Mercurial > repos > bornea > saint_protein_interactions

comparison ProteinInteractions.py @ 9:dd0b4c901d0a draft

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author bornea
date Wed, 23 Mar 2016 11:15:44 -0400
parents 355ad1ce474b
children
comparison
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8:355ad1ce474b 9:dd0b4c901d0a
79 return ReturnValue2(data, proteins, header) 79 return ReturnValue2(data, proteins, header)
80 80
81 81
82 def get_info(uniprot_accession_in): 82 def get_info(uniprot_accession_in):
83 # Get aa lengths and gene name. 83 # Get aa lengths and gene name.
84 print uniprot_accession_in
84 error = open('error proteins.txt', 'a+') 85 error = open('error proteins.txt', 'a+')
85 i = 0 86 i = 0
86 while i == 0: 87 while i == 0:
87 try: 88 try:
88 data = urllib2.urlopen("http://www.uniprot.org/uniprot/" + uniprot_accession_in 89 data = urllib2.urlopen("http://www.uniprot.org/uniprot/" + uniprot_accession_in
131 def dd_network(listfile, SAINTscore, CPDB_filter): 132 def dd_network(listfile, SAINTscore, CPDB_filter):
132 # Filter by SS and CPDB. 133 # Filter by SS and CPDB.
133 data = read_listfile(listfile).data 134 data = read_listfile(listfile).data
134 # Change to filtered list. 135 # Change to filtered list.
135 SS = (read_listfile(listfile).header).index("SaintScore") 136 SS = (read_listfile(listfile).header).index("SaintScore")
137 uni_ids = (read_listfile(listfile).header).index("PreyGene") - 1
136 filt_data = [] 138 filt_data = []
137 for i in data: 139 for i in data:
138 if i[SS] >= SAINTscore: 140 if i[SS] >= SAINTscore:
139 filt_data.append(i) 141 filt_data.append(i)
140 accessions = [] 142 accessions = []
141 for i in filt_data: 143 for i in filt_data:
142 accessions.append(get_info(i[1]).sp) 144 accessions.append(get_info(i[uni_ids]).sp)
143 GO = [] 145 GO = []
144 for i in CPDB[2:]: 146 for i in CPDB[2:]:
145 if i[3] >= CPDB_filter: 147 if i[3] >= CPDB_filter:
146 # Filter interaction confidence. 148 # Filter interaction confidence.
147 GO.append(i[2]) 149 GO.append(i[2])
178 180
179 def cytoscape(dd_network, listfile, SAINTscore): 181 def cytoscape(dd_network, listfile, SAINTscore):
180 with open('network.sif', 'wt') as y: 182 with open('network.sif', 'wt') as y:
181 data = read_listfile(listfile).data 183 data = read_listfile(listfile).data
182 SS = (read_listfile(listfile).header).index("SaintScore") 184 SS = (read_listfile(listfile).header).index("SaintScore")
185 uni_ids = (read_listfile(listfile).header).index("PreyGene") - 1
183 filt_data = [] 186 filt_data = []
184 for i in data: 187 for i in data:
185 if i[SS] >= SAINTscore: 188 if i[SS] >= SAINTscore:
186 filt_data.append(get_info(i[1]).sp) 189 filt_data.append(get_info(i[uni_ids]).sp)
187 for i in filt_data: 190 for i in filt_data:
188 if dd_network[i] != []: 191 if dd_network[i] != []:
189 lst = [] 192 lst = []
190 for j in dd_network[i]: 193 for j in dd_network[i]:
191 lst.append(j) 194 lst.append(j)