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Goalign: toolkit and api for alignment manipulation

Commands

rename

This command renames all sequences of the input alignment (fasta or phylip) in 3 ways:

  • Using a map file. The map file is tab separated, with the following fields:

    1. Current name of sequence
    2. New name of the sequence

    If option --revert is given, it is the other way.

    Note:

    • If a sequence name does not appear in the map file, it will not be renamed;
    • If a name that does not exist appears in the map file, it will not do anything;
    • If input is in Phylip format with several alignments, all of them will be renamed.

  • Using a regexp (-e|--regexp) and a replacement string (-b|--replace): will replace matching strings in sequence names by string given by -b, ex: goalign rename -i align.fasta --regexp 'Seq(\d+)' --replace 'Newname$1' -m map.txt this will replace all matches of 'Seq(\d+)' with 'NewName$1', with $1 being the matched string inside ().

  • With --clean-names option: Special characters in sequence names are replaced with '-'. Special characters are: \s\t[]();.,:|. And mapping between old and new names is written in the file potentially given with --map-file

In any case, option --unalign option will rename unaligned fasta files while ignoring formatting options (phylip, etc.).

Usage

Usage:
  goalign rename [flags]

Flags:
  --clean-names           Replaces special characters (tabs, spaces, newick characters)
                          with '-' from input sequence names before writing output alignment
  -h, --help              help for rename
  -m, --map-file string   Name Mapping infile (default "none")
  -o, --output string     renamed alignment output file (default "stdout")
  -e, --regexp string     rename alignment using given regexp (default "none")
  -b, --replace string    replaces regexp matching strings by this string (default "none")
  -r, --revert            Reverse orientation of mapfile

Global Flags:
  -i, --align string    Alignment input file (default "stdin")
      --auto-detect     Auto detects input format (overrides -p and -x)
      --input-strict    Strict phylip input format (only used with -p)
  -x, --nexus           Alignment is in nexus? default fasta
      --output-strict   Strict phylip output format (only used with -p)
  -p, --phylip          Alignment is in phylip? default fasta

Examples

  • Generating a random alignment and renaming sequences:
echo -e "Seq0000\tNewSeq" > map
goalign random -n 3 --seed 10 -l 10 | goalign rename -m map

It should give the following alignment:

>NewSeq
GATTAATTTG
>Seq0001
CCGTAGGCCA
>Seq0002
GAATCTGAAG
  • Generating a random alignment and renaming sequences with a regex:
goalign random -n 3 --seed 10 -l 10 | goalign rename --regexp 'Seq' --replace 'NewSeq' -m map.txt

It should give the following alignment:

>NewSeq0000
GATTAATTTG
>NewSeq0001
CCGTAGGCCA
>NewSeq0002
GAATCTGAAG
  • Cleaning input sequence names
input.fa
> S e q 0 0 00[]();.,
GATTA
> Se    q00 0 2  []();.,
CCGTA
>  Seq00  03[]();.,
GGCCA
>Se  q[]();.,0004
GAATC

goalign rename --clean-names -i input.fa

It should give the following alignment:

>S-e-q-0-0-00-
GATTA
>Se-q00-0-2-
CCGTA
>Seq00-03-
GGCCA
>Se-q-0004
GAATC