This command samples sites or sequences from an input alignment (fasta by default or phylip with -p):
goalign sample sites: take a random subalignment from the input alignment. If --consecutive is true, then a start position is randomly chosen, and the next "length" positions are extracted. Otherwise, if consecutive is false, then "length" positions are sampled without replacement from the original alignment (any order);goalign sample seqs: take a random subset of the sequences from an input alignment;goalign sample rarefy: Take a new sample taking into accounts counts. Each sequence in the alignment has associated counts. The sum s of the counts represents the number of sequences in the underlying initial dataset. The goal is to downsample (rarefy) the initial dataset, by sampling n sequences from s (n<s), and taking the alignment corresponding to this new sample, i.e by taking only unique (different) sequences from it.
If the input alignment contains several alignments (phylip), will process all of them.
- general command:
Available Commands:
rarefy Takes a new sample taking into accounts weights
seqs Samples a subset of sequences from the input alignment
sites Takes a random subalignment
Flags:
-h, --help help for sample
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 same sequences
--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
--seed int Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)
- seqs command
Usage:
goalign sample seqs [flags]
Flags:
-h, --help help for seqs
-s, --nb-samples int Number of samples to generate (default 1)
-n, --nb-seq int Number of sequences to sample from the alignment (default 1)
-o, --output string Sampled alignment output file (default "stdout")
--unaligned Considers sequences as unaligned and format fasta (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
--ignore-identical int Ignore duplicated sequences that have the same name and same sequences
--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
--seed int Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)
- sites command
Usage:
goalign sample sites [flags]
Flags:
--consecutive If sampled sites are consecutive (inactivate with --consecutive=false) (default true)
-h, --help help for sites
-l, --length int Length of the random sub alignment (default 10)
-n, --nsamples int Number of samples to generate (default 1)
-o, --output string Alignment output file (default "stdout")
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 same sequences
--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
--seed int Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)
- rarefy command
Usage:
goalign sample rarefy [flags]
Flags:
-c, --counts string Count file (tab separated), one line per sequence: seqname\tcount (default "stdin")
-h, --help help for rarefy
-n, --nb-seq int Number of sequences to sample from the repeated dataset (from counts) (default 1)
-o, --output string Rarefied alignment output file (default "stdout")
-r, --replicates int Number of replicates to generate (default 1)
--unaligned Considers sequences as unaligned and format fasta (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
--ignore-identical int Ignore duplicated sequences that have the same name and same sequences
--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
--seed int Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)
- Generating a random alignment and taking a subset of the sequences
goalign random -l 10 --seed 10 | goalign sample seqs -n 3 --seed 10
Should give the following alignment:
>Seq0001
CCGTAGGCCA
>Seq0002
GAATCTGAAG
>Seq0008
TTTAAACACT
- Generating a random alignment and taking a subsequence from it
goalign random -l 10 --seed 10 | goalign sample sites -l 5 --seed 10
Should give the following alignment:
>Seq0000
TTAAT
>Seq0001
GTAGG
>Seq0002
ATCTG
>Seq0003
CGAAC
>Seq0004
AAGTT
>Seq0005
TTCTA
>Seq0006
GAGGA
>Seq0007
TCATA
>Seq0008
TAAAC
>Seq0009
TACAT