def run(self, log, info): info['WORKFLOW'] = dropbox.extendWorkflowID(info['WORKFLOW']) info['DROPBOXSTAGE'] = dropbox.make_stagebox(log, info) info['EXPERIMENT_CODE'] = dropbox.get_experiment_code(info) keys = [Keys.PEPXML, 'PEPCSV', 'MAYUOUT'] dropbox.keys_to_dropbox(log, info, keys, info['DROPBOXSTAGE']) # protxml special naming filename = os.path.basename(info['DROPBOXSTAGE']) + '.prot.xml' filepath = os.path.join(info['DROPBOXSTAGE'], filename) shutil.copy(info['PROTXML'], filepath) #search.properties requires some specific fields sinfo = info.copy() sinfo['FDR'] = info['FDR'] sinfo['DBASENAME'] = os.path.splitext(os.path.split(info['DBASE'])[1])[0] sinfo['PARENT-DATA-SET-CODES'] = info[Keys.DATASET_CODE] # set values to NONE if they were e.g. "" before for key in ['STATIC_MODS', 'VARIABLE_MODS']: if info.get(key, "") == "": sinfo[key] = 'NONE' #lowercase required sinfo['experiment-code'] = info['EXPERIMENT_CODE'] path = os.path.join(info['DROPBOXSTAGE'], 'search.properties') IniInfoHandler().write(sinfo, path) #write mail to dropbox but do not send yet (after viewer only) info['MAILFILE'] = os.path.join(info['DROPBOXSTAGE'], 'mailtext.txt') self._writemail(info.copy()) info['DROPBOXSTAGE'] = dropbox.move_stage_to_dropbox(log, info['DROPBOXSTAGE'], info['DROPBOX'], keepCopy=True) return info
def run(self, log, info): info['WORKFLOW'] = dropbox.extendWorkflowID(info['WORKFLOW']) info['WORKFLOW'] += " msproteomicstools@" + subprocess.check_output( "git --git-dir=/cluster/apps/imsbtools/stable/msproteomicstools/master/.git rev-parse --short HEAD", shell=True).strip() info['WORKFLOW'] += " openms@" + subprocess.check_output( "git --git-dir=/cluster/apps/openms/2.0.0-memory/OpenMS/.git rev-parse --short HEAD", shell=True).strip() info['DROPBOXSTAGE'] = stagebox = dropbox.make_stagebox(log, info) expcode = dropbox.get_experiment_code(info) #copy and compress align.csv, but not the matrix REQUEST: expcode in name tgt = os.path.join(stagebox, expcode + '_' + os.path.basename(info['ALIGNMENT_TSV'])) shutil.copy(info['ALIGNMENT_TSV'], tgt) subprocess.check_call('gzip ' + stagebox + '/* 2>&1', shell=True) tgt = os.path.join(stagebox, expcode + '_' + os.path.basename(info['ALIGNMENT_MATRIX'])) shutil.copy(info['ALIGNMENT_MATRIX'], tgt) dropbox.keys_to_dropbox(log, info, ['ALIGNER_STDOUT'], stagebox) #compress all mprophet files into one zip archive = os.path.join(stagebox, 'pyprophet_stats.zip') if not 'MPROPHET_STATS' in info: info['MPROPHET_STATS'] = [] if not isinstance(info['MPROPHET_STATS'], list): info['MPROPHET_STATS'] = [info['MPROPHET_STATS']] for entry in info['MPROPHET_STATS']: subprocess.check_call('zip -j ' + archive + ' ' + entry + " 2>&1", shell=True) #PATCH: reimport old classifier if existing was used if 'MPR_LDA_PATH' in info and info['MPR_LDA_PATH'] != "": subprocess.check_call('zip -j ' + archive + ' ' + info['MPR_LDA_PATH'] + " 2>&1", shell=True) if 'MPR_WT_PATH' in info and info['MPR_WT_PATH'] != "": subprocess.check_call('zip -j ' + archive + ' ' + info['MPR_WT_PATH'] + " 2>&1", shell=True) #SPACE PROJECT given dsinfo = {} dsinfo['SPACE'] = info['SPACE'] dsinfo['PROJECT'] = info['PROJECT'] dsinfo['PARENT_DATASETS'] = info[Keys.DATASET_CODE] if info.get("DB_SOURCE", "") == "PersonalDB": if isinstance(dsinfo['PARENT_DATASETS'], list): dsinfo['PARENT_DATASETS'].append(info["DBASE"]) else: dsinfo['PARENT_DATASETS'] = [dsinfo['PARENT_DATASETS'], info['DBASE']] dsinfo['DATASET_TYPE'] = 'SWATH_RESULT' dsinfo['EXPERIMENT_TYPE'] = 'SWATH_SEARCH' dsinfo['EXPERIMENT'] = expcode path = os.path.join(stagebox, 'dataset.attributes') IniInfoHandler().write(dsinfo, path) expinfo = {} expinfo['PARENT-DATA-SET-CODES'] = dsinfo['PARENT_DATASETS'] expinfo['ALIGNER_DSCORE_CUTOFF'] = info['MPR_DSCORE_CUTOFF'] for key in ['WORKFLOW', 'COMMENT', 'TRAML', 'EXTRACTION_WINDOW', 'WINDOW_UNIT', 'RT_EXTRACTION_WINDOW', 'MIN_UPPER_EDGE_DIST', 'IRTTRAML', 'MIN_RSQ', 'MIN_COVERAGE', 'MPR_NUM_XVAL','MPR_LDA_PATH', 'MPR_WT_PATH', 'MPR_FRACT', 'MPR_SSL_IF', 'MPR_SSL_IL', 'MPR_SSL_TF', 'MPR_SSL_TL', 'MPR_SSL_NI', 'MPR_MAINVAR', 'MPR_VARS', 'ALIGNER_FRACSELECTED', 'ALIGNER_MAX_RT_DIFF', 'ALIGNER_METHOD', 'ALIGNER_FDR', 'ALIGNER_MAX_FDRQUAL', 'ALIGNER_TARGETFDR', 'ALIGNER_REALIGN_METHOD', 'DO_CHROMML_REQUANT', 'ALGNER_MST_USERTCORR','ALIGNER_MST_STDEVMULT', 'ISOTOPIC_GROUPING', 'REQUANT_METHOD', ]: if info.get(key, "") != "": expinfo[key] = info[key] path = os.path.join(stagebox, 'experiment.properties') IniInfoHandler().write(expinfo, path) #put a copy of the whole ini into the dropbox. copy() to prevent OUTPUT being removed from main ini IniInfoHandler().write(info.copy(), os.path.join(stagebox, 'input.ini')) mailtext = "" if info.get("RUNSWATH2VIEWER","") == "true": try: destdir = "/IMSB/ra/%s/html/tapir/%s" % (getpass.getuser(), dsinfo['EXPERIMENT']) makedirs_clean(destdir) shutil.copy(info['ALIGNMENT_TSV'],destdir) for chrom in info['CHROM_MZML']: shutil.copy(chrom,destdir) subprocess.call("gunzip -v %s/*.gz 2>&1" % destdir, shell=True) mailtext = "\n\nswath2viewer was enabled. To visualize results use e.g.\n" \ "user@crick# /opt/imsb/georger/py26/bin/python " \ "/opt/imsb/georger/msproteomicstools/gui/TAPIR.py --in %s/*" % destdir except Exception, e: log.warn("swath2viewer failed! " + e.message)