NAME

fasconvert - Convert sequences or alignments to or from fasta format.

SYNOPSIS

fasconvert -o <format> < fasta-file > other-format file

fasconvert -i <format> < other-format-file > fasta-file

fasconvert -fo <format> fasta-file1 fasta-file2 ...

fasconvert -fi <format> other-format-file1 other-format-file2 ...

DESCRIPTION

fasconvert converts multisequence or alignment data to or from fasta format. The alternative format must be explicitly specified using an option argument to either the --input/-i option or the --output/-o option. The format specifier is a single all-lower-case word corresponding to formats supported by the Bioperl Seq::IO and Align::IO modules. By default, input is from STDIN and output is to STDOUT. With the --files/-f option, input files are converted one-by-one to corresponding output files using extensions.

Options specific to fasconvert: -i, --input <format> convert from <format> to fasta -o, --output <format> convert from fasta to <format> -f, --files input file (not from stdin) -s, --sequential for phylip output, don't interleave sequences -M, --maxlength=<integer> for phylip output, truncate identifiers to specified length

Options general to FAST: -h, --help print a brief help message --man print full documentation --version print version -l, --log create/append to logfile -L, --logname=<string> use logfile name <string> -C, --comment=<string> save comment <string> to log

INPUT AND OUTPUT

fasconvert is part of FAST, the FAST Analysis of Sequences Toolbox, based on Bioperl. Most core FAST utilities expect input and return output in multifasta format. Input can occur in one or more files or on STDIN. Output occurs to STDOUT. The FAST utility fasconvert can reformat other formats to and from multifasta format. The FAST definition of fasta encompasses both single and multifasta formats and alignments.

OPTIONS

-i [format] --input [format]

Convert file from input format to FASTA format

-o [format] --output [format]

Convert file from FASTA format to output format

-f --files

Convert file in place. File name appended with format

-s --sequential

Used when the ouput format is phylip, specifies to not interleave sequences

-M [integer] --maxlength=[integer]

Used when the output format is phylip, this option truncates the identifiers to a specified maximum length. Default: [none]

-h, --help

Print a brief help message and exit.

--man

Print the manual page and exit.

--version

Print version information and exit.

-l, --log

Creates, or appends to, a generic FAST logfile in the current working directory. The logfile records date/time of execution, full command with options and arguments, and an optional comment.

-L [string], --logname=[string]

Use [string] as the name of the logfile. Default is "FAST.log.txt".

-C [string], --comment=[string]

Include comment [string] in logfile. No comment is saved by default.

EXAMPLES

Convert ClustalW to FASTA

cat data.aln | fasconvert -i clustalw > data.fas

SEE ALSO

man perlre

perldoc perlre

Documentation on perl regular expressions.

man FAST

perldoc FAST

Introduction and cookbook for FAST

The FAST Home Page"

CITING

If you use FAST, please cite Lawrence et al. (2015). FAST: FAST Analysis of Sequences Toolbox. and Bioperl Stajich et al..