| Previous changeset 20:26ec953069b3 (2019-06-03) Next changeset 22:98bd8a0f0901 (2019-06-04) |
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modified:
Tryp_V_T.py |
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| diff -r 26ec953069b3 -r 1b5bf8383973 Tryp_V_T.py --- a/Tryp_V_T.py Mon Jun 03 16:02:02 2019 -0400 +++ b/Tryp_V_T.py Tue Jun 04 01:29:12 2019 -0400 |
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| @@ -83,7 +83,7 @@ # we will not have the .gtf file so call cufflinks without -G option def transcriptAbundance(inputname): argString = "cufflinks -o "+inputname+".cuff -u -p 8 "+inputname+".sorted" - subprocess.call(argString, shell = True) + subprocess.call(argString, shell=True) os.remove(inputname+".sorted") #remove name.sorted os.remove(inputname+".sorted.bai") os.remove(inputname+".bam") @@ -96,7 +96,7 @@ dir_path = os.path.dirname(os.path.realpath(__file__)) # directory of this file refPath = dir_path + "/data/Reference/" + ref + "/" + refBase # eg refPath = data/Reference/Trinity/Trinity.fasta # used for dirty # refPath = 'Trinity.fasta' # dirty one - track_df = pd.read_csv(name+'.cuff/genes.fpkm_tracking', sep='\t') + track_df = pd.read_csv(dir_path+'/' + name + '.cuff/genes.fpkm_tracking', sep='\t') names = track_df['locus'] # print(len(names)) # print(names[:5]) @@ -234,13 +234,16 @@ return int(sac[1:i]) def combineFPMK(tdict): - fpkm_df = pd.read_csv(tdict['name']+'.cuff/genes.fpkm_tracking', sep='\t') + dir_path = os.path.dirname(os.path.realpath(__file__))+'/' + + fpkm_df = pd.read_csv(dir_path++tdict['name']+'.cuff/genes.fpkm_tracking', sep='\t') #fpkm_df = pd.read_csv('genes.fpkm_tracking',sep='\t') #print(fpkm_df.head()) fpkm_df['locus'] = fpkm_df['locus'].apply(lambda names: names[:names.find(':')]) #print(fpkm_df.head()) - reducedBlast_df = pd.read_csv(tdict['name']+'_transcript.csv') + + reducedBlast_df = pd.read_csv(dir_path + tdict['name']+'_transcript.csv') # reducedBlast_df = pd.read_csv('TrinityVT_transcript.csv') saccverSet = set(reducedBlast_df['saccver']) saccverList = list(saccverSet) @@ -398,12 +401,14 @@ # argdict = {'name':2, 'pdfexport': 3, 'refFastq': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8} def transcriptomicProcess(args,argdict): + dir_path = os.path.dirname(os.path.realpath(__file__)) tdict = {} tdict['name'] = args[argdict['name']] tdict['refFastq'] = args[argdict['refFastq']] tdict['forward'] = args[argdict['forward']] tdict['reverse'] = args[argdict['reverse']] - tdict['vivax_trans_database'] = 'data/vivax/Database/Phylotype_typeseqs.fas' + dir_path = os.path.dirname(os.path.realpath(__file__)) + tdict['vivax_trans_database'] = dir_path+'/data/vivax/Database/Phylotype_typeseqs.fas' tdict['pdf'] = args[argdict['pdfexport']] tdict['html_file'] = args[argdict['html_file']] tdict['html_resource'] = args[argdict['html_resource']] @@ -413,7 +418,7 @@ processSamFiles(tdict['name']) #uses samtools transcriptAbundance(tdict['name']) #uses cufflinks -> ?.cuff/*.* transcriptsForBlast(tdict['name'], tdict['refFastq']) #creates name+4blast.fa - blastContigs(tdict['name'], tdict['html_resource'], 'data/vivax/Database/Phylotype_typeseqs.fas') + blastContigs(tdict['name'], tdict['html_resource'], tdict['vivax_trans_database']) sum_df, sum2_df = combineFPMK(tdict) doBarChart(tdict, sum2_df) createHTML(tdict, sum_df) |