ufasta: utility to handle fasta files

Compilation

./configure
make
make install

If compiling from the git tree, first run autoreconf -fi.

For the grep sub-commands to work, the BOOST regexp library must be installed.

Usage

ufasta -h gives the list of subcommands: one, sizes, head, tail, rc, n50, stats, extract, format, hsort, sort, dsort, rsort, hgrep, dgrep, split. Similarly every subcommand has its own help. Here is a quick description of the subcommands:

• one: remove the new lines in the data section. Hence, all the sequences are written on one line. In some sense, it is the opposite of the format subcommand.
• format: reformat the data sections. The data is written in lines of the same length, it can changes the content in upper/lower case.
• sizes: print the amount of sequence in each section
• head: like UNIX head. Display the first 10 sequences
• tail: like UNIX tail. Display the last 10 sequences
• rc: reverse complement every sequence
• n50, stats: display stats about the sequences: N50, E size, total size, etc.
• extract: extract a sequence whose header match given names
• hsort, sort: sort file based on header content
• dsort: sort the data sections
• hgreap: output sequences whose header match the regular expression (if BOOST regexp available)
• dgresp: output sequences whose sequence match the regular expression (if BOOST regexp available)
• split: split a fasta file into many files