-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathclassify_ppi.py
executable file
·203 lines (158 loc) · 12.3 KB
/
classify_ppi.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
#AUTHOR: RATTINA Vimel - 2019/11/28 - SIB & Enyo Pharma
import sys #I/O files
import os, errno #create folder
import csv #parse tsv
import logging #log file
import pickle #store and use python object
logging.basicConfig(format='%(asctime)s\t%(levelname)s\t%(message)s', filename='main.log', level=logging.DEBUG)
###The aim of this script is to create a file to be integrated in neXtProt with no gene name and/or sequence changes and a file to be curated due to gene name and/or sequence changes
## INPUTS: ##
##-The flatten PPi file from ENYO (output of flatten_enyo_json.py),
##-The dictionnary object file with viral protein information about gene name and sequence from 2 versions of uniprot and if there is changes or not.
##-The dictionnary object file with human protein information about gene name and sequence from 2 versions of uniprot and if there is changes or not.
##-An output file name for the file to be integrated in neXtProt
##-An output file name for the file to be recurated by enyo & neXtProt
## OUTPUTS: ##
##-A first-version file (1/4) to be integrated by neXtProt with no gene name or sequence changes between 2 versions of uniprot i.e. the flatten PPi with in addition viral species, chain name and FTId
##-A file to be curated by enyo & nextprot with gene name and/or sequence changes between 2 versions of uniprot
###################
# FUNCTIONS #######
###################
###Function writting the output file ready to be integrated
def no_changes_for_sib(ppi, interactor1_ID, interactor2_ID, HP_dict, HorV_P_dict, outputfile):
##if changes status is available, the AC get downloaded
if ( ("Genename_changes" in HP_dict[interactor1_ID]) and ("Genename_changes" in HorV_P_dict[interactor2_ID])):
##if no gene name or sequence changed
if ( (HorV_P_dict[interactor2_ID]["Genename_changes"] == "no") and (HorV_P_dict[interactor2_ID]["Sequence_changes"] == "no") and (HP_dict[interactor1_ID]["Genename_changes"] == "no") and (HP_dict[interactor1_ID]["Sequence_changes"] == "no")):
common_core = ppi["ppi_type"]+"\t"+ppi["stable_id"]+"\t"+ppi["pmid"]+"\t"+ppi["psimi_id"]
common_core += "\t"+ppi["interactor1_accession"]+"\t"+ppi["interactor1_name"]+"\t"+ppi["interactor1_start"]+"\t"+ppi["interactor1_stop"]
common_core += "\t"+ppi["interactor2_accession"]+"\t"+ppi["interactor2_name"]+"\t"+ppi["interactor2_start"]+"\t"+ppi["interactor2_stop"]
common_core += "\t"+str(ppi["interactor1_mapping_sequence"])+"\t"+str(ppi["interactor1_isoform_accession"])+"\t"+str(ppi["interactor1_occurrence_start"])+"\t"+str(ppi["interactor1_occurrence_stop"])+"\t"+str(ppi["interactor1_occurrence_identity"])
common_core += "\t"+str(ppi["interactor2_mapping_sequence"])+"\t"+str(ppi["interactor2_isoform_accession"])+"\t"+str(ppi["interactor2_occurrence_start"])+"\t"+str(ppi["interactor2_occurrence_stop"])+"\t"+str(ppi["interactor2_occurrence_identity"])
##if VH PPi type every description will be associated to a viral species
if (ppi["ppi_type"] == "vh"):
common_core += "\t"+HorV_P_dict[interactor2_ID]["Uniprot_viral_species"]
##when chain name and FTId available write it otherwise write None
if HorV_P_dict[interactor2_ID].has_key("Chain_name"):
common_core += "\t"+HorV_P_dict[interactor2_ID]["FTId"]+"\t"+HorV_P_dict[interactor2_ID]["Chain_name"]
else:
common_core += "\tNone\tNone"
elif (ppi["ppi_type"] == "hh"):
common_core += "\t\t\t"
outputfile.write(common_core+"\n")
###Function writting the output file to be curated because of changes in gene name or sequence between the 2 UniProt versions
def changes_to_cure(ppi, interactor1_ID, interactor2_ID, HP_dict, HorV_P_dict, outputfile):
##if changes status is available, the AC get downloaded
if ( ("Genename_changes" in HP_dict[interactor1_ID]) and ("Genename_changes" in HorV_P_dict[interactor2_ID])):
##if changes repertoried in HP, print the pmid URL, gene name and sequence from the two UniProt versions
if ( (HP_dict[interactor1_ID]["Genename_changes"] == "yes") or (HP_dict[interactor1_ID]["Sequence_changes"] == "yes")):
print(interactor1_ID+"\tchanges")
debug = ppi["ppi_type"]+"\t"+ppi["stable_id"]+"\thttps://www.ncbi.nlm.nih.gov/pubmed/"+ppi["pmid"]
debug += "\t"+ppi["interactor1_accession"]+"\t"+ppi["interactor1_name"]
debug += "\t"+HP_dict[interactor1_ID]["Genename_changes"]+"\t"+HP_dict[interactor1_ID]["Sequence_changes"]
debug += "\t"+HP_dict[interactor1_ID]["Genename_ENYO"]+"\t"+HP_dict[interactor1_ID]["Genename_neXtProt"]
debug += "\t"+HP_dict[interactor1_ID]["Sequence_ENYO"]+"\t"+HP_dict[interactor1_ID]["Sequence_neXtProt"]
debug += "\t"+str(ppi["interactor1_isoform_accession"])+"\tHomo sapiens" ##Here the species is Homo sapiens
outputfile.write(debug+"\n")
##If changes repertoried in interactor2 so VP or HP depending on the PPi type
if ( (HorV_P_dict[interactor2_ID]["Genename_changes"] == "yes") or (HorV_P_dict[interactor2_ID]["Sequence_changes"] == "yes")):
print(interactor2_ID+"\tchanges")
debug = ppi["ppi_type"]+"\t"+ppi["stable_id"]+"\thttps://www.ncbi.nlm.nih.gov/pubmed/"+ppi["pmid"]
debug += "\t"+ppi["interactor2_accession"]+"\t"+ppi["interactor2_name"]
debug += "\t"+HorV_P_dict[interactor2_ID]["Genename_changes"]+"\t"+HorV_P_dict[interactor2_ID]["Sequence_changes"]
debug += "\t"+HorV_P_dict[interactor2_ID]["Genename_ENYO"]+"\t"+HorV_P_dict[interactor2_ID]["Genename_neXtProt"]
debug += "\t"+HorV_P_dict[interactor2_ID]["Sequence_ENYO"]+"\t"+HorV_P_dict[interactor2_ID]["Sequence_neXtProt"]
debug += "\t"+str(ppi["interactor2_isoform_accession"])
if (ppi["ppi_type"] == "vh"):
debug += "\t"+HorV_P_dict[interactor2_ID]["Uniprot_viral_species"]
elif (ppi["ppi_type"] == "hh"):
debug += "\tHomo sapiens"
outputfile.write(debug+"\n")
###Function filling the output file to be curated because no information was found
def no_information(ppi, interactor1_ID, interactor2_ID, HP_dict, HorV_P_dict, outputfile):
##if Genename_changes key does not exist, a problem occurs during download step
##if no changes in HP AC
if ("Genename_changes" not in HP_dict[interactor1_ID]):
print(interactor1_ID+"\tdoes not exist")
debug = ppi["ppi_type"]+"\t"+ppi["stable_id"]+"\thttps://www.ncbi.nlm.nih.gov/pubmed/"+ppi["pmid"]
debug += "\t"+ppi["interactor1_accession"]+"\t"+ppi["interactor1_name"]
debug += "\tyes\tyes\tNone\tNone\tNone\tNone" ##no gene name and sequence so put yes for both changes and None because no data were retrieved
debug += "\t"+str(ppi["interactor1_isoform_accession"]+"\thuman_failed") ##add a species name such as failed to highlight that the data could not be retrieved
outputfile.write(debug+"\n")
##If no changes in interactor2 so VP AC or HP AC
if ("Genename_changes" not in HorV_P_dict[interactor2_ID]):
print(interactor2_ID+"\tdoes not exist")
debug = ppi["ppi_type"]+"\t"+ppi["stable_id"]+"\thttps://www.ncbi.nlm.nih.gov/pubmed/"+ppi["pmid"]
debug += "\t"+ppi["interactor2_accession"]+"\t"+ppi["interactor2_name"]
debug += "\tyes\tyes\tNone\tNone\tNone\tNone"
if (ppi["ppi_type"] == "vh"):
debug += "\tNone\tvirus_failed"
elif (ppi["ppi_type"] == "hh"):
debug += "\tNone\thuman_failed"
outputfile.write(debug+"\n")
##Function creating the output files
def classify_ppi(flatfile, VP_dict_file, HP_dict_file, outputfile_raw_integrate, outputfile_recurate):
logging.info("Starts classifying PPi")
output_sib = open(outputfile_raw_integrate,"w")
output_cure = open(outputfile_recurate,"w")
with open(VP_dict_file, "rb") as viral_file:
VP_dict = pickle.loads(viral_file.read())
with open(HP_dict_file, "rb") as human_file:
HP_dict = pickle.loads(human_file.read())
##write the header in both output files
header_integrate = "ppi_type\tstable_id\tpmid\tpsimi_id"
header_integrate += "\tinteractor1_accession\tinteractor1_name\tinteractor1_start\tinteractor1_stop"
header_integrate += "\tinteractor2_accession\tinteractor2_name\tinteractor2_start\tinteractor2_stop"
header_integrate += "\tinteractor1_mapping_sequence\tinteractor1_isoform_accession"
header_integrate += "\tinteractor1_occurrence_start\tinteractor1_occurrence_stop\tinteractor1_occurrence_identity"
header_integrate += "\tinteractor2_mapping_sequence\tinteractor2_isoform_accession"
header_integrate += "\tinteractor2_occurrence_start\tinteractor2_occurrence_stop\tinteractor2_occurrence_identity"
header_integrate += "\tUniprot_viral_species\tFTId\tChain_name\n"
output_sib.write(header_integrate)
header_cure = "ppi_type\tstable_id\tpmid"
header_cure += "\tinteractor_accession\tinteractor_protein_name\tGenename_changes\tSequence_changes"
header_cure += "\tGenename_ENYO\tGenename_neXtProt\tSequence_ENYO\tSequence_neXtProt"
header_cure += "\tinteractor_isoform_AC\tspecies\n"
output_cure.write(header_cure)
with open(flatfile) as tsvfile:
reader = csv.DictReader(tsvfile, delimiter='\t')
for ppi in reader:
if (ppi["ppi_type"] == "vh"):
##recreate the keys, polyprotein name for viral protein and with isoform for human protein
interactor1_ID = ""
if (ppi["interactor1_mapping_sequence"] != ""): #None
interactor1_ID = ppi["interactor1_isoform_accession"]
else:
interactor1_ID = ppi["interactor1_accession"]
interactor2_ID = ppi["interactor2_accession"]+"_"+ppi["interactor2_name"]+"_"+ppi["interactor2_start"]+"_"+ppi["interactor2_stop"]
##function to write in the output files
no_changes_for_sib(ppi, interactor1_ID, interactor2_ID, HP_dict, VP_dict, output_sib)
changes_to_cure(ppi, interactor1_ID, interactor2_ID, HP_dict, VP_dict, output_cure)
no_information(ppi, interactor1_ID, interactor2_ID, HP_dict, VP_dict, output_cure)
if (ppi["ppi_type"] == "hh"):
interactor1_ID = ""
if (ppi["interactor1_mapping_sequence"] != ""): #None
interactor1_ID = ppi["interactor1_isoform_accession"]
else:
interactor1_ID = ppi["interactor1_accession"]
#print VP_dict[interactor1_ID]["Vprot_accession"]
interactor2_ID = ""
if (ppi["interactor2_mapping_sequence"] != ""): #None
interactor2_ID = ppi["interactor2_isoform_accession"]
else:
interactor2_ID = ppi["interactor2_accession"]
#print VP_dict[interactor1_ID]["Vprot_accession"]
no_changes_for_sib(ppi, interactor1_ID, interactor2_ID, HP_dict, HP_dict, output_sib)
changes_to_cure(ppi, interactor1_ID, interactor2_ID, HP_dict, HP_dict, output_cure)
no_information(ppi, interactor1_ID, interactor2_ID, HP_dict, HP_dict, output_cure)
output_cure.close()
output_sib.close()
logging.info("PPi classifying ends")
####################
# MAIN #############
####################
if len(sys.argv) < 6:
sys.exit('Usage: %s <flat_file> <VP_dict> <HP_dict> <outputfile_raw_integrate> <outputfile_recurate>\n<flat_file>: flatten json file from ENYO Pharma\n<VP_dict>: dictionnary of viral protein from update_ac_uniprot_information function\n<HP_dict>: dictionnary of human protein from update_ac_uniprot_information function\n<outputfile_raw_integrate>: first version (/4) of the file to be integrated in neXtProt (no gene name or sequence changes) with the same columns than flat_file\n<outputfile_recurate>: file to be recurate because of gene name and/or sequence changes or AC missing' % sys.argv[0])
if __name__ == "__main__":
classify_ppi(sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4], sys.argv[5])
#./classify_ppi.py vinland_flatfile.tsv results/2019_01/ results/2019_09/ theoutput_sib.tsv theoutput_recurate.tsv &> theoutput2.log