update May 16, 2013

NAME

gstat.py - calculate protein statistics

SYNOPSIS

DESCRIPTION

  Calculates the following statistics from protein sequences in a FASTA file

           1. the molecular weight of each protein.
           2. the theoretical pI value of each protein.
           3. the composition of each amino acid.
           4. the total number of amino acids in each protein

OPTIONS

Options:
  -kda     --- display molecular weights in kDa
  -img     --- display locus tags from IMG/ER FASTA files
  -aacount --- perform an amino acid count for each sequence
  -tsv     --- presents the output in a TSV format

EXAMPLES:
      gstat.py ecoli-k12.fsa
      gstat.py -kda ecoli-k12.fsa > data_save.csv
      gstat.py -img ecoli-k12.fsa ecoli-plasmid1.fsa
      gstat.py -kda -img ecoli-k12.fsa ecoli-plasmid1.fsa > data_save.csv

INPUT

Input is a file containing one or more proteins in FASTA format.

   The output of the program is CSV (tab delimited) via stdout.
    The columns outputted are as follows:

      NAME    Mol. Wt.    pI    COMPOSITION    SEQUENCE

    IF you are using multiple files, this program will print all
    of the sequences in succession to standard output.

NOTES

AUTHOR

Graham Alvare
Department of Plant Science
University of Manitoba
Winnipeg, MB  Canada R3T 2N2
alvare@cc.umanitoba.ca
http://home.cc.umanitoba.ca/~alvare

ACKNOWLEDGEMENTS/CO-AUTHORS
    Dr. Brian Fristensky - my work supervisor, and the man who introduced
                           me to the wonderful field of bioinformatics.
    Lukasz Kozlowski - bisection Henderson-Hasselbach algorithm
                       for determining the theoretical pI of proteins
                           Kozlowski L. 2007-2012 Isoelectric Point Calculator.
                       http://isoelectric.ovh.org
    Dr. Abby Perrill - amino acid pKa table
                           http://www.cem.msu.edu/~cem252/sp97/ch24/ch24aa.html

 QUESTIONS & COMMENTS
    If you have any questions, please contact me: alvare@cc.umanitoba.ca
    I usually get back to people within 1-2 weekdays (weekends, I am slower)

    P.S. please also let me know of any bugs, or if you have any suggestions
         I am generally happy to help create new tools, or modify my existing
         tools to make them more useful.

LICENSE
    This code is licensed under the Creative Commons 3.0
    Attribution + ShareAlike license - for details see:
       http://creativecommons.org/licenses/by-sa/3.0/