Goalign: toolkit and api for alignment manipulation

Commands

replace

This command replaces characters in sequences of an input alignment. The --regexp (-e) option considers the string to be replaced as a regular expression. Unless --unalignedis specified, the replacement should not change sequence lengths, otherwise it returns an error.

If --posfile is given, then --old and --new are not considered. Instead, characters at sites+sequences specified in the input file are replaced in the alignement. The format of the input posfile is tabulated with columns:

• 0: sequence name
• 1: site index
• 2: new character

Usage

Usage:
  goalign replace [flags]

Flags:
  -h, --help            help for replace
  -n, --new string      New string that will replace old string in sequences (default "none")
  -s, --old string      String to replace in the sequences (default "none")
  -o, --output string   Output alignment file (default "stdout")
  -e, --regexp          Considers Replace alignment using regexp
  -f, --posfile string  File containing sites to replace by give characters in given sequences (deactivates --old & --new) (default "none")
      --unaligned       Considers input sequences as unaligned and fasta format (phylip, nexus,... options 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
      --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

• Replacing all `` with --- (regex):

Input alignment:

   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 replace -s 'GA.' -n '---' -e -p -i input -o result

It should give the following alignment:

   10   20
Seq0000  ---TAATTTG CCGTAGGCCA
Seq0001  ---TCT---- --C---CACT
Seq0002  TTAAGTTTTC ACTTCTAATG
Seq0003  ---AG---TA GTTCATACTT
Seq0004  TTTAAACACT TTTACATCGA
Seq0005  TGTCG---CT AAGTATT---
Seq0006  TACAACGGTG TATTCCAGCG
Seq0007  GTG---AGGT CTATTTTTCC
Seq0008  GGTT---G-- -TCTA---CT
Seq0009  GTAAAGGGTA TGGCCATGTG

replace stops

Replace STOP codons in input nt sequences by NNN, in the given phase (except the last codon).

If --phase is given (>=0), then starts at the given offset (default=0)

Usage:
  goalign replace stops [flags]

Flags:
      --genetic-code string   Genetic Code: standard, mitoi (invertebrate mitochondrial) or mitov (vertebrate mitochondrial) (default "standard")
  -h, --help                  help for stops
      --phase int             Phase in which replace STOP codons

Global Flags:
  -i, --align string           Alignment input file (default "stdin")
      --alphabet string        Alignment/Sequences alphabet: auto (default), aa, or nt (default "auto")
      --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)
  -o, --output string          Output alignment file (default "stdout")
      --output-strict          Strict phylip output format (only used with -p)
  -p, --phylip                 Alignment is in phylip? default fasta
  -k, --stockholm              Alignment is in stockholm? default fasta
      --unaligned              Considers input sequences as unaligned and fasta format (phylip, nexus,... options are ignored)