diff datatypes/Datatype.py @ 1:85195e0d4b71 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes/Datatype.py	Fri Sep 29 13:32:23 2017 -0400
@@ -0,0 +1,205 @@
+#!/usr/bin/python
+# -*- coding: utf8 -*-
+
+"""
+Super Class of the managed datatype
+"""
+
+import os
+import tempfile
+import collections
+import util
+import logging
+import abc
+from abc import ABCMeta
+from TrackDb import TrackDb
+from datatypes.validators.DataValidation import DataValidation
+
+
+class Datatype(object):
+    __metaclass__ = ABCMeta
+
+    twoBitFile = None
+    chromSizesFile = None
+    input_fasta_file = None
+    extra_files_path = None
+    tool_directory = None
+
+    mySpecieFolderPath = None
+    myTrackFolderPath = None
+ 
+
+    def __init__(self):
+        not_init_message = "The {0} is not initialized." \
+                           "Did you use pre_init static method first?"
+        if Datatype.input_fasta_file is None:
+            raise TypeError(not_init_message.format('reference genome'))
+        if Datatype.extra_files_path is None:
+            raise TypeError(not_init_message.format('track Hub path'))
+        if Datatype.tool_directory is None:
+            raise TypeError(not_init_message.format('tool directory'))
+        self.inputFile = None
+        self.trackType = None
+        self.dataType = None
+        self.track = None
+        self.trackSettings = dict()
+        self.extraSettings = collections.OrderedDict()
+
+    @staticmethod
+    def pre_init(reference_genome, two_bit_path, chrom_sizes_file,
+                 extra_files_path, tool_directory, specie_folder, tracks_folder):
+        Datatype.extra_files_path = extra_files_path
+        Datatype.tool_directory = tool_directory
+
+        # TODO: All this should be in TrackHub and not in Datatype
+        Datatype.mySpecieFolderPath = specie_folder
+        Datatype.myTrackFolderPath = tracks_folder
+
+        Datatype.input_fasta_file = reference_genome
+
+        # 2bit file creation from input fasta
+        Datatype.twoBitFile = two_bit_path
+        Datatype.chromSizesFile = chrom_sizes_file
+    
+    def generateCustomTrack(self):
+        self.validateData()
+        self.initSettings()
+        #Create the track file
+        self.createTrack()
+        # Create the TrackDb Object
+        self.createTrackDb()
+        logging.debug("- %s %s created", self.dataType, self.trackName)  
+
+    
+    @abc.abstractmethod 
+    def validateData(self):
+        """validate the input data with DataValidation"""
+    
+    def initSettings(self):
+        #Initialize required fields: trackName, longLabel, shortLable
+        self.trackName = self.trackSettings["name"]
+        if self.trackSettings["long_label"]:
+            self.longLabel = self.trackSettings["long_label"]
+        else:
+            self.longLabel = self.trackName
+        if not "short_label" in self.trackSettings:
+            self.shortLabel = ""
+        else:
+            self.shortLabel = self.trackSettings["short_label"]
+        self.trackDataURL = os.path.join(self.myTrackFolderPath, self.trackName)
+        
+
+    @abc.abstractmethod
+    def createTrack(self):
+        """Create the final track file"""
+
+    def createTrackDb(self):
+        self.track = TrackDb(self.trackName, self.longLabel, self.shortLabel, self.trackDataURL, self.trackType, self.extraSettings)
+
+    
+   
+
+        
+    
+        
+    '''
+    def __init__(self):
+        not_init_message = "The {0} is not initialized." \
+                           "Did you use pre_init static method first?"
+        if Datatype.input_fasta_file is None:
+            raise TypeError(not_init_message.format('reference genome'))
+        if Datatype.extra_files_path is None:
+            raise TypeError(not_init_message.format('track Hub path'))
+        if Datatype.tool_directory is None:
+            raise TypeError(not_init_message.format('tool directory'))
+        self.track = None
+        self.extra_settings = collections.OrderedDict()
+        
+
+    @staticmethod
+    def pre_init(reference_genome, two_bit_path, chrom_sizes_file,
+                 extra_files_path, tool_directory, specie_folder, tracks_folder):
+        Datatype.extra_files_path = extra_files_path
+        Datatype.tool_directory = tool_directory
+
+        # TODO: All this should be in TrackHub and not in Datatype
+        Datatype.mySpecieFolderPath = specie_folder
+        Datatype.myTrackFolderPath = tracks_folder
+
+        Datatype.input_fasta_file = reference_genome
+
+        # 2bit file creation from input fasta
+        Datatype.twoBitFile = two_bit_path
+        Datatype.chromSizesFile = chrom_sizes_file
+ 
+    @staticmethod
+    def get_largest_scaffold_name(self):
+        # We can get the biggest scaffold here, with chromSizesFile
+        with open(Datatype.chromSizesFile.name, 'r') as chrom_sizes:
+            # TODO: Check if exists
+            return chrom_sizes.readline().split()[0]
+  
+
+    def createTrack(self, trackName, longLabel, shortLabel, trackDataURL, trackType, extra_settings=None):
+        self.track = TrackDb(trackName, longLabel, shortLabel, trackDataURL, trackType, extra_settings)
+
+    def initRequiredSettings(self, trackSettings, trackDataURL = None, trackType = None):
+        
+        #Initialize required fields: trackName, longLabel, shortLable
+      
+        self.trackSettings = trackSettings
+        self.trackName = self.trackSettings["name"]
+        #self.priority = self.trackSettings["order_index"]
+        #self.track_color = self.trackSettings["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        #self.group_name = self.trackSettings["group_name"]
+        #self.database = self.trackSettings["database"]
+        if self.trackSettings["long_label"]:
+            self.longLabel = self.trackSettings["long_label"]
+        else:
+            self.longLabel = self.trackName
+        if not "short_label" in self.trackSettings:
+            self.shortLabel = ""
+        else:
+            self.shortLabel = self.trackSettings["short_label"]
+        self.trackDataURL = trackDataURL
+        self.trackType = trackType
+    
+    def setExtLink(self, database, inputFile, seqType=None, useIframe=True, iframeHeight=None, iframeWidth=None):
+        if "NCBI" in database:
+            if not seqType:
+                self.seqType = int(self.getSeqType(inputFile))
+            else:
+                self.seqType = seqType
+            if self.seqType < 0:
+                print self.seqType
+                raise Exception("Sequence Type is not set for bigPsl. Stopping the application")
+            if self.seqType == 2:
+                self.extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/protein/$$"
+            elif self.seqType == 1:
+                self.extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/nuccore/$$"
+            else:
+                raise Exception("Sequence Type {0} is not valid for bigPsl. Stopping the application".format(self.seqType))
+        elif "UniProt" in database:
+            self.extra_settings["url"] = "http://www.uniprot.org/uniprot/$$"
+        elif "FlyBase" in database:
+            self.extra_settings["url"] = "http://flybase.org/reports/$$"
+        else:
+            self.extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$"
+        self.extra_settings["urlLabel"] = database + " Details:"
+        if useIframe:
+            self.extra_settings["iframeUrl"] = self.extra_settings["url"]
+            if not iframeHeight:
+                iframeHeight = "600"
+            if not iframeWidth:
+                iframeWidth = "800"
+            self.extra_settings["iframeOptions"] = "height= %s width= %s" % (iframeHeight, iframeWidth)
+
+    def getSeqType(self, inputFile):
+        with open(inputFile, "r") as bigpsl:
+            sampleSeq = bigpsl.readline().split()
+        if len(sampleSeq) == 25:
+            return sampleSeq[-1]
+        else:
+            return "-1"        
+    '''
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