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How to use copy_dir method in localstack

Best Python code snippet using localstack_python

srna_result.py

Source:srna_result.py

...102        self.diff_analy()103        self.miRNA_target_norefanimal()        104    def SuppFiles(self):105        SuppFilesdir = self.make_dir('SuppFiles')106        self.copy_dir(os.path.join(107                      self.projpath,'11.edit_family','edit_analy','known_novel_hairpin.fa'108                                  ),os.path.join(SuppFilesdir,'hairpin.fa')109                     )110        assert not os.system('cat {known_mature} {novel_mature} > {total_mature}'.format(111                                known_mature = os.path.join(self.result,'*Known_miRNA','mature.fa'),112                                novel_mature = os.path.join(self.result,'*Novel_miRNA','mature.fa'),113                                total_mature = os.path.join(SuppFilesdir,'mature.fa'))114                             )115                                     116        assert not os.system('{perlExec} {BioScripts}/Release/GO_class.pl {go} {GOseq} {outfile}'.format(117                                 perlExec = self.perlExec, BioScripts = self.BioScripts,go = self.go,118                                 GOseq = self.GOseq,outfile = os.path.join(SuppFilesdir,'gene.goannot.xls'))119                           )120                121        self.copy_dir(os.path.join(122                      self.projpath,'*.diff','diffAnalysisResult','{meanscount.txt,meanstpm.txt}'123                                  ),SuppFilesdir124                     )125        self.copy_dir(self.geneAnn,os.path.join(SuppFilesdir,'gene.description.xls'))126        self.copy_dir(os.path.join(127                      self.readme,'0.SuppFiles.Readme.txt'128                                  ),SuppFilesdir129                     )130        131        assert not os.system(132                             '{perlExec} {BioScripts}/Release/known_haipin_mature_result.pl \\\n'133                             '  -readcount {readcount} \\\n'134                             '  -h {hairpin} \\\n'135                             '  -m {mature} \\\n'136                             '  -pairs {hairpin_mature_pairs} \\\n'137                             '  -o {outfile} '.format(138                                      perlExec  = self.perlExec,BioScripts = self.BioScripts,139                                      readcount = os.path.join(self.projpath,'3.known/known_miRNAs/mature.readcount'),140                                      hairpin   = os.path.join(self.projpath,'3.known/known_miRNAs/hairpin.fa'),141                                      mature    = os.path.join(self.projpath,'3.known/known_miRNAs/mature.fa'),142                                      hairpin_mature_pairs = os.path.join(self.projpath,'3.known/known_miRNAs/hairpin_mature.pairs'),143                                      outfile   = os.path.join(SuppFilesdir,'known_hairpin_mature.xls')144                                                      )145                            )146        assert not os.system(147                             '{perlExec} {BioScripts}/Release/novel_haipin_mature_result.pl \\\n'148                             '  -readcount {readcount} \\\n'149                             '  -h {hairpin} \\\n'150                             '  -m {mature} \\\n'151                             '  -str {hairpin_str} \\\n'152                             '  -pos {hairpin_pos} \\\n'153                             '  -o {outfile} '.format(154                                      perlExec  = self.perlExec,BioScripts = self.BioScripts,155                                      readcount = os.path.join(self.projpath,'8.novel/novel_miRNAs/mature.readcount'),156                                      hairpin   = os.path.join(self.projpath,'8.novel/novel_miRNAs/hairpin.fa'),157                                      mature    = os.path.join(self.projpath,'8.novel/novel_miRNAs/mature.fa'),158                                      hairpin_str = os.path.join(self.projpath,'8.novel/novel_miRNAs/hairpin.str'),159                                      hairpin_pos = os.path.join(self.projpath,'8.novel/novel_miRNAs/hairpin.pos'),160                                      outfile   = os.path.join(SuppFilesdir,'novel_hairpin_mature.xls')161                                                     )162                            )163        if 'refanimal' in self.org:164            assert not os.system('{perlExec} {BioScripts}/Release/targets_pairs.transfer.v3.pl {inf} {ouf}'.format(165                                         perlExec  = self.perlExec,BioScripts = self.BioScripts,166                                         inf = os.path.join(self.result,'*miRNA_target/all_target_gene.xls'),167                                         ouf = os.path.join(SuppFilesdir,'targets.pairs.allcom')168                                         )169                                )170        else:171            assert not os.system('{perlExec} {BioScripts}/Release/targets_pairs.transfer.v3.pl {inf} {ouf}'.format(172                                         perlExec  = self.perlExec,BioScripts = self.BioScripts,173                                         inf = os.path.join(self.result,'*miRNA_target/*_targets.pairs'),174                                         ouf = os.path.join(SuppFilesdir,'targets.pairs.allcom')175                                         )176                                )177            178        assert not os.system("sed -e 's/,/\\t/g' {inf} > {ouf}".format(179                                      inf = os.path.join(SuppFilesdir,'targets.pairs.allcom'),180                                      ouf = os.path.join(SuppFilesdir,'targets.pairs.alltab')181                                      )182                            )183        184        if 'noref' not in self.org:185            if 'refplant' in self.org:186                self.copy_dir(self.gene,os.path.join(SuppFilesdir,'gene.fa'))187            else:188                self.copy_dir(self.utr3,os.path.join(SuppFilesdir,'3_utr.fa'))189                190    def Example_data(self):191        192        #RawDatadir,CleanDatadir,order = self.make_dir('Example_data',['1.RawData','2.CleanData'])193        CleanDatadir,order = self.make_dir('Example_data',['1.CleanData'])       194        ''' 195        for eachsample in self.samples:196            files = glob.glob(self.projpath+'/raw_data/'+eachsample+'/'+eachsample+'.fq.gz')[0]197            f_in = gzip.open(files,'rb')198            f_out = [f_in.readline() for num in range(20)]199            f_out_name = os.path.join(RawDatadir,eachsample+'.example.raw.fastq')200            open(f_out_name,'w').writelines(f_out)201            f_in.close()202        shutil.copy('{}/1.1RawData.txt'.format(self.readme),os.path.join(RawDatadir,order+'.1.RawData.Readme.txt'))203        '''        204        for eachsample in self.samples:205            files=glob.glob(self.projpath+'/1.QC/'+eachsample+'/clean_data/'+eachsample+'_remain_total.fa')[0]206            f_in=open(files,'rb')207            f_out=[f_in.readline() for num in range(20)]208            f_out_name = os.path.join(CleanDatadir,eachsample+'.example.clean.fastq')209            open(f_out_name,'w').writelines(f_out)210            f_in.close()211        #shutil.copy('{}/1.2CleanData.txt'.format(self.readme),os.path.join(CleanDatadir,order+'.2.CleanData.Readme.txt'))212        shutil.copy('{}/1.2CleanData.txt'.format(self.readme),os.path.join(CleanDatadir,order+'.1.CleanData.Readme.txt'))213    def qc(self):214        #RawData_ErrorRate,RawData_Stat,ReadsClassification,Length_Filter,order = self.make_dir(215        #    'QualityControl',['1.RawData_ErrorRate','2.RawData_Stat','3.ReadsClassification','4.Length_Filter']216        #)217        218        Length_Filter,order = self.make_dir('QualityControl',['1.Length_Filter'])219        #qc_report = os.path.join(self.projpath,self.project+'_QC_results','results')220        #dirname = os.path.dirname(RawData_ErrorRate)221        #self.copy_dir(os.path.join(qc_report,'1RawData_ErrorRate/*'),RawData_ErrorRate)222        #self.copy_dir(os.path.join(qc_report,'2RawData_Stat/*'),RawData_Stat)223        #self.copy_dir(os.path.join(qc_report,'3ReadsClassification/*'),ReadsClassification)224        self.copy_dir(os.path.join(self.projpath,'1.QC/*/clean_data/*len_distribution.p*'),Length_Filter)225        #shutil.copy(226        #            '{}/2.1RawData_ErrorRate.txt'.format(self.readme),227        #            os.path.join(RawData_ErrorRate,order+'.1.RawData_ErrorRate.txt')228        #            )229        #shutil.copy(230        #            '{}/2.2RawData_Stat.txt'.format(self.readme),231        #            os.path.join(RawData_Stat,order+'.2.RawData_Stat.txt')232        #            )233        #shutil.copy(234        #            '{}/2.3ReadsClassification.txt'.format(self.readme),235        #            os.path.join(ReadsClassification,order+'.3.ReadsClassification.txt')236        #            )237        shutil.copy(238                    '{}/2.4Length_Filter.txt'.format(self.readme),239                    os.path.join(Length_Filter,order+'.1.Length_Filter.txt')240                    )241        #shutil.copy(242        #            '{}/2QC_2.txt'.format(self.readme),243        #            os.path.join(dirname,order+'.QC.Readme.txt')244        #            )     245        if 'y' in self.common :246            assert not os.system('mkdir -p {}'.format(os.path.join(dirname,order+'.5.Common_Specific_sRNA')))247            self.copy_dir(os.path.join(self.projpath,'1.QC','*_vs_*/*venn*'),dirname)248            shutil.copy(249                        '{}/2.5Common-Specific_sRNA.txt'.format(self.readme),250                        os.path.join(dirname,order+'.5.Common_Specific_sRNA',order+'.5.Common_Specific_sRNA.Readme.txt')251                        )252    def mapping(self):253        Mapping_Stat,order = self.make_dir('Mapping_Stat')254        analydir = os.path.join(self.projpath,'2.map')255        shutil.copy(256                    os.path.join(analydir,'reference.mapping.stat'),257                    Mapping_Stat258                   )259        for eachsample in self.samples:260            shutil.copy(261                        os.path.join(analydir,eachsample,eachsample+'.mapping.stat'),262                        Mapping_Stat263                       )264            if 'noref' not in self.org:265                shutil.copy(266                            os.path.join(analydir,eachsample,'Circos',eachsample+'_circos.png'),267                            os.path.join(Mapping_Stat,eachsample+'.circos.png')268                           )269                shutil.copy(270                            os.path.join(analydir,eachsample,'Circos',eachsample+'_circos.svg'),271                            os.path.join(Mapping_Stat,eachsample+'.circos.svg')272                           )        273        self.copy_dir(os.path.join(274                                   self.readme,'3Mapping_Stat.txt'275                                  ),os.path.join(Mapping_Stat,order+'.Mapping_Stat.Readme.txt')276                     )277    def known_miRNA(self):278        279        known_miRNA,order = self.make_dir('Known_miRNA')280        analydir = os.path.join(self.projpath,'3.known')        281        assert not os.system('mkdir -p {}'.format(282                             os.path.join(known_miRNA,'Structure_plot_example'))283                            )284        assert not os.system('tar -zcf {tardir} -C {rawdir} {file}'.format(285                             tardir = os.path.join(known_miRNA,'Structure_plot.tar.gz'),286                             rawdir = os.path.join(analydir,'known_miRNAs'),287                             file = 'image')288                             )289        assert not os.system('ls {} 2>&1 | head -n 10 | xargs -n1 -i cp {{}} {}'.format(290                            os.path.join(analydir,'known_miRNAs','image/*jpg'),291                            os.path.join(known_miRNA,'Structure_plot_example'))292                            )293        self.copy_dir(os.path.join(294                      analydir,'known_miRNAs','{hairpin*,mature*,known*.map.*,miRBase.mrd}'295                                  ),known_miRNA296                     )297                             298        for eachsample in self.samples:        299            shutil.copy(300                        os.path.join(analydir,eachsample+'.firstbase.png'),301                        known_miRNA302                       )303            shutil.copy(304                        os.path.join(analydir,eachsample+'.position.png'),305                        known_miRNA306                       )307        self.copy_dir(os.path.join(308                                   self.readme,'4Known_miRNA.txt'309                                  ),os.path.join(known_miRNA,order+'.Known_miRNA.Readme.txt')310                     )311        312    def ncRNA(self):313        ncRNA,order = self.make_dir('ncRNA')314        analydir = os.path.join(self.projpath,'4.ncRNA')315        self.copy_dir(os.path.join(316                      analydir,'output','{*.map.fas,rc.stat,uc.stat}'317                                  ),ncRNA318                     )319        self.copy_dir(os.path.join(320                      self.readme,'5ncRNA.txt'321                                  ),os.path.join(ncRNA,order+'.ncRNA.Readme.txt')322                     )                    323    def repeat(self):324        repeat,order = self.make_dir('Repeat')325        analydir = os.path.join(self.projpath,'5.repeat')326        self.copy_dir(os.path.join(327                      analydir,'{repeat.map.fas,repeat.rc.stat,repeat.uc.stat,*bar.png,*bar.pdf}'328                                  ),repeat329                     )330        self.copy_dir(os.path.join(331                      self.readme,'6Repeats.txt'332                                  ),os.path.join(repeat,order+'.Repeats.Readme.txt')333                     )334    def NAT(self):335        NAT,order = self.make_dir('NAT')336        analydir = os.path.join(self.projpath,'6.NAT')337        self.copy_dir(os.path.join(338                      analydir,'output','{*.map.fas,rc.stat,uc.stat,NAT.rc.stat,NAT.uc.stat}'339                                  ),NAT340                     )341        self.copy_dir(os.path.join(342                      self.readme,'7NAT.txt'343                                  ),os.path.join(NAT,order+'.NAT.Readme.txt')344                     )345    def geneAnalysis(self):346        gene,order = self.make_dir('gene')347        analydir = os.path.join(self.projpath,'7.gene')348        self.copy_dir(os.path.join(349                      analydir,'output','{*.map.fas,rc.stat,uc.stat}'350                                  ),gene351                     )352        self.copy_dir(os.path.join(353                      self.readme,'8gene.txt'354                                  ),os.path.join(gene,order+'.gene.Readme.txt')355                     )356    def novel_miRNA(self):357        Novel_miRNA,order = self.make_dir('Novel_miRNA')358        analydir = os.path.join(self.projpath,'8.novel')        359        assert not os.system('mkdir -p {}'.format(360                             os.path.join(Novel_miRNA,'Structure_plot_example'))361                            )362        assert not os.system('tar -zcf {tardir} -C {rawdir} {file}'.format(363                             tardir = os.path.join(Novel_miRNA,'Structure_plot.tar.gz'),364                             rawdir = os.path.join(analydir,'novel_miRNAs'),365                             file = 'image')366                             )367        assert not os.system('ls {} 2>&1 | head -n 10 | xargs -n1 -i cp {{}} {}'.format(368                            os.path.join(analydir,'novel_miRNAs','image/*jpg'),369                            os.path.join(Novel_miRNA,'Structure_plot_example'))370                            )371        self.copy_dir(os.path.join(372                      analydir,'novel_miRNAs','{hairpin*,mature*,novel*.map.*,miRBase.mrd,star*}'373                                  ),Novel_miRNA374                     )375                             376        for eachsample in self.samples:        377            shutil.copy(378                        os.path.join(analydir,eachsample+'.firstbase.png'),379                        Novel_miRNA380                       )381            shutil.copy(382                        os.path.join(analydir,eachsample+'.position.png'),383                        Novel_miRNA384                       )385        self.copy_dir(os.path.join(386                                   self.readme,'9Novel_miRNA.txt'387                                  ),os.path.join(Novel_miRNA,order+'.Novel_miRNA.Readme.txt')388                     )389            390    def TAS(self):391        392        tas,order = self.make_dir('TAS')393        analydir = os.path.join(self.projpath,'9.TAS')394        self.copy_dir(os.path.join(395                      analydir,'output','{TAS.map.fas,TAS.rc.stat,TAS.uc.stat}'396                                  ),tas397                     )398        self.copy_dir(os.path.join(399                      self.readme,'10TAS.txt'400                                  ),os.path.join(tas,order+'.TAS.Readme.txt')401                     )402        403    def Category(self):404        category,order = self.make_dir('Category')405        analydir = os.path.join(self.projpath,'10.Category')406        self.copy_dir(os.path.join(407                      analydir,'{*_full.txt,*pie.png,*pie.pdf}'408                                  ),category409                     )410        self.copy_dir(os.path.join(411                      self.readme,'11Category.txt'412                                  ),os.path.join(category,order+'.Category.Readme.txt')413                     )414    def miRNA_editing(self):415        miRNA_editing,order = self.make_dir('miRNA_editing')416        analydir = os.path.join(self.projpath,'11.edit_family')417        self.copy_dir(os.path.join(418                      analydir,'edit_analy','*editing_stats*.txt'419                                  ),miRNA_editing420                     )421        self.copy_dir(os.path.join(422                      self.readme,'12miRNA_editing.txt'423                                  ),os.path.join(miRNA_editing,order+'.miRNA_editing.Readme.txt')424                     )425        426    427    def miRNA_family(self):428        miRNA_family,order = self.make_dir('miRNA_family')429        analydir = os.path.join(self.projpath,'11.edit_family')430        self.copy_dir(os.path.join(431                      analydir,'family_analy','*_family.*.txt'432                                  ),miRNA_family433                     )434        self.copy_dir(os.path.join(435                      self.readme,'13miRNA_family.txt'436                                  ),os.path.join(miRNA_family,order+'.miRNA_family.Readme.txt')437                     )438    def diff_analy(self):439        analydir = os.path.join(self.projpath,'13.diff')440        if len(self.samples) == 1:441            miRNAExp,miRNAExpdensity,order = self.make_dir('DiffExprAnalysis',442                    ['1.miRNAExp','2.miRNAExpdensity'])443        else:444            if self.venn_cluster:445                (miRNAExp,miRNAExpdensity,CorAnalysis,DiffExprAnalysis,446                     DEsFilter,DEcluster,DEvenn,order) = self.make_dir('DiffExprAnalysis',[447                        '1.miRNAExp','2.miRNAExpdensity','3.CorAnalysis','4.DiffExprAnalysis',448                        '5.DEsFilter','6.DEcluster','7.DEvenn'449                         ])450            else:451                (miRNAExp,miRNAExpdensity,CorAnalysis,DiffExprAnalysis,452                     DEsFilter,DEcluster,order) = self.make_dir('DiffExprAnalysis',[453                        '1.miRNAExp','2.miRNAExpdensity','3.CorAnalysis',454                        '4.DiffExprAnalysis','5.DEsFilter','6.DEcluster'455                         ])456        self.copy_dir(os.path.join(457                        analydir,'diffAnalysisResult','{Readcount_TPM.xls,TPM_interval.xls}'458                            ),miRNAExp459                     )460        self.copy_dir(os.path.join(461                      self.readme,'14.1miRNAExp.txt'462                                  ),os.path.join(miRNAExp,order+'.1.miRNAExp.Readme.txt')463                     )464        465        self.copy_dir(os.path.join(466                        analydir,'diffAnalysisResult','{TPM_density_distribution.*,TPM_boxplot.*}'467                            ),miRNAExpdensity468                     )469        self.copy_dir(os.path.join(470                      self.readme,'14.2miRNAExpdensity.txt'471                                  ),os.path.join(miRNAExpdensity,order+'.2.miRNAExpdensity.Readme.txt')472                     )473        474        if len(self.samples) != 1:475        476            self.copy_dir(os.path.join(477                            analydir,'diffAnalysisResult','corr_plot/*'478                                ),CorAnalysis479                         )480            self.copy_dir(os.path.join(481                          self.readme,'14.3CorAnalysis.txt'482                                      ),os.path.join(CorAnalysis,order+'.3.CorAnalysis.Readme.txt')483                         )484            485            for each_compare in self.comparename.replace(':','vs').split(','):486                assert not os.system('mkdir -p {}'.format(os.path.join(DiffExprAnalysis,each_compare))) 487                self.copy_dir(os.path.join(488                                analydir,'diffAnalysisResult',each_compare,'{*vs*xls,*vs*txt}'489                                          ),os.path.join(DiffExprAnalysis,each_compare)490                             )491                self.copy_dir(os.path.join(492                                analydir,'diffAnalysisResult',each_compare,'*Volcanoplot*'493                                          ),DEsFilter494                             )                495            self.copy_dir(os.path.join(496                          self.readme,'14.4DiffExprAnalysis.txt'497                                      ),os.path.join(DiffExprAnalysis,order+'.4.DiffExprAnalysis.Readme.txt')498                         )499        500            self.copy_dir(os.path.join(501                          self.readme,'14.5DEsFilter.txt'502                                      ),os.path.join(DEsFilter,order+'.5.DEsFilter.Readme.txt')503                         )504            505            #self.copy_dir(os.path.join(506            #                analydir,'diffAnalysisResult',507            #                '{*heatmap.png,*heatmap.pdf,DE_union_for_cluster,SOM_cluster,K_means_cluster}'508            #                    ),DEcluster509            #             )510            #self.copy_dir(os.path.join(511            #              self.readme,'14.6DEcluster.txt'512            #                          ),os.path.join(DEcluster,order+'.6.DEcluster.Readme.txt')513            #             )514            if self.venn_cluster:515                516                self.copy_dir(os.path.join(517                                analydir,'diffAnalysisResult','venn'518                                    ),DEvenn519                             )520                assert not os.system('rm -rf {}'.format(os.path.join(521                                    DEvenn,'venn','{type.txt,Signature.xls,plot_venn.R}'))522                                )523                self.copy_dir(os.path.join(524                              self.readme,'14.7DEvenn.txt'525                                          ),os.path.join(DEvenn,order+'.7.DEvenn.Readme.txt')526                             )527            if len(self.groupname.split(','))==2:528                529                tmpdir = os.path.dirname(os.path.abspath(miRNAExp))530                DEvenn = os.path.join(tmpdir,order+'.7.DEvenn')531                assert not os.system('mkdir -p {}'.format(DEvenn))532                               533                self.copy_dir(os.path.join(534                                analydir,'diffAnalysisResult','venn'535                                    ),DEvenn536                             )537                self.copy_dir(os.path.join(538                              self.readme,'14.8DEvenn.txt'539                                          ),os.path.join(DEvenn,order+'.7.DEvenn.Readme.txt')                             )540                541                542    def miRNA_target_refanimal(self):543        544        miRNA_target,order = self.make_dir('miRNA_target')545        analydir = os.path.join(self.projpath,'12.target')546        self.copy_dir(os.path.join(547                      analydir,'Common','{commom_target.xls,all_target_gene.xls,commom_target_example.xls,all_target_gene.xls.annotate}'548                                  ),miRNA_target549                     )550        assert not os.system('gzip -c {}/miRanda/miranda_targets_out.fmt > {}/miranda_targets_out.fmt.gz'.format(analydir,miRNA_target))551        assert not os.system('gzip -c {}/RNAhybrid/RNAhybrid_miRNA_target_pairs > {}/RNAhybrid_miRNA_target_pairs.gz'.format(analydir,miRNA_target))       552        assert not os.system('gzip -c {}/PITA/PITA_pita_results_targets.tab > {}/PITA_pita_results_targets.tab.gz'.format(analydir,miRNA_target)) 553        self.copy_dir(os.path.join(554                      self.readme,'15miRNA_target.txt'555                                  ),os.path.join(miRNA_target,order+'.miRNA_target.Readme.txt')556                     )557    def miRNA_target_plant(self):558        559        miRNA_target,order = self.make_dir('miRNA_target')560        analydir = os.path.join(self.projpath,'12.target')561        self.copy_dir(os.path.join(562                    analydir,'{*targets.txt,*_example.xls,*targets.pairs.annotate,*targets.pairs}'563                            ),miRNA_target564                     )565        self.copy_dir(os.path.join(566                      self.readme,'15miRNA_target.txt'567                                  ),os.path.join(miRNA_target,order+'.miRNA_target.Readme.txt')568                     )  569    570        571    def miRNA_target_norefanimal(self):572        573        miRNA_target,order = self.make_dir('miRNA_target')574        analydir = os.path.join(self.projpath,'12.target')575        self.copy_dir(os.path.join(576                    analydir,'{*targets,*_example.xls,*targets.pairs.annotate,*targets.pairs}'577                            ),miRNA_target578                     )579        assert not os.system('gzip -c {}/mature.miranda_targets_out.fmt > {}/mature.miranda_targets_out.fmt.gz'.format(analydir,miRNA_target))580        self.copy_dir(os.path.join(581                    self.readme,'15miRNA_target.txt'582                            ),os.path.join(miRNA_target,order+'.miRNA_target.Readme.txt')583                     )584    def single_sample_Enrichment(self):585        586        Enrichment,order = self.make_dir('Enrichment')587        analydir = os.path.join(self.projpath,'14.enrich')588        godir    = os.path.join(Enrichment,self.samples[0],'GOenrichment') 589        keggdir  = os.path.join(Enrichment,self.samples[0],'KEGGenrichment')590        assert not os.system('mkdir -p {}'.format(godir))591        assert not os.system('mkdir -p {}'.format(keggdir))592        self.copy_dir(os.path.join(593                      analydir,'GO_enrichment','{*DEG*,*png,*pdf}'594                                  ),godir595                     )596        self.copy_dir(os.path.join(597                      analydir,'Pathway','{*scatterplot.png,*scatterplot.pdf,src}'598                                  ),keggdir599                     )600        self.copy_dir(os.path.join(601                      analydir,self.samples[0],'Pathway','*html'),602                      os.path.join(603                      keggdir,self.samples[0]+'.DEG_enriched_KEGG_pathway_API.html')604                      )605        self.copy_dir(os.path.join(606                      analydir,'Pathway',self.samples[0]+'.identify.xls'),607                      os.path.join(608                      keggdir,self.samples[0]+'.DEG_KEGG_pathway_enrichment_result.xls')609                      )610        self.copy_dir(os.path.join(611                      analydir,'Pathway','top*.xls'),612                      os.path.join(613                      keggdir,self.samples[0]+'.DEG_enriched_KEGG_pathway_top20.xls')614                     )615        self.copy_dir(os.path.join(616                      self.readme,'16Enrichment.txt'617                                  ),os.path.join(os.path.dirname(GOenrichment),order+'.Enrichment.Readme.txt')618                     )619    def multi_sample_Enrichment(self):620        Enrichment,order = self.make_dir('Enrichment')621        analydir = os.path.join(self.projpath,'14.enrich')622        self.copy_dir(os.path.join(623                      self.readme,'16Enrichment.txt'624                                  ),os.path.join(Enrichment,order+'.Enrichment.Readme.txt')625                     )626        for each_compare in self.comparename.replace(':','vs').split(','):627            temdir = os.path.join(Enrichment,each_compare)628            assert not os.system('mkdir -p {}'.format(temdir))629            self.copy_dir(os.path.join(630                          analydir,each_compare,'{*diffmiRNA-geneid,*diffmiRNAID,*diffmiRNA-gene.pairs}'631                                      ),temdir632                         )633            tmpgodir   = os.path.join(temdir,'GOenrichment')634            assert not os.system('mkdir -p {}'.format(tmpgodir))635            self.copy_dir(os.path.join(636                          analydir,each_compare,'GO2','*DEG*'637                                      ),tmpgodir638                          )639            os.system('rm -rf {}'.format(os.path.join(tmpgodir,640                                  '{*classification2_gene_count.txt,*classification2.pdf,*classification2.png}')641                                        )642                     )643            tmpkeggdir = os.path.join(temdir,'KEGGenrichment')644            assert not os.system('mkdir -p {}'.format(tmpkeggdir))645            self.copy_dir(os.path.join(646                          analydir,each_compare,'Pathway','{*scatterplot.pdf,*scatterplot.png,src}'647                                      ),tmpkeggdir648                         )649            650            self.copy_dir(os.path.join(651                          analydir,each_compare,'Pathway','*html'),652                          os.path.join(653                          tmpkeggdir,each_compare+'.DEG_enriched_KEGG_pathway_API.html')654                         )655            if 'noref' not in self.org:656 657                self.copy_dir(os.path.join(658                              analydir,each_compare,'Pathway',each_compare+'.identify.xls'),659                              os.path.join(660                              tmpkeggdir,each_compare+'.DEG_KEGG_pathway_enrichment_result.xls')661                              )662                self.copy_dir(os.path.join(663                              analydir,each_compare,'Pathway','top*.xls'),664                              os.path.join(665                              tmpkeggdir,each_compare+'.DEG_enriched_KEGG_pathway_top20.xls')666                              )667                668            else:669                670                self.copy_dir(os.path.join(671                              analydir,each_compare,'Pathway',each_compare+'*result.xls'),672                              os.path.join(673                              tmpkeggdir,each_compare+'.DEG_KEGG_pathway_enrichment_result.xls')674                              )675                self.copy_dir(os.path.join(676                              analydir,each_compare,'Pathway','*_top20.xls'),677                              os.path.join(678                              tmpkeggdir,each_compare+'.DEG_enriched_KEGG_pathway_top20.xls')679                              )680    def make_dir(self,analysis,subdirs=None):681        subdirL = list()682        order = self.order683        analydir = os.path.join(self.result,order + '.' + analysis)684        if 'SuppFiles' in analysis:685            SupFdir = os.path.join(self.result,'0.SuppFiles')686            assert not os.system(687                                'mkdir -p {}'.format(SupFdir)688                                )689            return SupFdir690        else:691            if subdirs:692                for subdir in subdirs:693                    absubdir = os.path.join(analydir,order + '.' + subdir)694                    assert not os.system('mkdir -p {}'.format(absubdir))695                    subdirL.append(absubdir)696                subdirL.append(order)697                return subdirL698            else:699                assert not os.system('mkdir -p {}'.format(analydir))700                return analydir,order701    @staticmethod702    def copy_dir(rawdir,newdir):703        if os.path.isfile(rawdir):704            assert not os.system(705                        'cp -f {rawdir} {newdir}'.format(706                        rawdir = rawdir, newdir = newdir)707                        )708        else:709            ## assert not os.system(710            os.system(711                        'cp -rf {rawdir} {newdir}'.format(712                        rawdir = rawdir, newdir = newdir)713                        )714def Argument():715    parser = argparse.ArgumentParser(716    description = 'srna pipline result v1.0',...

test_executers.py

Source:test_executers.py

1import shutil2import os3import _executers4import _config5from .sample_data import SAMPLE_DIR, none_dir, copy_dir, move_dir6def _clean_sample_data_dir():7    if os.path.isdir(SAMPLE_DIR):8        shutil.rmtree(SAMPLE_DIR)9    assert not os.path.isdir(SAMPLE_DIR)10def _create_folders_if_dont_exist(sample_data: _config.UserDir):11    _executers._create_folders_if_dont_exists(12        [sample_data.in_, sample_data.out]13    )14def _fill_with_sample_files_with_extension(15    directory: str, num_files: int, extension: str16) -> None:17    for filename in [f"sample{x}.{extension}" for x in range(0, num_files)]:18        with open(os.path.join(directory, filename), "w") as f:19            f.write("sample data")20def test_none_executer_creates_directory():21    _clean_sample_data_dir()22    executer = _executers.NoneExecuter(23        none_dir.in_, none_dir.out, none_dir.filter_24    )25    executer.run()26    assert os.path.isdir(SAMPLE_DIR)27def test_copy_executer_copy_all_files():28    _clean_sample_data_dir()29    _create_folders_if_dont_exist(copy_dir)30    _fill_with_sample_files_with_extension(copy_dir.in_, 3, "jpg")31    _fill_with_sample_files_with_extension(copy_dir.in_, 2, "txt")32    assert len(os.listdir(copy_dir.in_)) == 533    assert len(os.listdir(copy_dir.out)) == 034    executer = _executers.CopyExecuter(35        copy_dir.in_, copy_dir.out, copy_dir.filter_36    )37    executer.run()38    assert len(os.listdir(copy_dir.in_)) == 539    assert len(os.listdir(copy_dir.out)) == 340def test_copy_executer_copy_existing_files():41    _clean_sample_data_dir()42    _create_folders_if_dont_exist(copy_dir)43    _fill_with_sample_files_with_extension(copy_dir.in_, 3, "jpg")44    _fill_with_sample_files_with_extension(copy_dir.out, 1, "jpg")45    _fill_with_sample_files_with_extension(copy_dir.in_, 2, "txt")46    assert len(os.listdir(copy_dir.in_)) == 547    assert len(os.listdir(copy_dir.out)) == 148    executer = _executers.CopyExecuter(49        copy_dir.in_, copy_dir.out, copy_dir.filter_50    )51    executer.run()52    assert len(os.listdir(copy_dir.in_)) == 553    assert len(os.listdir(copy_dir.out)) == 354def test_move_executer_all_files():55    _clean_sample_data_dir()56    _create_folders_if_dont_exist(move_dir)57    _fill_with_sample_files_with_extension(move_dir.in_, 3, "jpg")58    _fill_with_sample_files_with_extension(move_dir.in_, 2, "txt")59    assert len(os.listdir(move_dir.in_)) == 560    assert len(os.listdir(move_dir.out)) == 061    executer = _executers.MoveExecuter(62        move_dir.in_, move_dir.out, move_dir.filter_63    )64    executer.run()65    assert len(os.listdir(move_dir.in_)) == 266    assert len(os.listdir(move_dir.out)) == 367def test_copy_executer_move_existing_files():68    _clean_sample_data_dir()69    _create_folders_if_dont_exist(move_dir)70    _fill_with_sample_files_with_extension(move_dir.in_, 3, "jpg")71    _fill_with_sample_files_with_extension(move_dir.in_, 2, "txt")72    _fill_with_sample_files_with_extension(move_dir.out, 1, "jpg")73    assert len(os.listdir(move_dir.in_)) == 574    assert len(os.listdir(move_dir.out)) == 175    executer = _executers.MoveExecuter(76        move_dir.in_, move_dir.out, move_dir.filter_77    )78    executer.run()79    assert len(os.listdir(move_dir.in_)) == 280    assert len(os.listdir(move_dir.out)) == 381def test_copy_over_same_out_path():82    _clean_sample_data_dir()83    _create_folders_if_dont_exist(copy_dir)84    _fill_with_sample_files_with_extension(copy_dir.out, 3, "jpg")85    _fill_with_sample_files_with_extension(copy_dir.out, 2, "txt")86    assert len(os.listdir(copy_dir.out)) == 587    executer = _executers.CopyExecuter(88        copy_dir.out, copy_dir.out, copy_dir.filter_89    )90    executer.run()91    assert len(os.listdir(copy_dir.out)) == 592def test_move_executer_same_out_path():93    _clean_sample_data_dir()94    _create_folders_if_dont_exist(move_dir)95    _fill_with_sample_files_with_extension(move_dir.out, 3, "jpg")96    _fill_with_sample_files_with_extension(move_dir.out, 2, "txt")97    assert len(os.listdir(move_dir.out)) == 598    executer = _executers.MoveExecuter(99        move_dir.out, move_dir.out, move_dir.filter_100    )101    executer.run()...

Automation Testing Tutorials

Learn to execute automation testing from scratch with LambdaTest Learning Hub. Right from setting up the prerequisites to run your first automation test, to following best practices and diving deeper into advanced test scenarios. LambdaTest Learning Hubs compile a list of step-by-step guides to help you be proficient with different test automation frameworks i.e. Selenium, Cypress, TestNG etc.