havugimana MMC ppi, starting to rearrange data files

data/.gitignore

@@ -0,0 +1 @@
+

src/pappi/ppis/havu.py

@@ -0,0 +1,28 @@
+# import the module for the super-class PPI
+from .ppi import PPI
+
+
+class Havugimana(PPI):
+ """
+ The PPI network from the Havugimana paper:
+ A census of human soluble protein complexes
+ http:https://www.ncbi.nlm.nih.gov/pubmed/22939629
+ """
+
+ def __init__(self, filename, sql_connection):
+ """
+ Creates a new PPI network, with the given filename and sql
+ connection object.
+
+ Parameter:
+ - filename: Filename of the ppi network file.
+ - sql_connection: SQL connection object for the database,
+ into which the PPI network is to be
+ imported.
+ """
+ # create super class with all necessary paramenters
+ PPI.__init__(self, filename, sql_connection, "havu",
+ "Gene1", "Gene2", "uniprot")
+
+ self.has_header = True
+ self.file_field_seperator = '\t'

src/test_mapping.py

@@ -1,18 +1,23 @@
 import pappi.id_mapping
 import pappi.sql
-#import pappi.ppi_import
-from pappi.ppi.ccsb import CCSB
-from pappi.ppi.bossi_lehner import Bossi_Lehner
+#import pappi.ppis_import
+from pappi.ppis.ccsb import CCSB
+from pappi.ppis.bossi_lehner import Bossi_Lehner
+from pappi.ppis.havu import Havugimana
 import os
 
 DATA_FOLDER = '/home/patrick/dev/bio/data/'
+INT_DATA_FOLDER = '/home/patrick/dev/bio/pappi/data/'
 
 HGNC_FILE = DATA_FOLDER + 'hgnc_entrez_ensembl_uniprot.txt'
 BIOMART_FILE = DATA_FOLDER + 'mart_export.csv'
 DATABASE = DATA_FOLDER + 'test_matching.sqlite'
 CCSB_FILE = DATA_FOLDER + 'HI_2012_PRE.tsv'
 BOSSI_FILE = DATA_FOLDER + 'CRG.integrated.human.interactome.txt'
 
+HAVU_FILE = INT_DATA_FOLDER + 'cell_havugimana_ppi.tsv'
+
+
 # first delete an old DB, to make sure everything is new
 if (os.path.exists(DATABASE)):
  os.remove(DATABASE)
@@ -30,7 +35,7 @@
 
 #ccsb_file = open(CCSB_FILE)
 #print("Importing CCSB data ...")
-#pappi.ppi_import.import_ccsb_file(ccsb_file, con, 'ccsb')
+#pappi.ppis_import.import_ccsb_file(ccsb_file, con, 'ccsb')
 
 #pappi.id_mapping.map_identifier('ccsb', ['Gene_IDA', 'Gene_IDB'], 'entrez',
 # 'ccsb_hgnc1', 'hgnc', con, True)
@@ -42,3 +47,6 @@
 bossi_ppi = Bossi_Lehner(BOSSI_FILE, con)
 #bossi_ppi.import_raw_file()
 bossi_ppi.init_ppi(True)
+
+havu_ppi = Havugimana(HAVU_FILE, con)
+havu_ppi.init_ppi(True)