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Goalign: toolkit and api for alignment manipulation

Commands

mask

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

It takes an alignment and replaces positions defined by start (0-based inclusive) and length by N (nucleotide alignment) or X (amino-acid alignment).

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.

The output format is the same than input format.

Usage

Usage:
  goalign mask [flags]

Flags:
  -h, --help            help for mask
  -l, --length int      Length of the sub alignment (default 10)
  -o, --output string   Alignment output file (default "stdout")
  -s, --start int       Start position (0-based inclusive)

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
      --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