Beispiel #1
0
    def __call_peaks_wo_control (self):
        """To call peaks w/o control data.

        """
        #self.lambda_bg = float(self.scan_window)*self.treat.total/self.gsize
        #self.debug("#3 background lambda: %.2f " % (self.lambda_bg))
        #self.min_tags = poisson_cdf_inv(1-pow(10,self.pvalue/-10),self.lambda_bg)+1
        #self.debug("#3 min tags: %d" % (self.min_tags))

        self.info("#3 shift treatment data")
        self.__shift_trackI(self.treat)
        self.info("#3 merge +/- strand of treatment data")
        self.treat.merge_plus_minus_locations_naive ()

        self.debug("#3 after shift and merging, tags: %d" % (self.treat.total))
        if self.opt.store_bdg:
            self.info("#3 save the shifted and merged tag counts into bedGraph file...")
            zbdg_write(self.treat,self.opt.wig_dir_tr,self.zwig_tr,self.d,log=self.info,single=self.opt.single_profile)
        elif self.opt.store_wig:
            self.info("#3 save the shifted and merged tag counts into wiggle file...")
            #if self.opt.wigextend:
            #    zwig_write(self.treat,self.opt.wig_dir_tr,self.zwig_tr,self.opt.wigextend,log=self.info,space=self.opt.space,single=self.opt.single_profile)
            #else:
            zwig_write(self.treat,self.opt.wig_dir_tr,self.zwig_tr,self.d,log=self.info,space=self.opt.space,single=self.opt.single_profile)
        self.info("#3 call peak candidates")
        peak_candidates = self.__call_peaks_from_trackI (self.treat)
        self.info("#3 use self to calculate local lambda and  filter peak candidates...")
        self.final_peaks = self.__filter_w_control(peak_candidates,self.treat,self.treat,pass_sregion=True)
        return self.final_peaks
Beispiel #2
0
    def __call_peaks_wo_control(self):
        """To call peaks w/o control data.

        """
        #self.lambda_bg = float(self.scan_window)*self.treat.total/self.gsize
        #self.debug("#3 background lambda: %.2f " % (self.lambda_bg))
        #self.min_tags = poisson_cdf_inv(1-pow(10,self.pvalue/-10),self.lambda_bg)+1
        #self.debug("#3 min tags: %d" % (self.min_tags))

        self.info("#3 shift treatment data")
        self.__shift_trackI(self.treat)
        self.info("#3 merge +/- strand of treatment data")
        self.treat.merge_plus_minus_locations_naive()

        self.debug("#3 after shift and merging, tags: %d" % (self.treat.total))
        if self.opt.store_bdg:
            self.info(
                "#3 save the shifted and merged tag counts into bedGraph file..."
            )
            zbdg_write(self.treat,
                       self.opt.wig_dir_tr,
                       self.zwig_tr,
                       self.d,
                       log=self.info,
                       single=self.opt.single_profile)
        elif self.opt.store_wig:
            self.info(
                "#3 save the shifted and merged tag counts into wiggle file..."
            )
            #if self.opt.wigextend:
            #    zwig_write(self.treat,self.opt.wig_dir_tr,self.zwig_tr,self.opt.wigextend,log=self.info,space=self.opt.space,single=self.opt.single_profile)
            #else:
            zwig_write(self.treat,
                       self.opt.wig_dir_tr,
                       self.zwig_tr,
                       self.d,
                       log=self.info,
                       space=self.opt.space,
                       single=self.opt.single_profile)
        self.info("#3 call peak candidates")
        peak_candidates = self.__call_peaks_from_trackI(self.treat)
        self.info(
            "#3 use self to calculate local lambda and  filter peak candidates..."
        )
        self.final_peaks = self.__filter_w_control(peak_candidates,
                                                   self.treat,
                                                   self.treat,
                                                   pass_sregion=True)
        return self.final_peaks
Beispiel #3
0
    def __call_peaks_w_control(self):
        """To call peaks with control data.

        A peak info type is a: dictionary

        key value: chromosome

        items: (peak start,peak end, peak length, peak summit, peak
        height, number of tags in peak region, peak pvalue, peak
        fold_enrichment) <-- tuple type
        """
        #self.lambda_bg = float(self.scan_window)*self.treat.total/self.gsize
        #self.debug("#3 background lambda: %.2f " % (self.lambda_bg))
        #self.min_tags = poisson_cdf_inv(1-pow(10,self.pvalue/-10),self.lambda_bg)+1
        #self.debug("#3 min tags: %d" % (self.min_tags))

        self.ratio_treat2control = float(self.treat.total) / self.control.total
        if self.ratio_treat2control > 2 or self.ratio_treat2control < 0.5:
            self.warn(
                "Treatment tags and Control tags are uneven! FDR may be wrong!"
            )
        self.info("#3 shift treatment data")
        self.__shift_trackI(self.treat)
        self.info("#3 merge +/- strand of treatment data")

        self.treat.merge_plus_minus_locations_naive()

        self.debug("#3 after shift and merging, tags: %d" % (self.treat.total))
        if self.opt.store_bdg:
            self.info(
                "#3 save the shifted and merged tag counts into bedGraph file..."
            )
            zbdg_write(self.treat,
                       self.opt.wig_dir_tr,
                       self.zwig_tr,
                       self.d,
                       log=self.info,
                       single=self.opt.single_profile)
        elif self.opt.store_wig:
            self.info(
                "#3 save the shifted and merged tag counts into wiggle file..."
            )
            #if self.opt.wigextend:
            #    zwig_write(self.treat,self.opt.wig_dir_tr,self.zwig_tr,self.opt.wigextend,log=self.info,space=self.opt.space,single=self.opt.single_profile)
            #else:
            zwig_write(self.treat,
                       self.opt.wig_dir_tr,
                       self.zwig_tr,
                       self.d,
                       log=self.info,
                       space=self.opt.space,
                       single=self.opt.single_profile)
        self.info("#3 call peak candidates")
        peak_candidates = self.__call_peaks_from_trackI(self.treat)

        self.info("#3 shift control data")
        self.info("#3 merge +/- strand of control data")
        self.__shift_trackI(self.control)
        self.control.merge_plus_minus_locations_naive()

        self.debug("#3 after shift and merging, tags: %d" %
                   (self.control.total))
        if self.opt.store_bdg:
            self.info(
                "#3 save the shifted and merged tag counts into bedGraph file..."
            )
            zbdg_write(self.control,
                       self.opt.wig_dir_ctl,
                       self.zwig_ctl,
                       self.d,
                       log=self.info,
                       single=self.opt.single_profile)
        if self.opt.store_wig:
            self.info(
                "#3 save the shifted and merged tag counts into wiggle file..."
            )
            #if self.opt.wigextend:
            #    zwig_write(self.control,self.opt.wig_dir_ctl,self.zwig_ctl,self.opt.wigextend,log=self.info,space=self.opt.space,single=self.opt.single_profile)
            #else:
            zwig_write(self.control,
                       self.opt.wig_dir_ctl,
                       self.zwig_ctl,
                       self.d,
                       log=self.info,
                       space=self.opt.space,
                       single=self.opt.single_profile)
        self.info("#3 call negative peak candidates")
        negative_peak_candidates = self.__call_peaks_from_trackI(self.control)

        # build score
        #if self.save_score:
        #    self.info("#4 build scores")
        #    scoreswig = self.__build_score_wigtrackI(treatwig,controlbkI,self.d,space=self.opt.space,bglambda=self.lambda_bg)
        #    zwigfile = file(self.opt.name+".score.wig","w")
        #    self.info("#4.1 save scores to wiggle file")
        #    scoreswig.write_wig(zwigfile,"score")
        #    self.info("compress the wiggle file using gzip...")
        #    os.system("gzip "+self.opt.name+".score.wig")

        self.info("#3 use control data to filter peak candidates...")
        #self.final_peaks = self.__filter_w_control(peak_candidates,self.treat,self.control, self.ratio_treat2control,fake_when_missing=True)
        self.final_peaks = self.__filter_w_control(
            peak_candidates,
            self.treat,
            self.control,
            fake_when_missing=True,
            to_small_sample=self.opt.tosmall)
        self.info("#3 find negative peaks by swapping treat and control")

        #self.final_negative_peaks = self.__filter_w_control(negative_peak_candidates,self.control,self.treat, 1.0/self.ratio_treat2control,fake_when_missing=True)
        self.final_negative_peaks = self.__filter_w_control(
            negative_peak_candidates,
            self.control,
            self.treat,
            fake_when_missing=True,
            to_small_sample=self.opt.tosmall)
        return self.__add_fdr(self.final_peaks, self.final_negative_peaks)
Beispiel #4
0
    def __call_peaks_w_control (self):
        """To call peaks with control data.

        A peak info type is a: dictionary

        key value: chromosome

        items: (peak start,peak end, peak length, peak summit, peak
        height, number of tags in peak region, peak pvalue, peak
        fold_enrichment) <-- tuple type
        """
        #self.lambda_bg = float(self.scan_window)*self.treat.total/self.gsize
        #self.debug("#3 background lambda: %.2f " % (self.lambda_bg))
        #self.min_tags = poisson_cdf_inv(1-pow(10,self.pvalue/-10),self.lambda_bg)+1
        #self.debug("#3 min tags: %d" % (self.min_tags))

        self.ratio_treat2control = float(self.treat.total)/self.control.total
        if self.ratio_treat2control > 2 or self.ratio_treat2control < 0.5:
            self.warn("Treatment tags and Control tags are uneven! FDR may be wrong!")
        self.info("#3 shift treatment data")
        self.__shift_trackI(self.treat)
        self.info("#3 merge +/- strand of treatment data")

        self.treat.merge_plus_minus_locations_naive ()

        self.debug("#3 after shift and merging, tags: %d" % (self.treat.total))
        if self.opt.store_bdg:
            self.info("#3 save the shifted and merged tag counts into bedGraph file...")
            zbdg_write(self.treat,self.opt.wig_dir_tr,self.zwig_tr,self.d,log=self.info,single=self.opt.single_profile)
        elif self.opt.store_wig:
            self.info("#3 save the shifted and merged tag counts into wiggle file...")
            #if self.opt.wigextend:
            #    zwig_write(self.treat,self.opt.wig_dir_tr,self.zwig_tr,self.opt.wigextend,log=self.info,space=self.opt.space,single=self.opt.single_profile)
            #else:
            zwig_write(self.treat,self.opt.wig_dir_tr,self.zwig_tr,self.d,log=self.info,space=self.opt.space,single=self.opt.single_profile)
        self.info("#3 call peak candidates")
        peak_candidates = self.__call_peaks_from_trackI (self.treat)

        self.info("#3 shift control data")
        self.info("#3 merge +/- strand of control data")
        self.__shift_trackI(self.control)
        self.control.merge_plus_minus_locations_naive ()

        self.debug("#3 after shift and merging, tags: %d" % (self.control.total))
        if self.opt.store_bdg:
            self.info("#3 save the shifted and merged tag counts into bedGraph file...")
            zbdg_write(self.control,self.opt.wig_dir_ctl,self.zwig_ctl,self.d,log=self.info,single=self.opt.single_profile)
        if self.opt.store_wig:
            self.info("#3 save the shifted and merged tag counts into wiggle file...")
            #if self.opt.wigextend:
            #    zwig_write(self.control,self.opt.wig_dir_ctl,self.zwig_ctl,self.opt.wigextend,log=self.info,space=self.opt.space,single=self.opt.single_profile)
            #else:
            zwig_write(self.control,self.opt.wig_dir_ctl,self.zwig_ctl,self.d,log=self.info,space=self.opt.space,single=self.opt.single_profile)
        self.info("#3 call negative peak candidates")
        negative_peak_candidates = self.__call_peaks_from_trackI (self.control)

        # build score
        #if self.save_score:
        #    self.info("#4 build scores")
        #    scoreswig = self.__build_score_wigtrackI(treatwig,controlbkI,self.d,space=self.opt.space,bglambda=self.lambda_bg)
        #    zwigfile = file(self.opt.name+".score.wig","w")
        #    self.info("#4.1 save scores to wiggle file")            
        #    scoreswig.write_wig(zwigfile,"score")
        #    self.info("compress the wiggle file using gzip...")
        #    os.system("gzip "+self.opt.name+".score.wig")
        
        self.info("#3 use control data to filter peak candidates...")
        #self.final_peaks = self.__filter_w_control(peak_candidates,self.treat,self.control, self.ratio_treat2control,fake_when_missing=True)
        self.final_peaks = self.__filter_w_control(peak_candidates,self.treat,self.control, fake_when_missing=True, to_small_sample=self.opt.tosmall)
        self.info("#3 find negative peaks by swapping treat and control")

        #self.final_negative_peaks = self.__filter_w_control(negative_peak_candidates,self.control,self.treat, 1.0/self.ratio_treat2control,fake_when_missing=True)
        self.final_negative_peaks = self.__filter_w_control(negative_peak_candidates,self.control,self.treat, fake_when_missing=True, to_small_sample=self.opt.tosmall)
        return self.__add_fdr (self.final_peaks, self.final_negative_peaks)