File	Date	Author	Commit
LICENSE	2014-07-10	Stefano Manzini	[d1af75] Initial commit
README	2014-07-10	Stefano Manzini	[d1af75] Initial commit
dnarand.py	2014-07-10	Stefano Manzini	[d1af75] Initial commit

Read Me

dnarand, version 0.6 17/06/2014

This program produces random DNA sequences.
Author: Manzini Stefano; stefano.manzini@gmail.com

** How to use this program **
http://stefanomanzini.xoom.it/dnarand.php

usage: dnarand.py [-h] [-c ORF_LENGTH] [-C ORF_CODE] [-t GENETIC_CODE]
                      [-p] [-f] [-r GC_RATIO] [-V] [-v]
                      length lines filename

positional arguments:
  length                specifies the length of each sequence to be randomized
  lines                 specifies the number of random sequences to be generated
                        (one sequence per line)
  filename              name of the file to write to

optional arguments:
  -h, --help            show this help message and exit
  -c ORF_LENGTH, --coding ORF_LENGTH
                        determines whether there are open reading frames of a
                        specified lenght in base pairs (rounded to closest
                        integer codons) within each sequence produced, and
                        stores everything in orfs_<filename>". Open reading
                        frames are parsed using standard genetic code,
                        unless -C/--orf-code option in specified
  -C ORF_CODE, --orf-code ORF_CODE
                        if specified, tells dnarand to look for coding
                        sequences with the specified genetic code instead
                        of the standard genetic code.
  -t GENETIC_CODE, --translate-sequence GENETIC_CODE
                        translates open reading frames found using a genetic
                        code of choice, then writes the protein sequences to
                        prots_<filename>. Requires the -c/--coding option.
                        A different genetic code than the one supplied with
                        -C/--orf-code can be specified.
                        
                        The genetic_code must be specified via one of these
                        for either -C/--orf-code and -t/--translate-sequence
                        options:
                        
                        standard                          | Ncbi transl_table=1
                        vertebrate-mitochondrial          | Ncbi transl_table=2
                        yeast-mitochondrial               | Ncbi transl_table=3
                        mold-mitochondrial                | Ncbi transl_table=4
                        invertebrate-mitochondrial        | Ncbi transl_table=5
                        ciliate-nuclear                   | Ncbi transl_table=6
                        flatworm-mitochondrial            | Ncbi transl_table=9
                        euplotid-nuclear                  | Ncbi transl_table=10
                        bacterial-archaeal-plastid        | Ncbi transl_table=11
                        alternative-yeast-nuclear         | Ncbi transl_table=12
                        ascidian-mitochondrial            | Ncbi transl_table=13
                        alternative-flatworm-mitochondrial| Ncbi transl_table=14
                        chlorophycean-mitochondrial       | Ncbi transl_table=16
                        trematode-mitochondrial           | Ncbi transl_table=21
                        scenedesmus-mitochondrial         | Ncbi transl_table=22
                        thraustochytrium-mitochondrial    | Ncbi transl_table=23
                        pterobranchia-mitochondrial       | Ncbi transl_table=24
                        gracilibacteria                   | Ncbi transl_table=25
                        
                        If you are unsure what to do, you probably want
                        -t standard
                        for translating with the standard genetic code
                        
  -p, --permissive      requires -c/--coding option. If specified, tells dnarand
                        to search for open reading frames using all documented
                        initiation codons (in addition to ATG) for which there
                        is evidence in literature for the genetic code specified
  -f, --fasta           writes each sequence with a FASTA descriptor
  -r GC_RATIO, --ratio GC_RATIO
                        sets the desired GC ratio [0.00 - 100]. If none is
                        specified, default GC content is 50
  -V, --verbose         dnarand becomes verbose, and displays some information
                        about what it's doing. Turning this option off for long
                        jobs increases computation speed
  -v, --version         show program's version number and exit

** Bug reporting, feature request, any feedback **
stefano.manzini@gmail.com

** Changelog **

dnarand 0.6 release 17/06/2014
- -C/--orf-code option added. It is now possible to look for open reading frames of specified lenght within the newly produced random sequences by parsing them with the genetic code of preference, instead of only the standard genetic code. By supplying the -t option, is is then possible to translate them into proteins by using a translation table of another (or just the same) genetic code.
- -p/--permissive option added. It is now possible to look for open reading frames of specified lenght within the newly produced random sequences by parsing them with the genetic code of preference, telling dnarand to use all known translation initiation codons, instead of only ATG. More information: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c

dnarand 0.5 release 11/06/2014
- added multiple genetic codes

dnarand 0.4c release 09/06/2014
- -t/--translate-sequence option added.
- bug fix: now it is possible to run without -c/--coding option without getting an error
- bug fix: now it accepts both uppercase and lowercase input answers from the user

dnarand 0.4b release 06/06/2014
- -c/--coding option added.
- various bug fixes