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annotate Datatype.py @ 10:acc233161f50 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
author rmarenco
date Thu, 21 Jul 2016 05:58:51 -0400
parents 816956489fe9
children d05236b15f81
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1 #!/usr/bin/python
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2 # -*- coding: utf8 -*-
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4 """
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5 Super Class of the managed datatype
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6 """
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8 import os
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9 import tempfile
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11 from util import subtools
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14 class Datatype(object):
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16 twoBitFile = None
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18 input_fasta_file = None
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19 extra_files_path = None
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20 tool_directory = None
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22 mySpecieFolderPath = None
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23 myTrackFolderPath = None
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25 twoBitFile = None
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26 chromSizesFile = None
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28 def __init__(self):
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30 not_init_message = "The {0} is not initialized." \
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31 "Did you use pre_init static method first?"
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32 if Datatype.input_fasta_file is None:
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33 raise TypeError(not_init_message.format('reference genome'))
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34 if Datatype.extra_files_path is None:
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35 raise TypeError(not_init_message.format('track Hub path'))
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36 if Datatype.tool_directory is None:
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37 raise TypeError(not_init_message.format('tool directory'))
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40 @staticmethod
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41 def pre_init(reference_genome, two_bit_path, chrom_sizes_file,
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42 extra_files_path, tool_directory, specie_folder, tracks_folder):
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43 Datatype.extra_files_path = extra_files_path
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44 Datatype.tool_directory = tool_directory
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46 # TODO: All this should be in TrackHub and not in Datatype
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47 Datatype.mySpecieFolderPath = specie_folder
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48 Datatype.myTrackFolderPath = tracks_folder
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50 Datatype.input_fasta_file = reference_genome
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52 # 2bit file creation from input fasta
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53 Datatype.twoBitFile = two_bit_path
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54 Datatype.chromSizesFile = chrom_sizes_file
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56 @staticmethod
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57 def get_largest_scaffold_name(self):
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58 # We can get the biggest scaffold here, with chromSizesFile
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59 with open(Datatype.chromSizesFile.name, 'r') as chrom_sizes:
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60 # TODO: Check if exists
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61 return chrom_sizes.readline().split()[0]
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63 # TODO: Rename for PEP8
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64 def getShortName( self, name_to_shortify ):
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65 # Slice to get from Long label the short label
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66 short_label_slice = slice(0, 15)
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68 return name_to_shortify[short_label_slice]