Difference between revisions of "Python code created by Shim"

Latest revision as of 08:29, 11 April 2014

Using class as a high speed searchable variation

    class ClassName:
         def __init__(self,variation1,variation2,,,,):
              self.variation1=variation1
              self.variation2=variation2
              ...

Import the files include this class Then, input data which you'd like to input to an instance like this way

    ClassName(Data4variation1,Data4variation2,,,,)

If you want to search the instance which you've made, firstly, you have to state variation. However, creating variation repeatedly is not possible in python. So, dictionary used as a searching table.

    Gene_dict = {'Glyma01g01110':1,'Glyma02g01230':2,,,,}
    instance_list = [ ClassName('Glyma01g01110',,,,),ClassName('Glyma02g01230',,,,,),,,,]

Variation typing code

annotate genomic features of variation included in variant calling format

    location: 63server:/home/kev8305/pythonShim/[SNP]variation_type.py
    mannual: python [SNP]variation_type.py (reference.fa) (reference.gff3) (vcf_from_reference_seqeuncing)

count variation for several types of genomic feature

    location: 63server:/home/kev8305/pythonShim/[SNP]vcf_2_count.py
    mannual: python [SNP]vcf_2_count.py (vcf_file_annotated_by_variation_type.py)

Useful annotation code for one who is not familiar with python

    location: 63server:/home/kev8305/pythonShim/[annotation]phytozome_annot.py
    mannual: python [annotation]phytozome_annot.py --help
    caution: not compatible with other plant species annotaion(only in Gmax)