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23
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24 optional arguments:
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25 -h, --help show this help message and exit
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26 --cmd activates the command-line interface
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27 --allow_empty_sequences
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28 set this to keep the empty sequences in the output
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29 file
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30 --disable_automatic_renaming
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31 disables automatic renaming, may result in duplicate
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32 sequence names in Phylip and Nexus files
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33 --informat INFORMAT format of the input file
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34 --outformat OUTFORMAT
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35 format of the output file
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36
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37 ### Batch processing
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38
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39 If `infile` is a directory, all files in it will be converted. In this case `informat` and `outformat` arguments are required.
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40
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41 Specifying names of the output files:
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42 * `outfile` contains a '#' character: '#' will be replaced with the base names of input files.
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43 * `outfile` is a directory: the output files will be written in it, with the same names as input files.
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44
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45 ## Supported formats
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46 * `tab`: [Internal tab format][1]
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47 * `tab_noheaders`: [Internal tab format][1] without headers
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48 * `fasta`: FASTA format
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49 * `relaxed_phylip`: relaxed Phylip format
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50 * `fasta_hapview`: FASTA format for Haplotype Viewer
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51 * `phylip`: Phylip format
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52 * `fastq`: FASTQ format
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53 * `fasta_gbexport`: FASTA format for export into Genbank repository
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54 * `nexus`: NEXUS format
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55 * `nexml`: DnaCharacterMatrix in NeXML format
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56 * `genbank`: Genbank flat file format
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57 * `mold_fasta`: FASTA format with sequence name matching requirements for the tool MolD
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58
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59 ## Recognised extension
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60 If format is not provided, the program can infer it from the file extension
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61
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62 Currently recognised:
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63 * `.tab`, `.txt`, `.tsv`: [Internal tab format][1]
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64 * `.fas`, `.fasta`, `.fna`: FASTA format
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65 * `.rel.phy`: relaxed Phylip format
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66 * `.hapv.fas`: FASTA format for Haplotype Viewer
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67 * `.phy`: Phylip format
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68 * `.fastq`, `.fq`: FASTQ format
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69 * `.fastq.gz`, `.fq.gz`: FASTQ format compressed with Gzip
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70 * `.gb.fas`: FASTA format for export into Genbank repository
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71 * `.nex`: NEXUS format
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72 * `.xml`: NeXML format
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73 * `.gb`: Genbank flat file format
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74
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75 Files with extension `.gz` are uncompressed automatically
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76
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77 ## Adding new formats
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78 [Link to documentation](docs/ADDING_FORMATS.md)
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79
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80 [1]: docs/TAB_FORMAT.md
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81
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82 ## Options
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83 DNAconvert uses two parsers for NEXUS format: internal (default) and the one from python-nexus package.
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84
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85 In the file `DNAconvert/config.json` (found in `%APPDATA%\iTaxoTools` or in `$XDG_CONFIG_HOME$/`) the key-value pair
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86 ```
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87 "nexus_parser" : "(method)""
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88 ```
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89 determines the parser. `(method)` is either `internal` or `python-nexus`.
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90
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91 ## Generating an executable
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92 Using [PyInstaller](http://www.pyinstaller.org) is recommended. You should first clone the repository and install DNAconvert with all dependencies (includes PyInstaller):
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93 ```
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94 git clone https://github.com/iTaxoTools/DNAconvert.git
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95 cd DNAconvert
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96 pip install ".[dev]"
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97 ```
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98
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99 After the following instruction, the directory `dist` will be created (among others) and the executable will be inside it:
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100 ```
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101 pyinstaller scripts/DNAconvert.spec
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102 ```
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103
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104 ## Dependencies
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105 Automatically installed when using pip:
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106 * [python\-nexus](https://pypi.org/project/python-nexus/)
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107 * [dendropy](https://pypi.org/project/DendroPy/)