s_mart: smart_toolShed/SMART/Java/Python/structure/TranscriptContainer.py annotate

annotate smart_toolShed/SMART/Java/Python/structure/TranscriptContainer.py @ 1:30c5431d8ce4

Uploaded

author	yufei-luo
date	Thu, 17 Jan 2013 11:01:51 -0500
parents	e0f8dcca02ed
children

rev	line source
0 e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	1 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	2 # Copyright INRA-URGI 2009-2010
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	3 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	4 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	5 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	6 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	7 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	8 # "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	9 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	10 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	11 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	12 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	13 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	14 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	15 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	16 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	17 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	18 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	19 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	20 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	21 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	22 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	23 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	24 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	25 # same conditions as regards security.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	26 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	27 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	28 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	29 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	30 import re
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	31 import sys
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	32 from commons.core.parsing.ParserChooser import ParserChooser
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	33 from SMART.Java.Python.mySql.MySqlTranscriptTable import MySqlTranscriptTable
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	34 from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	35
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	36 class TranscriptContainer(object):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	37 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	38 An interface class that contains a list of transcripts, handle different formats
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	39 @ivar container: container of the data
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	40 @type container: string
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	41 @ivar format: format of the data
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	42 @type format: string
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	43 @ivar transcriptListParser: possibly contains a parser to a list of transcripts
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	44 @type transcriptListParser: L{TranscriptListParser<TranscriptListParser>} or None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	45 @ivar mappingListParser: possibly contains a parser to a list of mappings
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	46 @type mappingListParser: L{MapperParser<MapperParser>} or None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	47 @ivar transcriptTables: possibly contains the mySQL tables
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	48 @type transcriptTables: dict of L{MySqlTranscriptTable<MySqlTranscriptTable>} or None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	49 @ivar mySqlConnection: connection to a MySQL database
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	50 @type mySqlConnection: class L{MySqlConnection<MySqlConnection>}
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	51 @ivar type: type of the data (transcripts, mappings or mySQL)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	52 @type type: string
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	53 @ivar verbosity: verbosity
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	54 @type verbosity: int
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	55 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	56
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	57 def __init__(self, container, format, verbosity = 0):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	58 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	59 Constructor
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	60 @param container: container of the data
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	61 @type container: string
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	62 @param format: format of the data
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	63 @type format: string
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	64 @param verbosity: verbosity
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	65 @type verbosity: int
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	66 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	67 self.container = container
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	68 self.format = format
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	69 self.verbosity = verbosity
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	70 self.transcriptListParser = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	71 self.mappingListParser = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	72 self.transcriptTables = {}
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	73 self.mySqlConnection = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	74 self.foundData = False
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	75 self.nbTranscripts = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	76 self.nbNucleotides = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	77 self.chromosomes = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	78 self.type = None
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	79 if self.container == None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	80 sys.exit("Error! Container input file name is empty!")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	81 if self.format == None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	82 sys.exit("Error! Container input format is empty!")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	83
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	84
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	85 def findData(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	86 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	87 Load data
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	88 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	89 if self.format == None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	90 sys.exit("Error! Format is not specified!")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	91 if self.format == "sql":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	92 self.transcriptTables = {}
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	93 self.chromosomes = []
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	94 self.nbTranscripts = 0
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	95 self.nbNucleotides = 0
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	96 self.type = "sql"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	97 query = self.mySqlConnection.executeQuery("SELECT name FROM sqlite_master WHERE type LIKE 'table' AND name LIKE '%s_%%_transcripts'" % (self.container))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	98 for line in query.getIterator():
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	99 tableName = line[0]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	100 m = re.search(r"^(\S*)_transcripts$", tableName[len(self.container)+1:])
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	101 if m == None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	102 sys.exit("Table '%s' has a strange name" % (tableName))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	103 chromosome = m.group(1)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	104 self.transcriptTables[chromosome] = MySqlTranscriptTable(self.mySqlConnection, self.container, chromosome, self.verbosity)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	105 self.chromosomes.append(chromosome)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	106 for transcript in self.transcriptTables[chromosome].getIterator():
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	107 self.nbTranscripts += 1
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	108 self.nbNucleotides += transcript.getSize()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	109 if self.type == None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	110 parserChooser = ParserChooser(self.verbosity)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	111 parserChooser.findFormat(self.format)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	112 self.type = parserChooser.getType()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	113 if self.type == "transcript":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	114 self.transcriptListParser = parserChooser.getParser(self.container)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	115 elif self.type == "mapping":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	116 self.mappingListParser = parserChooser.getParser(self.container)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	117 else:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	118 sys.exit("Error! Cannot handle format '%s'!" % (self.format))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	119 if self.type == None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	120 sys.exit("Error! Cannot handle format '%s'!" % (self.format))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	121
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	122 if self.transcriptListParser != None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	123 if self.type == "transcript":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	124 self.nbTranscripts = self.transcriptListParser.getNbTranscripts()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	125 self.nbNucleotides = self.transcriptListParser.getNbNucleotides()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	126 self.chromosomes = self.transcriptListParser.getChromosomes()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	127 if self.mappingListParser != None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	128 if self.type == "mapping":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	129 self.nbTranscripts = self.mappingListParser.getNbMappings()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	130 self.nbNucleotides = self.mappingListParser.getNbNucleotides()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	131 self.chromosomes = self.mappingListParser.getChromosomes()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	132
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	133 self.foundData = True
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	134
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	135
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	136 def getNbTranscripts(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	137 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	138 Get the number of transcripts
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	139 @return: the number of transcripts
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	140 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	141 if not self.foundData:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	142 self.findData()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	143 return self.nbTranscripts
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	144
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	145
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	146 def getNbItems(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	147 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	148 Same as getNbTranscripts
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	149 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	150 return self.getNbTranscripts()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	151
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	152
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	153 def getNbNucleotides(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	154 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	155 Get the number of nucleotides
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	156 @return: the number of nucleotides
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	157 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	158 if not self.foundData:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	159 self.findData()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	160 return self.nbNucleotides
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	161
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	162
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	163 def getChromosomes(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	164 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	165 Get the chromosomes
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	166 @return: the chromosomes
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	167 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	168 if not self.foundData:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	169 self.findData()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	170 return self.chromosomes
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	171
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	172
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	173 def getIterator(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	174 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	175 An iterator
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	176 @return: an iterator to a list of transcripts
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	177 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	178 if not self.foundData:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	179 self.findData()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	180 if self.type == "sql":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	181 for chromosome in self.transcriptTables:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	182 for transcript in self.transcriptTables[chromosome].getIterator():
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	183 yield transcript
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	184 return
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	185 if self.type == "transcript":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	186 for transcript in self.transcriptListParser.getIterator():
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	187 yield transcript
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	188 return
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	189 if self.type == "mapping":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	190 for mapping in self.mappingListParser.getIterator():
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	191 yield mapping.getTranscript()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	192 return
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	193 sys.exit("Error! No valid transcript container given!")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	194
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	195
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	196 def storeIntoDatabase(self, name = None):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	197 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	198 Store the current transcript / mapping list into database
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	199 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	200 if not self.foundData:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	201 self.findData()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	202
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	203 if (self.transcriptListParser == None and self.mappingListParser == None) or len(self.transcriptTables.keys()) != 0:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	204 return
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	205
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	206 mySqlTranscriptWriter = MySqlTranscriptWriter(self.mySqlConnection, name, self.verbosity)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	207 mySqlTranscriptWriter.addTranscriptList(self.transcriptListParser if self.transcriptListParser else self.mappingListParser)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	208 mySqlTranscriptWriter.write()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	209 self.transcriptTables = mySqlTranscriptWriter.getTables()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	210 self.type = "sql"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	211
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	212
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	213 def getTables(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	214 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	215 Accessor to the mySQL tables
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	216 @return: the mySQL tables
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	217 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	218 return self.transcriptTables
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	219
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	220
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	221 def setDefaultTagValue(self, name, value):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	222 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	223 Set the given tag to the value for all transcripts
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	224 @param name: name of the tag
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	225 @type name: string
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	226 @param value: value of the tag
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	227 @type value: string
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	228 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	229 if self.type == "sql":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	230 for chromosome in self.transcriptTables:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	231 self.transcriptTables[chromosome].setDefaultTagValue(name, value)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	232 elif self.type == "transcript":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	233 self.transcriptListParser.setDefaultTagValue(name, value)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	234 elif self.type == "mapping":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	235 self.mappingListParser.setDefaultTagValue(name, value)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	236

Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/structure/TranscriptContainer.py @ 1:30c5431d8ce4