--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ProteinInteractions.py	Tue Mar 15 15:36:27 2016 -0400
@@ -0,0 +1,204 @@
+################################################################################
+# This program will read in a SAINT 'list.txt' file and the interactions from
+# the consensus path db database and return all the interactions that we saw in
+# our experiment in a format suitable for cytoscape. This allows us to filter
+# before getting PPIs so that it doesn't affect our SAINT score or include
+# interactions that don't score well
+################################################################################
+# Copyright (C)  Brent Kuenzi.
+# Permission is granted to copy, distribute and/or modify this document
+# under the terms of the GNU Free Documentation License, Version 1.3
+# or any later version published by the Free Software Foundation;
+# with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
+# A copy of the license is included in the section entitled "GNU
+# Free Documentation License".
+################################################################################
+## REQUIRED INPUT ##
+
+# 1) listfile: SAINTexpress output
+# 2) SAINT_cutoff: Saint score cutoff for import (between 0 and 1)
+# 3) Int_conf: Confidence of PPI from CPDB to include
+#       - low: no filtering
+#       - medium: >0.5
+#       - high: >0.7
+#       - very high: >0.9
+# 4) Species: Human, Yeast, or Mouse
+################################################################################
+
+
+import urllib2
+import itertools
+import sys
+import os
+
+
+listfile = sys.argv[1]
+SAINT_cutoff = sys.argv[2]
+Int_conf = sys.argv[3]
+Species = sys.argv[4]
+cyto_file = sys.argv[5]
+db_path = sys.argv[6]
+
+class ReturnValue1(object):
+    def __init__(self, uniprot_acc, gene, swissprot):
+        self.up = uniprot_acc
+        self.gn = gene
+        self.sp = swissprot
+class ReturnValue2(object):
+    def __init__(self, getdata, getproteins, getheader):
+        self.data = getdata
+        self.proteins = getproteins
+        self.header = getheader
+
+
+def main(listfile, SAINT_cutoff, Int_conf, Species):
+    cytoscape(dd_network(listfile, SAINT_cutoff, Int_conf), listfile, SAINT_cutoff)
+
+
+def readtab(infile):
+    with open(infile, 'r') as file_to_read:
+    # Read in tab-delim text.
+        output = []
+        for line in file_to_read:
+            line = line.strip()
+            temp = line.split('\t')
+            output.append(temp)
+    return output
+
+
+def read_listfile(listfile): 
+    # Get data, proteins and header from scaffold output
+    dupes = readtab(listfile)
+    header = dupes[0]
+    prot_start = header.index("PreyGene")-1
+    data = dupes[1:]
+    # Cut off blank line and END OF FILE.
+    proteins = []
+    for protein in data:
+        proteins.append(protein[prot_start])
+    return ReturnValue2(data, proteins, header)
+
+
+def get_info(uniprot_accession_in): 
+    # Get aa lengths and gene name.
+    error = open('error proteins.txt', 'a+')
+    i = 0
+    while i == 0:
+        try:
+            data = urllib2.urlopen("http://www.uniprot.org/uniprot/" + uniprot_accession_in
+                + ".fasta")
+            break
+        except urllib2.HTTPError, err:
+            i = i + 1
+            if i == 50:
+                sys.exit("More than 50 errors. Check your file or try again later.")
+            if err.code == 404:
+                error.write(uniprot_accession_in + '\t' + "Invalid URL. Check protein" + '\n')
+                seqlength = 'NA'
+                genename = 'NA'
+                return ReturnValue1(seqlength, genename)
+            elif err.code == 302:
+                sys.exit("Request timed out. Check connection and try again.")
+            else:
+                sys.exit("Uniprot had some other error")
+    lines = data.readlines()
+    header = lines[0]
+    lst = header.split('|')
+    lst2 = lst[2].split(' ')
+    swissprot = lst2[0]
+    uniprot_acc = lst[1]
+    if lines == []:
+        error.write(uniprot_accession_in + '\t' + "Blank Fasta" + '\n')
+        error.close
+        uniprot_acc = 'NA'
+        genename = 'NA'
+        return ReturnValue1(uniprot_acc, genename, swissprot)
+    if lines != []:
+        seqlength = 0
+        header = lines[0]
+        if 'GN=' in header:
+            lst = header.split('GN=')
+            lst2 = lst[1].split(' ')
+            genename = lst2[0]
+            error.close
+            return ReturnValue1(uniprot_acc, genename, swissprot)
+        if 'GN=' not in header:
+            genename = 'NA'
+            error.close
+            return ReturnValue1(uniprot_acc, genename, swissprot)
+
+
+def dd_network(listfile, SAINTscore, CPDB_filter): 
+    # Filter by SS and CPDB.
+    data = read_listfile(listfile).data
+    # Change to filtered list.
+    SS = (read_listfile(listfile).header).index("SaintScore")
+    filt_data = []
+    for i in data:
+        if i[SS] >= SAINTscore:
+            filt_data.append(i)
+    accessions = []
+    for i in filt_data:
+        accessions.append(get_info(i[1]).sp)
+    GO = []
+    for i in CPDB[2:]:
+        if i[3] >= CPDB_filter:
+        # Filter interaction confidence.
+            GO.append(i[2])
+            # All known interactions.
+    GO2 = []
+    for i in GO:
+        GO2.append(i.split(','))
+        # Make interactions list friendly.
+    unfiltered_network = {}
+    for i in accessions:
+        interactions = []
+        for j in GO2:
+            if i in j:
+            # Find the interactions.
+                if j not in interactions:
+                # Dont add duplicate interactions.
+                    interactions.append(j)
+        merged = list(itertools.chain(*interactions))
+        # Flatten list of lists.
+        unfiltered_network[i] = merged
+        # Assign all possible interactions to protein in a dictionary.
+    dd_network = {}
+    # Data dependent network.
+    for i in unfiltered_network:
+        temp = []
+        for j in unfiltered_network[i]:
+            if j in accessions:
+                if j not in temp:
+                    if j != i:
+                        temp.append(j)
+        dd_network[i] = temp
+    return dd_network
+
+
+def cytoscape(dd_network, listfile, SAINTscore):
+    with open('network.sif', 'wt') as y:
+        data = read_listfile(listfile).data
+        SS = (read_listfile(listfile).header).index("SaintScore")
+        filt_data = []
+        for i in data:
+            if i[SS] >= SAINTscore:
+                filt_data.append(get_info(i[1]).sp)
+        for i in filt_data:
+            if dd_network[i] != []:
+                lst = []
+                for j in dd_network[i]:
+                    lst.append(j)
+                for j in lst:
+                    y.write(i+'\t'+'pp'+'\t' + j+'\n')
+
+
+if Species == "Human":
+    CPDB = readtab(str(db_path) + 'ConsensusPathDB_human_PPI.txt')
+if Species == "Yeast":
+    CPDB = readtab(str(db_path) + 'ConsensusPathDB_yeast_PPI.txt')
+if Species == "Mouse":
+    CPDB = readtab(str(db_path) +'ConsensusPathDB_mouse_PPI.txt')
+if __name__ == '__main__':
+    main(listfile, SAINT_cutoff, Int_conf, Species)
+    os.rename('network.sif', str(cyto_file))