fasconvert - Convert sequences or alignments to or from fasta format.
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 ...
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
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.
Convert file from input format to FASTA format
Convert file from FASTA format to output format
Convert file in place. File name appended with format
Used when the ouput format is phylip, specifies to not interleave sequences
Used when the output format is phylip, this option truncates the identifiers to a specified maximum length. Default: [none]
Print a brief help message and exit.
Print the manual page and exit.
Print version information and exit.
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.
Use [string] as the name of the logfile. Default is "FAST.log.txt".
Include comment [string] in logfile. No comment is saved by default.
Convert ClustalW to FASTA
cat data.aln | fasconvert -i clustalw > data.fas
man perlre
perldoc perlre
Documentation on perl regular expressions.
man FAST
perldoc FAST
Introduction and cookbook for FAST
If you use FAST, please cite Lawrence et al. (2015). FAST: FAST Analysis of Sequences Toolbox. and Bioperl Stajich et al..
To install FAST, copy and paste the appropriate command in to your terminal.
cpanm
cpanm FAST
CPAN shell
perl -MCPAN -e shell install FAST
For more information on module installation, please visit the detailed CPAN module installation guide.