mfsizes

*** mfsizes v. 1.8.4 - 2013-06-22 - by J Program to count the size of each sequence in a FASTA file, amount of Ns per sequence, calculate the total and weighted average size for the total set of sequences, GC% for each sequence (Met proportion and total, if protein), and N50, 90 and 95. Optionally, calculate the GC content for each codon position separately. * Normal usage: mfsizes -i filename [-o outfile] [-p] [-c] [-q] [-e] * Options: -i Input FASTA file, mandatory; -o Output file (optional); -p Input sequences are protein (default: DNA); -c Calculate GC separately for each codon position (default: no); -e Ignore "empty" sequences (default: no); -q Quiet output, see below (default: detailed output); -n Do NOT sort (descrescing) sequences by size (default: sort); -v Prints program version and exits; -h Prints this help message and exits. - Order of options is irrelevant, and switches can be bundled (e.g. -cq); - If the output file is not specified (-o option), the program will generate an outfile with the same name of the input file, but with .sizes extension added; - If your sequences are protein, use the -p switch, otherwise meaningless results will be produced; - For "quiet" output (no general statistics, no comments, just each sequence's ID, size and GC or Met content), use the -q switch; - Use -e to ignore "empty" sequences (definition lines after which there is no sequence) in the output -- these sequences are never used to calculate the averages, even if not ignored, so it is safe to use the default behavior; - The -c switches on the separate codon position calculation of GC (output will also have three GC compositions for each sequence, one for each codon position). This is ignored if you use -p, and might give meaningless results if sequences are not protein coding (as well as some warnings or even errors); - The program will list each sequence's name followed by its size and percent GC (or %Met and total number of Met). At the end of the file, the average size, standard deviation and weigthed average GC (or Met). Copyright J.M.P. Alves 2003-2013 (alvesjmp@yahoo.com) This software is licensed under the GNU General Public License v. 3. Please see http://www.fsf.org/licensing/licenses/gpl.html for details.