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1 import sys,os
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2 import logging
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3 import galaxy.datatypes.data
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4 from galaxy.datatypes.data import Text
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5 from galaxy.datatypes.metadata import MetadataElement
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6
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7 class ShearSvIndex( Text ):
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8 MetadataElement( name="base_name", desc="base name for this index set", default='shear_ref', set_in_upload=True, readonly=True )
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9 """
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10 generated files:
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11 copy fasta:
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12 base_name.fa
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13 index fasta with samtools index:
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14 base_name.fa.fai
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15 create 2bit with faToTwoBit:
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16 base_name.2bit
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17 create bwa index:
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18 base_name.fa.amb
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19 base_name.fa.ann
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20 base_name.fa.bwt
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21 base_name.fa.pac
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22 base_name.fa.rbwt
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23 base_name.fa.rpac
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24 base_name.fa.rsa
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25 base_name.fa.sa
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26 """
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27 file_ext = 'shear.svidx'
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28 composite_type = 'auto_primary_file'
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29 allow_datatype_change = False
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30
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31 def __init__(self, **kwd):
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32 """Initialize datatype"""
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33 Text.__init__( self, **kwd )
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34
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35 def init_meta( self, dataset, copy_from=None ):
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36 Text.init_meta( self, dataset, copy_from=copy_from )
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37
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38 def generate_primary_file( self, dataset = None ):
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39 """
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40 This is called only at upload to write the html file
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41 cannot rename the datasets here - they come with the default unfortunately
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42 """
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43
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44 def regenerate_primary_file(self,dataset):
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45 """
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46 cannot do this until we are setting metadata
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47 """
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48 bn = dataset.metadata.base_name
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49 f = file(dataset.file_name,'w')
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50 f.write(bn)
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51 f.close()
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52
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53 def set_meta( self, dataset, overwrite = True, **kwd ):
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54 efp = dataset.extra_files_path
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55 flist = os.listdir(efp)
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56 for i,fname in enumerate(flist):
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57 if fname.endswith('.fa'):
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58 dataset.metadata.base_name = fname[:-3]
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59 break
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60 if fname.endswith('.2bit'):
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61 dataset.metadata.base_name = fname[:-5]
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62 break
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63 self.regenerate_primary_file(dataset)
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64
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65
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