SNP consensus sequence to CDS mapping
Copyright © 2013 Richard J. Edwards - See source code for GNU License Notice
See SLiMSuite Blog for further documentation. See
This module is in development. The following documentation should be considered aspirational rather than accurate!
This module is for mapping SNPs onto a genbank file (or similar feature annotation) and reporting the possible effect of SNPs in addition to more detailed output for individual genes and proteins. The main SNP output will be restricted to feature reporting and coding changes.
NOTE: At present, this does not handle indels properly, nor multiple SNPS affecting the same amino acid. It cannot deal with introns.
Primary input for this program is:
1. Reference genome sequence. This should be a DNA sequence file in which the accession numbers match the
2. A feature table with the headers:
locus feature position start end product gene_synonym note db_xref locus_tag details
If this is not given, a
3. The SNP file (
The default FTBest hierarchy for
To be added
Sequence output and recognition of BCF files to be added.
This module reads in an alignment of a coding sequence with a consensus sequence and a list of polymorphic sites
Basic SNP mapping functions
Old Options (need reviving)
Obsolete Options (roll back to pre v0.3.0 if required)
See also rje.py generic commandline options.
History Module Version History
# 0.0 - Initial Compilation. Batch mode for mapping SNPs needs updating. # 0.1 - SNP mapping against a GenBank file. # 0.2 - Fixed complement strand bug. # 0.3.0 - Updated to work with RATT(/Mummer?) snp output file. Improved docs. # 0.4.0 - Major reworking for easier updates and added functionality. (Convert to 1.0.0 when complete.) # 0.5.0 - Added CDS rating. # 0.6.0 - Added AltFT mapping mode (map features to AltLocus and AltPos) # 0.7.0 - Added additional fields for processing Snapper output. (Hopefully will still work for SAMTools etc.) # 0.8.0 - Added parsing of GFF file from Prokka. # 0.8.1 - Corrected "intron" classification for first position of features. Updated FTBest defaults. # 1.0.0 - Version that works with Snapper V1.0.0. Not really designed for standalone running any more. # 1.1.0 - Added pNS and modified the "Positive" CDS rating to be pNS < 0.05. # 1.1.1 - Updated pNS calculation to include EXT mutations and substitution frequency. # 1.2.0 - SNPByFType=T/F : Whether to output mapped SNPs by feature type (before FTBest filtering) [False] # 1.2.1 - Fixed GFF parsing bug.
SNP_Mapper REST Output formatsRun with
which is formatted as follows:
###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~### # OUTFMT: ... contents for OUTFMT section ...
Available REST OutputsThere is currently no specific help available on REST output for this program.
© 2015 RJ Edwards. Contact: firstname.lastname@example.org.