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rje_genbank V1.5.2

RJE GenBank Module

Module: rje_genbank
Description: RJE GenBank Module
Version: 1.5.2
Last Edit: 05/09/16

Copyright © 2011 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_db rje_obj rje_sequence rje_taxonomy rje_zen


See SLiMSuite Blog for further documentation.

Function

This module is for parsing information out of GenBank files and converting them to other formats.

Input Options

seqin=FILE : Input Genbank file []
fetchuid=LIST : Genbank retrieval to of a list of nucleotide entries to generate seqin=FILE []
spcode=X : Overwrite species read from file (if any!) with X [None]
taxdir=PATH : Path to taxonomy files for species code extraction. (Will not use if blank or None) [./SourceData/]
addtags=T/F : Add locus_tag identifiers if missing - needed for gene/cds/prot fasta output [False]

Output Options

basefile=FILE : Root of output file names (same as input file by default) []
tabout=T/F : Delimited table output of features [False]
features=LIST : Subset of features to extract from Genbank file (blank for all) []
details=LIST : List of feature details to extract into own columns []
detailskip=LIST : Subset of feature details to exclude from extraction [translation]
fasout=LIST : Types of sequences to output into files (full/gene/cds/prot) as *.*.fas []
geneacc=X : Feature detail to use for gene sequence accession number (added to details) [locus_tag]
protacc=X : Feature detail to use for protein sequence accession number (added to details) [protein_id]
locusout=T/F : Whether to generate output by locus (True, locus as basefile) or combined (False) [False]
locusdir=PATH : Directory in which to generate output by locus [./]

See also rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - Modified and Tidied output a little.
    # 0.2 - Added details to skip and option to use different detail for protein accession number.
    # 0.3 - Added reloading of features.
    # 1.0 - Basic functioning version. Added fetchuid=LIST Genbank retrieval to generate seqin=FILE.
    # 1.1 - Added use of rje_taxonomy for getting Species Code from TaxID.
    # 1.2 - Modified to deal with genbank protein entries.
    # 1.2.1 - Fixed feature bug that was breaking parser and removing trailing '*' from protein sequences.
    # 1.2.2 - Fixed more features that were breaking parser.
    # 1.3.0 - Added split viral output.
    # 1.3.1 - Fixed bug in split viral output.
    # 1.3.2 - Fixed bug in reverse complement sequences with introns.
    # 1.4.0 - Added addtags=T/F : Add locus_tag identifiers if missing - needed for gene/cds/prot fasta output [False]
    # 1.4.1 - Fixed genetic code warning.
    # 1.5.0 - Added setupRefGenome() method based on PAGSAT code.
    # 1.5.1 - Fixed logskip append locus sequence file bug.
    # 1.5.2 - Fixed addtag(s) bug.

rje_genbank REST Output formats

Run with &rest=docs for program documentation and options. A plain text version is accessed with &rest=help.
&rest=OUTFMT can be used to retrieve individual parts of the output, matching the tabs in the default
(&rest=format) output. Individual OUTFMT elements can also be parsed from the full (&rest=full) server output,
which is formatted as follows:
###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~###
# OUTFMT:
... contents for OUTFMT section ...

Available REST Outputs

There is currently no specific help available on REST output for this program.

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.