https://github.com/warelab/drunken-noodle

https://github.com/warelab/drunken-noodle

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• Host: GitHub
• URL: https://github.com/warelab/drunken-noodle
• Owner: warelab
• Created: 2013-12-02T16:22:39.000Z (about 11 years ago)
• Default Branch: master
• Last Pushed: 2014-05-07T20:23:02.000Z (over 10 years ago)
• Last Synced: 2024-06-11T16:41:20.060Z (7 months ago)
• Size: 6.6 MB
• Stars: 1
• Watchers: 21
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Operation Drunken Noodle

Comparative maps, etc.  A complete rewrite of CMap 

(http://gmod.org/wiki/CMap).  See "doc" directory for PPT/PDF overview of

goals.

# Author

Ken Youens-Clark 

# Map data formats

## Tab-delimited

A basic tab-delimite file with the following format (from CMap 1):

         map_name: T1

     feature_name: T1.1

    feature_start: 0

     feature_stop: 1000

 feature_type_acc: contig

  feature_aliases: T1.A,T1.AA

## GFF

Ben Faga proposed a variation on GFF format for CMap data imports:

  ##gff-version 3

  ##cmap-gff-version 1

  # This file was produced from a CMap database using Bio::GMOD::CMap::Admin::GFFProducer

  # Data was created by Apurva Narechania of the Gramene Project

    

  ##cmap_species  species_acc=oryza_sativa;species_common_name=O.%20sativa;species_full_name=Oryza%20sativa;display_order=1

    

  ###

  ##cmap_map_set  map_set_name=Chromosomes;map_set_short_name=Chromosomes;map_type_acc=Seq;map_set_acc=osc1;shape=box;color=blue;width=7;published_on=2008-06-25;unit_modifier=1

  ##cmap_map  map_name=1;map_start=1.00;map_stop=43596771.00;display_order=1

  ##sequence-region   1   1.00    43596771.00

  1   CMap    syntenic_block  272.00  770372.00   .   -   .   ID=syntenic_block5279691;Name=sb3_272-770372;corr_by_id=syntenic_block5279692 synteny

  1   CMap    syntenic_block  771644.00   865909.00   .   +   .   ID=syntenic_block5279693;Name=sb3_771644-865909;corr_by_id=syntenic_block5279694 synteny