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Goalign: toolkit and api for alignment manipulation

Commands

subseq

This command takes a sub-alignment (slice) from the input alignment.

It takes an alignment and extracts sub-sequences from it, given a start position (0-based inclusive) and a length. If the length is after the end of the alignment, will stop at the end of the alignment.

(start,length) can be specified on the alignment coordinate system (default) or on a given sequence coordinate system without gaps (--ref-seq). It allows to extract sub alignment by just knowing coordinates on a given unaligned sequence.

For example:

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

This will extract a sub-alignment going from 10th position of the alignemnt, with a length of 10.

The output format is the same than input format.

If --ref-seq <name> is specified, then the coordinates are specified on the given sequence coordinate system without considering gaps.

For example:

If al.fa is:

>s1
--ACG--AT-GC
>s2
GGACGTTATCGC

Then:

goalign subseq -i al.fa -s 0 -l 4 --ref-seq s1

will output:

>s1
ACG--A
>s2
ACGTTA

--ref-seq is currently not not compatible with --step

Sliding window:

If --step is given and > 0, then Several sub-alignments will be produced, and corresponding to all alignments in windows of sizes -l, and with starts: [start, start+step, ..., end-length].

Example with an alignment al.phy of size 10 (0123456789)

goalign subseq -i al.phy -s 0 -l 5 --step 1

will produce alignments with positions:

01234
 12345
  23456
   34567
    45678
     56789

Warning: If output is stdout, it works only if input format is Phylip, because it is possible to split alignments afterwards (with goalign divide for example).

--step is currently not compatible with --ref-seq.

Several alignments:

If several alignments are present in the input file and the output is a file (not stdout or -) , then :

  • First alignment, first subalignment: results will be placed in the given file (ex out.fasta)
  • First alignment, other subalignments (sliding windows): results will be placed in file with the given name with _sub<i> suffix (ex: out_sub1.fasta, out_sub2.fasta, etc.)
  • Other alignments, first subalignment: results will be placed in the given file with _al<i> suffix (ex out_al1.fasta, out_al2.fasta, etc.)
  • Other alignments, other subalignments: results will be placed in the given file with _al<i> and _sub<i> suffixes (ex out_al1_sub1.fasta, out_al1_sub2.fasta, etc.)

In any case:

If --reverse is given, all positions but the given subsequence is output. In case of a sliding window, it will correspond to sliding subsequence "deletion". In case of reference sequence coordinates, the subsequence is first computed, then all positions of the alignment but this subsequence are given in output.

Usage

Usage:
  goalign subseq [flags]
  
Flags:
  -l, --length int      Length of the sub alignment (default 10)
  -o, --output string   Alignment output file (default "stdout")
  -s, --start int       Start position
      --step int        Step: If > 0, then will generate several alignments, 
                        for each window of length l, with starts: 
                        [start,start+step, ..., end-l]*

Global Flags:
  -i, --align string   Alignment input file (default "stdin")
  -p, --phylip         Alignment is in phylip? False=Fasta
  --input-strict       Strict phylip input format (only used with -p)
  --output-strict      Strict phylip output format  (only used with -p)

Examples

  • Generating a random alignment and taking a sub-alignment of length 10 from position 5:
goalign random -n 4 --seed 10 -l 100 | goalign subseq -l 10 -s 5

It should give the following alignment:

>Seq0000
ATTTGCCGTA
>Seq0001
GACCTAAGTA
>Seq0002
CGCGGGCGGA
>Seq0003
GAGGCTTTAT