Metadata-Version: 1.0
Name: revtrans
Version: 1.4
Summary: revtrans - performs a reverse translation of a peptide alignment
Home-page: http://pypi.python.org/pypi/revtrans
Author: Rasmus Wernersson
Author-email: UNKNOWN
License: GNU General Public License 2
Description: 
        NAME
        	revtrans - performs a reverse translation of a peptide alignment
        
        SYNOPSIS
        	revtrans dnafile pepfile [-v] [-h] [-gapin chars] [-gapout char]
        	 [-Idna format] [-Ipep format] [-mtx tablename/file] [-match method]
        	 [-O format] [outfile]
        
        DESCRIPTION
               Reads a set of aligned peptide sequences from pepfile and uses
               the corresponding DNA sequences from dnafile to construct a
               reverse translated version of the alignment.
        
               By default the input file formats are auto detected and the
               corresponding DNA and peptide sequences is found by translation.
        
               In the typical case this means that the user only need to
               supply the DNA and peptide sequences, and may safely ignore
               the more advanced options. E.g :
        
        	       revtrans kinases.dna.fsa kinases.prot.aln
        
               The final alignment is written to STDOUT or outfile if specified,
               and is by default in FASTA format.
        
        OPTIONS
        	-h
        		Help. Print this help information.
        
        	-gapin chars
        		Specify gap characters in the input sequences.
        		Default is '.-~'
        
        	-gapout	char
        		Specify which character should be used for gaps in the
        		output.
        		Default is '-'
        
        	-Idna format
        		Specify format of the input DNA file.
        		Valid formats are: auto (default), fasta, msf and aln
        
        	-Ipep format
        		Specify format of the input peptide file.
        		Valid formats are: auto (default), fasta, msf and aln
        
        	-O format
        		Specify format of the output file.
        		Valid formats are: fasta (default), msf and aln
        
        	-mtx tablename/file
        		Use alternative translation matrix instead of the build-in
        		Standard Genetic Code for translation.
        
        		If "tablename" is 1-6,9-16 or 21-23 one of the alternative
        		translation tables defined by the NCBI taxonomy group will be
        		used.
        
        		Briefly, the following tables are defined:
        		-----------------------------------------
        		 1: The Standard Code
        		 2: The Vertebrate Mitochondrial Code
        		 3: The Yeast Mitochondrial Code
        		 4: The Mold, Protozoan, and Coelenterate Mitochondrial Code
        		    and the Mycoplasma/Spiroplasma Code
        		 5: The Invertebrate Mitochondrial Code
        		 6: The Ciliate, Dasycladacean and Hexamita Nuclear Code
        		 9: The Echinoderm and Flatworm Mitochondrial Code
        		10: The Euplotid Nuclear Code
        		11: The Bacterial and Plant Plastid Code
        		12: The Alternative Yeast Nuclear Code
        		13: The Ascidian Mitochondrial Code
        		14: The Alternative Flatworm Mitochondrial Code
        		15: Blepharisma Nuclear Code
        		16: Chlorophycean Mitochondrial Code
        		21: Trematode Mitochondrial Code
        		22: Scenedesmus obliquus mitochondrial Code
        		23: Thraustochytrium Mitochondrial Code
        
        		See http://www.ncbi.nlm.nih.gov/Taxonomy [Genetic Codes]
        		for a detailed description. Please notice that the table
        		of start codons is also used (see the -allinternal option
        		below for details).
        
        		If a filename is supplied the translation table is read from
        		file instead.
        
        		The file should contain one line per codon in the format:
        
        		codon<whitespace>aa-single letter code
        
        		All 64 codons must be included. Stop codons is specified
        		by "*". T and U is interchangeable. Blank lines and lines
        		starting with "#" are ignored.
        
        		See the "gcMitVertebrate.mtx" file in the RevTrans source
        		distribution for a well documented example.
        
        	-allinternal
        		By default the very first codon in each sequences is assumed
        		to be the initial codon on the transcript. This means certain
        		non-methionine codons actually codes for metionine at this
        		position. For example "TTG" in the standard genetic code (see
        		above).
        
        		Selecting this option treats all codons as internal codons.
        
        	-readthroughstop
        		Allow the translation to continue after a stop codon is reached.
        		The stop codon will be marked as "*".
        
        		Be careful that stop codons have been addressed in the same manner
        		in the input peptide alignment.
        
        	-match method
        		Specify how to match the corresponding DNA and peptide
        		sequences. Valid methods are: trans (default), name and pos.
        
        		Please note that both DNA and peptide sequence should have
        		unique names, regardless of the matching method.
        
        		trans:
        			Match sequences by translation. The DNA sequences are
        			translated using the standard genetic code (default)
        			or an alternative translation matrix if the -mtx
        			option is used.
        
        		name:
        			Match sequences by name. Please note that for FASTA
        			files everything after the ">" is considered the
        			sequence name.
        
        		pos:
        			Match by position. The sequence are matched by position
        			in the files (first DNA sequence with first peptide
        			sequence etc.).
        	-v
        		Verbose. Print extra information about files, sequences
        		and the progress in general to STDERR.
        
        		The verbose level can be set to three degrees of
        		detail.
        
        		-v:   verbose level 1
        			Info about files, number of sequences read etc.
        			Use this as the first try if something needs
        			investigation.
        
        		-vv:  verbose level 2
        			As level 1 +
        			Print detailed info about all the sequence names.
        
        		-vvv: verbose level 3
        			As level 2 +
        			Do a sanity check on the degapped length of the
        			sequences. Warn if the sizes do not match.
        
        AUTHOR
        	Rasmus Wernersson, raz@cbs.dtu.dk
        	September 2002, February 2003, July 2004, April 2005
        
        FILES
        	revtrans.py, mod_translate.py, mod_seqfiles.py,
        	ncbi_genetic_codes.py
        
        WEB PAGE
        	http://www.cbs.dtu.dk/services/RevTrans/
        
        REFERENCE
        	Rasmus Wernersson and Anders Gorm Pedersen.
        	RevTrans - Constructing alignments of coding DNA from aligned amino
        	acid sequences.
        	Nucl. Acids Res., 2003, 31(13), 3537-3539.
        
Platform: UNKNOWN
