dnarand, version 0.6b 17/07/2014
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: dnarand0.6b.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
-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
coding DNA options:
-c/--coding option can be further customized with these options:
-C ORF_CODE, --orf-code ORF_CODE
requires the -c/--coding option. 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
requires the -c/--coding option. Translates open
reading frames found using a genetic code of choice,
then writes the protein sequences to prots_<filename>.
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
** Bug reporting, feature request, any feedback **
stefano.manzini@gmail.com
** Changelog **
dnarand 0.6b release 17/07/2014
- bug fix: -C option now explicitly requires -c option and does not end the program weirdly if invoked without -c
- now all of the options depending on -c/--coding have been grouped for enhanced help readability
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 length 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
