Mercurial > repos > johnheap > vapper

comparison Tryp_V_T.py @ 26:7983a9305b53 draft

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Uploaded
author johnheap
date Wed, 05 Jun 2019 05:54:10 -0400
parents c0a6a170163e
children 92c5ecb025b6
comparison
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25:c0a6a170163e 26:7983a9305b53
94 refBase = os.path.basename(refFastq) 94 refBase = os.path.basename(refFastq)
95 ref = os.path.splitext(refBase)[0] # 'mydata/test.fasta' -> 'test' 95 ref = os.path.splitext(refBase)[0] # 'mydata/test.fasta' -> 'test'
96 dir_path = os.path.dirname(os.path.realpath(__file__)) # directory of this file 96 dir_path = os.path.dirname(os.path.realpath(__file__)) # directory of this file
97 refPath = dir_path + "/data/Reference/" + ref + "/" + refBase # eg refPath = data/Reference/Trinity/Trinity.fasta 97 refPath = dir_path + "/data/Reference/" + ref + "/" + refBase # eg refPath = data/Reference/Trinity/Trinity.fasta
98 # used for dirty # refPath = 'Trinity.fasta' # dirty one 98 # used for dirty # refPath = 'Trinity.fasta' # dirty one
99 track_df = pd.read_csv(dir_path+'/' + name + '.cuff/genes.fpkm_tracking', sep='\t') 99 cur_path = os.getcwd()
100 track_df = pd.read_csv(cur_path+'/' + name + '.cuff/genes.fpkm_tracking', sep='\t')
100 names = track_df['locus'] 101 names = track_df['locus']
101 # print(len(names)) 102 # print(len(names))
102 # print(names[:5]) 103 # print(names[:5])
103 104
104 nlist = [] 105 nlist = []