Difference between revisions of "Python code created by Shim"
From Crop Genomics Lab.
Sangrea Shim (Talk | contribs) |
Sangrea Shim (Talk | contribs) |
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| − | ''' | + | '''Using class as a high speed searchable variation''' |
class ClassName: | class ClassName: | ||
| Line 7: | Line 7: | ||
... | ... | ||
| − | + | Import the files include this class | |
| − | + | Then, input data which you'd like to input to an instance like this way | |
ClassName(Data4variation1,Data4variation2,,,,) | 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''' | '''Variation typing code''' | ||
determine variation type from three files: fasta, gff3, vcf(generated by samtools pipeline) | determine variation type from three files: fasta, gff3, vcf(generated by samtools pipeline) | ||
Revision as of 01:26, 28 March 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
determine variation type from three files: fasta, gff3, vcf(generated by samtools pipeline)
