NAME

alignment-find - Extract the first or last FASTA alignment from a stream.

SYNOPSIS

alignment-find [OPTIONS] < alignments-file > alignment.fasta

DESCRIPTION

Read standard input and write one alignment in FASTA format to standard output. By default, select the last alignment; use --first to select the first. Input filenames are not command-line arguments: use shell input redirection or a pipe.

An alignment starts with a FASTA header whose first character is > and ends at an empty line or the end of input. Separate successive alignments with empty lines. Text before an alignment, or between alignments, is skipped while searching for the next header. This allows extraction from a stream containing sample labels and FASTA alignment blocks. PHYLIP input is not supported by this tool.

Sequence letters are converted to uppercase, and spaces and tabs within sequences are removed. Sequence lengths and all columns are preserved, including columns containing only -, ?, or =. Symbols are not interpreted using an alphabet. The output is FASTA with normalized formatting.

With --first, reading stops after the first alignment. With --last, the stream is read until its end or an alignment cannot be loaded. A loading error produces a warning on standard error and stops the search; if an earlier alignment was successfully loaded, that alignment is returned. Thus successful exit does not necessarily mean that every input alignment was valid. If no alignment was loaded, the program reports an error.

OPTIONS

-h, --help

Print usage information and exit.

--first

Select the first alignment. Cannot be combined with --last.

--last

Select the last successfully loaded alignment. This is the default when neither selection flag is given. Cannot be combined with --first.

EXAMPLES

Extract the last alignment in a sample file:

alignment-find < samples.fastas > last.fasta

Extract the first alignment:

alignment-find --first < samples.fastas > first.fasta

Convert the selected alignment to PHYLIP:

alignment-find < samples.fastas | alignment-cat -o phylip > last.phy

EXIT STATUS

Returns 0 on success (including --help) and 1 when an error is reported. Warnings and error messages are written to standard error.

SEE ALSO

alignment-cat(1), alignment-chop-internal(1), cut-range(1)

REPORTING BUGS

BAli-Phy online help: http://www.bali-phy.org/docs.php.

Please send bug reports to bali-phy-users@googlegroups.com.