Alignment Conversion
Segul can convert a single file, multiple file in the same directory, or multiple files in multiple directory.
Converting a single file
To convert a single file, use the --input or -i.
segul align convert --input [a-path-to-file] --output-format [sequence-format]
segul should be able to infer the input file format based on the extension of your file. If your file extension is uncommon (for example .aln instead of .fas), specify the --input-format:
segul align convert --input [a-path-to-file] --input-format [sequence-format] --output-format [sequence-format]
For example, here we will convert a nexus file containing DNA sequence named loci.nexus to fasta format:
segul align convert --input alignments/loci.nexus -output-format fasta
You can ignore specifying the output format if you would like the output files in nexus format. For example, we will convert loci.fasta to nexus format:
segul align convert --input alignments/loci.fasta
Some segul arguments available in short format, notice the uppercase 'F' for the output format:
segul align convert -i alignments/loci.nexus -f nexus -F fasta --datatype aa -o alignment-fasta
Note that, when converting alignments,
segulwill only change the file extension and will maintain the original file names for the output files. This behavior is the same for a single or multiple file format conversion. This way it gives the app the flexibility to convert many files in a single command.
Batch converting sequence files in a directory
We have to option to provide the input files to the progam. First, using the --dir or -d input. For a directory input, it is required to specify the --input-format:
segul align convert --dir [path-to-your-repository] --input-format [sequence-format] --output [your-output-dir-name] --output-format [sequence-format]
In short format:
segul align convert -d [path-to-your-repository] -f [sequence-format] -o [your-output-dir-name]
For example, suppose we want to convert all the nexus files in the directory below to fasta formats and name the output directory alignments-fas:
alignments/
├── locus_1.nexus
├── locus_2.nexus
└── locus_3.nexus
The command will be:
segul align convert -d alignments/ -f nexus -F fasta -o alignments-fas
We can also input wildcard (*) using the --input or -i option to achieve the same results:
segul align convert -i alignments/*.nexus -f nexus -F fasta -o alignments-fas
The outputs will be:
alignments-fas/
├── locus_1.fas
├── locus_2.fas
└── locus_3.fas
Batch converting multiple files in multiple directories
To convert multiple files in multiple directories, we will inputs multiple paths with wildcards and use the --input or -i option:
segul align convert -i [wildcard-1] [wildcard-2] [wildcard-3] -o [your-output-dir-name]
For example:
segul align convert -i alignments-1/*.nexus alignments-2/*.nexus alignments-3/*.nexus -F fasta -o alignments-fas
You can also convert multiple files in different formats. Because segul maintain the original file name for the output, the filename for each input file should be unique regardless of the extension. Otherwise, segul will failed to write the output.
For example:
segul align convert -i alignments-1/*.nexus alignments-2/*.fasta alignments-3/*.fasta -F phylip -o alignments-phylip
Depending on the size of your RAM, you can provide as many input paths as possible. The output files, however, will all be saved in the same directory.
Converting amino acid sequences
By default, segul datatype is set for converting DNA sequence. If your file contains amino acid sequence, use the argument --datatype aa. For example:
segul align convert --input alignments/loci.nexus -output-format fasta --datatype aa
Specifying the output directory
By default segul will write the result in a directory called SEGUL-convert. If you would like to specify the output directory, use the --output argument. For example, here we will specify the output directory to alignment-fasta.
segul align convert --input alignments/loci -output-format fasta --datatype aa --output alignment-fasta
Sorting the output sequences
By default, segul maintain the original order of the sequences in the input file(s). Using the --sort flag, you can sort the sequences in alphabetical order based on their IDs:
segul align convert --input alignments/loci -output-format fasta --datatype aa --output alignment-fasta --sort
Terminal output for file conversion
For sequence format conversion, segul terminal output consists of three parts. The first part is the input information. It contains information from your command input. The second part is the spinner. It will show you the state of the program as it is processing the file. The third part is the output information. It shows the information of the output directory relative to the current working directory, the output format, and the log file path. With the exception of the spinner (include the spinning emoji and its text), all the terminal output is written into the log file.
Below is an example of terminal output when you use the argument --input or -i to input the files:
=========================================================
SEGUL v0.11.1
An alignment tool for phylogenomics
---------------------------------------------------------
Input : STDIN
File counts : 1
Input format : Auto
Data type : DNA
Task : Sequence format conversion
🌘 Finished converting sequence format!
Output
Output dir : SEGUL-Convert
Output format : Nexus Sequential
Log file : segul.log
Execution time : 9.7194ms
For --dir or -d input, notice the input file path is printed in the terminal:
=========================================================
SEGUL v0.11.1
An alignment tool for phylogenomics
---------------------------------------------------------
Input dir : align-fas/
File counts : 1
Input format : Fasta
Data type : DNA
Task : Sequence format conversion
🌘 Finished converting sequence format!
Output
Output dir : SEGUL-Convert
Output format : Nexus Sequential
Log file : segul.log
Execution time : 13.5741ms