Mercurial > repos > johnheap > vapper

comparison Tryp_T.py @ 4:8f6469ffef85 draft

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planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
author johnheap
date Thu, 19 Jul 2018 06:38:58 -0400
parents 36cb22bd911d
children 25226d33642e
comparison
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3:4432e4183ebd 4:8f6469ffef85
87 dir_path = os.path.dirname(os.path.realpath(__file__)) 87 dir_path = os.path.dirname(os.path.realpath(__file__))
88 refName = dir_path + "/data/Reference/ORFAnnotation.gtf" # default 88 refName = dir_path + "/data/Reference/ORFAnnotation.gtf" # default
89 if strain == "Tc148": 89 if strain == "Tc148":
90 refName = dir_path + "/data/Reference/148_prot.fasta" 90 refName = dir_path + "/data/Reference/148_prot.fasta"
91 if strain == "IL3000": 91 if strain == "IL3000":
92 refName = dir_path + "data/Reference/IL3000_prot.fasta" 92 refName = dir_path + "/data/Reference/IL3000_prot.fasta"
93 93
94 cuff_df = pd.read_csv(inputName+".cuff/genes.fpkm_tracking", sep='\t') 94 cuff_df = pd.read_csv(inputName+".cuff/genes.fpkm_tracking", sep='\t')
95 cuff_df = cuff_df[(cuff_df['FPKM'] > 0)] 95 cuff_df = cuff_df[(cuff_df['FPKM'] > 0)]
96 cuff_df.to_csv("cuffTest.csv") 96 cuff_df.to_csv("cuffTest.csv")
97 gene_id_List = cuff_df['gene_id'].tolist() 97 gene_id_List = cuff_df['gene_id'].tolist()
122 line = ref.readline() 122 line = ref.readline()
123 if line: 123 if line:
124 while line[0] != '>': 124 while line[0] != '>':
125 outfile.write(line) 125 outfile.write(line)
126 line=ref.readline() 126 line=ref.readline()
127 if not line:
128 break;
127 else: 129 else:
128 line = ref.readline() 130 line = ref.readline()
129 else: 131 else:
130 line =ref.readline() 132 line =ref.readline()
131 ref.close() 133 ref.close()