• Intro

  • step_01
  • step_02
  • step_03
  • step_04
  • step_05
  • step_06
  • step_07
  • step_08
  • step_09
  • step_10
  • step_11
  • step_12
  • step_13
  • step_14
  • step_15
  • step_16
  • step_17
  • step_18
  • step_19
  • step_20
  • step_21
  • step_22
  • step_23
  • step_24

  • Credits

    UC Davis

    Step 10: Processing of the CAP3 output
    Generation of the "Alignment Files"

    Then we have used Python_CAP3_ContigExtractor_Feb_27_2004.py script with option "2" to process CAP3 output and generate "Alignment Files" in the new directory "tomato_alignments". Dialog is shown below:

    $ python Python_CAP3_ContigExtractor_Feb_27_2004.py
    What type of output do you want? (1/2): 2
    Enter the SOURCE file name: tomato_ABC.cap3.out
    Enter the DESTINATION directory with alignments: tomato_alignments
    Default contig file extension is ali
    Enter the contig file extension :aln
    Default contig file name prefix is Contig
    Enter the contig file name prefix:L_ABC_Contig

    Upon execution, a new directory "tomato_alignments" will be created and files with ".aln" extention will be generated for every contig in the assembly. The example of an "Alignment File" fragment is shown below:

    [text in red and dot actually are not displayed in the "Alignment File". We need some extra steps to find polymorphic sites]