Sequence Transposition

Transpose locus alignments into per-sample sequence files. Locus alignments store one locus per file with a sequence for each sample. Transposing creates one file for each sample with a sequence for each locus. This is useful for creating sample-level reference sequences, for example, to map reads from each sample back to its own loci.

Note

This feature is available in SEGUL v0.24.0 and later versions. To check your SEGUL version, run in your terminal:

segul --version
# Compatible version example:
# segul 0.24.0

Check the Installation Guide to update SEGUL to the latest version.

Quick example

Assume we have two alignment files in FASTA format. locus_1.fas:

>sample1
AT-GC?
>sample2
ATTGCA

And locus_2.fas, which does not have sample2:

>sample1
--GGCC

To transpose the alignments, use the following command:

segul sequence transpose --dir alignments/

SEGUL creates one file for each sample. Each sequence is named after the locus it comes from, and gaps (-) and missing data (?) are removed. Sequence-Transpose/sample1/sample1.fas:

>locus_1
ATGC
>locus_2
GGCC

Sequence-Transpose/sample2/sample2.fas:

>locus_1
ATTGCA

Detailed usage

Transposing sequences

To transpose sequences, use the sequence transpose command:

segul sequence transpose --dir <alignment-dir>

The locus name is the input file name without its extension. Samples missing from a locus are skipped for that locus, so each sample file only contains the loci where the sample is present.

For amino acid sequences, use the --datatype aa option:

segul sequence transpose --dir alignments/ --datatype aa

Specifying the output directory and format

By default, the output directory is Sequence-Transpose. Each sample is written to its own folder: Sequence-Transpose/<sample>/<sample>.fas. You can change the output directory name using the --output or -o option:

segul sequence transpose --dir alignments/ --output sample-references

Because gaps are removed, the output sequences are unaligned and are always in FASTA format. Use the --output-format or -F option to choose between sequential (fasta, the default) and interleaved (fasta-int) FASTA:

segul sequence transpose --dir alignments/ --output-format fasta-int

More ways to specify input files

You can also specify input files using the --input or -i option. For example:

segul sequence transpose --input alignments/*.fasta

All options

Option	Description
-d, --dir	Directory with alignments
-i, --input	Alignment files. Allows wildcards
-f, --input-format	Input format: auto (default), fasta, nexus, or phylip
--datatype	Data type: dna (default), aa, or ignore
-F, --output-format	Output format: fasta (default) or fasta-int
-o, --output	Output directory. Default: Sequence-Transpose
--force	Overwrite an existing output directory
--log	Log file path. Default: segul.log