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Goalign: toolkit and api for alignment manipulation

Commands

mask

Mask a part of the input alignment (replace by N|X or a specified character)

It takes an alignment and replaces some characters by "N" or "X" by default.

By default, it masks positions defined by start (0-based inclusive) and length with N (nucleotide alignment) or X (amino-acid alignment) by default. If the length is after the end of the alignment, will stop at the end of the alignment.

For example:

goalign mask -p -i al.phy -s 9 -l 10

This will replace 10 positions with N|X from the 10th position.

If --no-gaps is specified, then does not replace gaps.

If --no-ref is specified, then does not replace the character if it is the same as the reference sequences (only with --ref-seq).

If --ref-seq is specified, then coordinates are considered on the given reference sequence without considering gaps. In that case, if the range of masked sites incorporates gaps in the reference sequence, these gaps will also be masked in the output alignment.

If --unique is specified, goalign mask --unique will replace characters that are unique (defined by --at-most option) in their column (except GAPS) with N or X. In that case, if --ref-seq option is given, then a unique character is masked if: 1) It is different from the given reference sequence 2) Or the reference is a GAP In this case, --length, --start, and --no-gaps, --no-ref are ignored.

Option --replace defines the replacement character. If --replace is "" (default), then, masked characters are replaced by "N" or "X" depending on the alphabet. Orherwise:

  1. if --replace is AMBIG: just like ""
  2. if --replace is MAJ: Masked characters are replaced by the most frequent character of the column (without considering the reference sequence when --ref-seq is given)
  3. if --replace is GAP: Replacing character is a GAP

The output format is the same than input format.

Usage

Usage:
  goalign mask [flags]

Flags:
      --at-most int      The number of occurences that defines the uniqueness of the characher in the column (only used with --unique) (default 1)
  -h, --help             help for mask
  -l, --length int       Length of the sub alignment (default 10)
      --no-gaps          Do not mask gaps (has no effect on --unique --at-most options, for which gaps are not taken into account anyway)
      --no-ref           Do not mask if same as reference (only with --ref-seq, and has no effect on --unique --at-most options
  -o, --output string    Alignment output file (default "stdout")
      --ref-seq string   Coordinates are considered wrt. to the given reference sequence (with --unique, it masks unique characters that are different from the reference sequence) (default "none")
      --replace string   Replacement character. If AMBIG: N or X (depending on alphabet), if GAP: -, if MAJ: the main character of the column, or can be any other character (default "AMBIG")
  -s, --start int        Start position (0-based inclusive)
      --unique           If given, then masks characters that are unique (defined with --at-most) in their columns (start and length are ignored)

Global Flags:
  -i, --align string           Alignment input file (default "stdin")
      --auto-detect            Auto detects input format (overrides -p, -x and -u)
  -u, --clustal                Alignment is in clustal? default fasta
      --ignore-identical int   Ignore duplicated sequences that have the same name and potentially have same sequences, 0 : Does not ignore anything, 1: Ignore sequences having the same name (keep the first one whatever their sequence), 2: Ignore sequences having the same name and the same sequence
      --input-strict           Strict phylip input format (only used with -p)
  -x, --nexus                  Alignment is in nexus? default fasta
      --no-block               Write Phylip sequences without space separated blocks (only used with -p)
      --one-line               Write Phylip sequences on 1 line (only used with -p)
      --output-strict          Strict phylip output format (only used with -p)
  -p, --phylip                 Alignment is in phylip? default fasta

Examples

align.phy :

   10   20
Seq0000  GATTAATTTG CCGTAGGCCA
Seq0001  GAATCTGAAG ATCGAACACT
Seq0002  TTAAGTTTTC ACTTCTAATG
Seq0003  GAGAGGACTA GTTCATACTT
Seq0004  TTTAAACACT TTTACATCGA
Seq0005  TGTCGGACCT AAGTATTGAG
Seq0006  TACAACGGTG TATTCCAGCG
Seq0007  GTGGAGAGGT CTATTTTTCC
Seq0008  GGTTGAAGGA CTCTAGAGCT
Seq0009  GTAAAGGGTA TGGCCATGTG

goalign mask -i align.phy -p -s 0 -l 2

Should print:

   10   20
Seq0000  NNTTAATTTG CCGTAGGCCA
Seq0001  NNATCTGAAG ATCGAACACT
Seq0002  NNAAGTTTTC ACTTCTAATG
Seq0003  NNGAGGACTA GTTCATACTT
Seq0004  NNTAAACACT TTTACATCGA
Seq0005  NNTCGGACCT AAGTATTGAG
Seq0006  NNCAACGGTG TATTCCAGCG
Seq0007  NNGGAGAGGT CTATTTTTCC
Seq0008  NNTTGAAGGA CTCTAGAGCT
Seq0009  NNAAAGGGTA TGGCCATGTG