bicluster.py

#################################################################
# @Program: bicluster.py                                        #
# @Version: 1                                                   #
# @Author: Chris Plaisier                                       #
# @Sponsored by:                                                #
# Nitin Baliga, ISB                                             #
# Institute for Systems Biology                                 #
# 1441 North 34th Street                                        #
# Seattle, Washington  98103-8904                               #
# (216) 732-2139                                                #
# @Also Sponsored by:                                           #
# Luxembourg Systems Biology Grant                              #
#                                                               #
# If this program is used in your analysis please mention who   #
# built it. Thanks. :-)                                         #
#                                                               #
# Copyrighted by Chris Plaisier  12/8/2009                      #
#################################################################

import os
from pssm import PSSM
import sqlite3 as lite

class Bicluster:
    """A class designed to hold the information pertaining to a bicluster
    and be able to output this in many different formats."""
    def __init__(self, k, maxIter, de_novo_method_upstream=None, de_novo_method_3pUTR=None, sqliteDb=None):
        self.k = k
        self.maxIter = maxIter
        self.attributes = {}
        self.sqliteDb = sqliteDb
        self.name = 'Bicluster %d' % k
        self.__read_data(de_novo_method_upstream, de_novo_method_3pUTR)

    # Reads in the bicluster file generated by cMonkeyWrapper
    def __read_data(self, de_novo_method_upstream=None, de_novo_method_3pUTR=None):
        # Attach to the database
        con = lite.connect(self.sqliteDb)
        con.row_factory = lite.Row
        cur = con.cursor()
        # Get the number of biclusters in run
        q1 = 'SELECT name FROM row_members, row_names WHERE row_members.cluster='+str(self.k)+' and row_members.iteration='+str(self.maxIter)+' and row_members.order_num=row_names.order_num'
        cur.execute(q1)
        data = cur.fetchall()
        self.genes = [str(i['name']) for i in data]
        # Read in conditions
        q1 = 'SELECT name FROM column_members, column_names WHERE column_members.cluster='+str(self.k)+' and column_members.iteration='+str(self.maxIter)+' and column_members.order_num=column_names.order_num'
        cur.execute(q1)
        data = cur.fetchall()
        self.conditions = [i['name'] for i in data]
        # Read in residuals
        q1 = 'SELECT residual FROM cluster_stats WHERE cluster='+str(self.k)+' and iteration='+str(self.maxIter)
        cur.execute(q1)
        data = cur.fetchall()
        self.norm_residual = float(data[0]['residual'])
        # At some point might be nice to figure out how to include this
        """# Read in associations with clinical traits
        self.cor = {}
        corFile = open('biclust/'+str(self.k)+'/correlation.csv','r')
        corFile.readline() # Skip header
        for line in corFile.readlines():
            splitUp = line.strip().split(',')
            self.cor[splitUp[0].strip('"')] = {'cor':splitUp[1],'pValue':splitUp[2]}
        corFile.close()
        self.surv = {}
        survFile = open('biclust/'+str(self.k)+'/survival.csv','r')
        survFile.readline() # Skip header
        for line in survFile.readlines():
            splitUp = line.strip().split(',')
            self.surv[splitUp[0]] = {'zScore':splitUp[1],'pValue':splitUp[2]}
        survFile.close()
        """
        # Now load up the PSSMs
        q1 = 'SELECT rowid, seqtype, motif_num, evalue FROM motif_infos WHERE cluster='+str(self.k)+' and iteration=2001'
        cur.execute(q1)
        motifs = cur.fetchall()
        # Set the de novo method
        if not de_novo_method_upstream==None:
            de_novo_method = de_novo_method_upstream
        else:
            de_novo_method = de_novo_method_3pUTR
        self.pssms_upstream = []
        self.pssms_3putr = []
        for motif in motifs:
            name = str(self.k)+'_motif'+str(motif['motif_num'])+'_'+de_novo_method
            q1 = 'SELECT row_names.name, motif_annotations.position, motif_annotations.reverse, motif_annotations.pvalue FROM motif_annotations, row_names WHERE motif_annotations.motif_info_id='+str(motif['rowid'])+' and motif_annotations.gene_num=row_names.order_num'
            cur.execute(q1)
            sites = [[str(i['name']), i['position'], i['reverse'], i['pvalue']] for i in cur.fetchall()]
            nsites = len(sites)
            eValue = motif['evalue']
            q1 = 'SELECT a, c, g, t FROM motif_pssm_rows WHERE motif_info_id='+str(motif['rowid']) #+' and iteration='+str(self.maxIter)
            cur.execute(q1)
            matrix = [[i['a'], i['c'], i['g'], i['t']] for i in cur.fetchall()]
            genes = list(set([i[0] for i in sites]))
            if motif['seqtype']=='upstream':
                self.pssms_upstream.append(PSSM(name, nsites, eValue, matrix, genes, de_novo_method))
            else:
                self.pssms_3putr.append(PSSM(name, nsites, eValue, matrix, genes, de_novo_method))
        con.close()

    def num_genes(self):
        return len(self.genes)

    def num_conditions(self):
        return len(self.conditions)

    # Returns a list of the upstream pssms for this biclutster
    def pssm_upstream(self, name):
        for i in self.pssms_upstream:
            if i.name == name:
                return i
        return 'No such PSSM with that name!'

    def pssm_3putr(self, name):
        for i in self.pssms_3putr:
            if i.name == name:
                return i
        return 'No such PSSM with that name!'

    def pssm_names_upstream(self):
        return [pssm.name for pssm in self.pssms_upstream]

    def pssm_names_3putr(self):
        return [pssm.name for pssm in self.pssms_3putr]

    # Adds a PSSM to a bicluster
    def add_pssm_upstream(self, pssm):
        self.pssms_upstream.append(pssm)

    # Adds a PSSM to a bicluster
    def add_pssm_3putr(self, pssm):
        self.pssms_3putr.append(pssm)

    # Add attribute
    def add_attribute(self, key, value):
        if key is None or value is None:
            print 'Error:  Key or Value have no data'
        self.attributes[key] = value