changeset 9:9c3d2b1d0c1c draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SAINT_preprocessing_v6_mq_pep.py	Tue Nov 10 13:15:41 2015 -0500
@@ -0,0 +1,262 @@
+#######################################################################################
+# Python-code: SAINT pre-processing from maxquant "Samples Report" output
+# Author: Brent Kuenzi
+#######################################################################################
+# This program reads in a raw maxquant "Samples Report" output and a user generated
+# bait file and autoformats it into prey and interaction files for SAINTexpress 
+# analysis
+#######################################################################################
+import sys
+import urllib2
+import os
+#######################################################################################
+## REQUIRED INPUT ##
+
+# 1) infile: maxquant "Samples Report" output
+# 2) baitfile: SAINT formatted bait file generated in Galaxy
+# 3) prey: Y or N for generating a prey file (requires internet connection)
+#######################################################################################
+mq_file = sys.argv[1]
+cmd = r"Rscript /home/bornea/galaxy_moffitt_dev/tools/Moffitt_Tools/bubblebeam/pre_process_protein_name_set.R " + str(mq_file) 
+os.system(cmd)
+
+infile = "./tukeys_output.txt" #maxquant "Samples Report" output
+prey = sys.argv[2] # Y or N
+fasta_db = sys.argv[3]
+if fasta_db == "None":
+    fasta_db = "/home/bornea/galaxy_moffitt_dev/tools/Moffitt_Tools/bubblebeam/SwissProt_HUMAN_2014_08.fasta"
+make_bait= sys.argv[6]
+
+def bait_create(baits, infile):
+    #Takes the Bait specified by the user and makes them into a Bait file and includes a check to make sure they are using valid baits.
+    baits = make_bait.split()
+    i = 0
+    bait_file_tmp = open("bait.txt", "wr")
+    order = [] 
+    bait_cache = []
+    while i < len(baits):
+        if baits[i+2] == "true":
+            T_C = "C"
+        else:
+            T_C = "T"
+        line1 = baits[i] + "\t" + baits[i+1] + "\t" + T_C + "\n"
+        q = open(infile,"r")
+        for line2 in q:
+           line2 = line2.replace("\"", "")
+           line2 = line2.replace(r"Intensity.", "") #R coerces "-" into "." this changes them back and remove Intensity from the Bait names.
+           line2 = line2.replace(r".", r"-")
+           temp = line2.split()
+           if "mapped_protein" in str(temp):
+                #If the bait is in the original file then write to cache it if not exit.
+                if baits[i] in temp:
+                    number_bait = temp.index(str(baits[i]))
+                    number_bait = number_bait - 9
+                    bait_cache.append((number_bait, str(line1)))
+                else:
+                    print "Error: bad bait " + str(baits[i])
+                    sys.exit()
+           else: 
+                pass                    
+        i = i + 3
+    #Writes cache to file.
+    bait_cache.sort()
+    for line in bait_cache:
+        bait_file_tmp.write(line[1])            
+        
+    bait_file_tmp.close()  
+
+
+baitfile = "bait.txt"
+
+class ReturnValue1(object):
+    def __init__(self, sequence, gene):
+     self.seqlength = sequence
+     self.genename = gene
+class ReturnValue2(object):
+    def __init__(self, getdata, getproteins, getheader):
+        self.data = getdata
+        self.proteins = getproteins
+        self.header = getheader
+
+def main(maxquant_input, make_bait):  
+    bait_create(make_bait, infile)
+    baitfile = "bait.txt"
+    #bait_check(baitfile, maxquant_input)
+    make_inter(maxquant_input)
+    if prey == 'true':
+        make_prey(maxquant_input)
+        no_error_inter(maxquant_input)
+        os.rename('prey.txt', sys.argv[5])
+    elif prey == 'false':
+        if os.path.isfile('error proteins.txt') == True:
+            no_error_inter(maxquant_input)
+        pass
+    elif prey != 'true' or 'false':
+        sys.exit("Invalid Prey Argument: Y or N")
+    os.rename('inter.txt', sys.argv[4])
+    os.rename("bait.txt", sys.argv[7])
+
+
+def get_info(uniprot_accession_in): # get aa lengths and gene name
+    error = open('error proteins.txt', 'a+')
+#    while True:
+#        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")
+#
+#
+#    if lines == []:
+#        error.write(uniprot_accession_in + '\t' + "Blank Fasta" + '\n')
+#        error.close
+# if lines == []:
+#        error.write(uniprot_accession_in + '\t' + "Blank Fasta" + '\n')
+#        error.close
+#        seqlength = 'NA'
+#        genename = 'NA'
+#        return ReturnValue1(seqlength, genename)
+#    if lines != []:
+#        seqlength = 0
+#        header = lines[0]
+#        for line in lines[1:]:
+#            line = line.replace("\n","") # strip \n or else it gets counted in the length
+#            seqlength += len(line) 
+#        if 'GN=' in header:
+#            lst = header.split('GN=')
+#            lst2 = lst[1].split(' ')
+#            genename = lst2[0]
+#            error.close
+#            return ReturnValue1(seqlength, genename)
+#        if 'GN=' not in header:
+#            genename = 'NA'
+#            error.close
+#            return ReturnValue1(seqlength, genename)
+
+    data = open(fasta_db,'r')
+    lines = data.readlines()
+    db_len = len(lines)
+    seqlength = 0
+    count = 0
+    for i in lines:           
+        if ">sp" in i:
+            if uniprot_accession_in == i.split("|")[1]:
+                match = count+1
+                if 'GN=' in i:
+                    lst = i.split('GN=')
+                    lst2 = lst[1].split(' ')
+                    genename = lst2[0]
+                if 'GN=' not in i:
+                    genename = 'NA'
+                while ">sp" not in lines[match]:
+                    if match <= db_len:
+                        seqlength = seqlength + len(lines[match].strip())
+                        match = match + 1
+                    else:
+                        break
+                return ReturnValue1(seqlength, genename)
+        count = count + 1
+        
+
+    if seqlength == 0:
+        error.write(uniprot_accession_in + '\t' + "Uniprot not in Fasta" + '\n')
+        error.close
+        seqlength = 'NA'
+        genename = 'NA'
+        return ReturnValue1(seqlength, genename)
+
+
+def readtab(infile):
+    with open(infile,'r') as x: # read in tab-delim text
+        output = []
+        for line in x:
+            line = line.strip()
+            temp = line.split('\t')
+            output.append(temp)
+    return output
+def read_maxquant(maxquant_input): # Get data, proteins and header from maxquant output
+    dupes = readtab(maxquant_input)
+    header_start = 0 
+    header = dupes[header_start]
+    for i in header:
+        i = i.replace(r"\"", "")
+        i = i.replace(r"Intensity.", r"")
+        i = i.replace(r".", r"-")
+    data = dupes[header_start+1:len(dupes)] #cut off blank line and END OF FILE
+    proteins = []
+    for protein in data:
+        proteins.append(protein[0])
+    return ReturnValue2(data, proteins, header)
+def make_inter(maxquant_input):
+    bait = readtab(baitfile)
+    data = read_maxquant(maxquant_input).data
+    header = read_maxquant(maxquant_input).header
+    proteins = read_maxquant(maxquant_input).proteins
+    bait_index = []
+    for i in bait:
+        bait_index.append(header.index("mapped_protein") + 1) # Find just the baits defined in bait file
+    with open('inter.txt', 'w') as y:
+            a = 0; l=0
+            for bb in bait:
+                for lst in data:
+                    y.write(header[bait_index[l]] + '\t' + bb[1] + '\t' + proteins[a] + '\t' + lst[bait_index[l]] + '\n')
+                    a+=1
+                    if a == len(proteins):
+                        a = 0; l+=1
+def make_prey(maxquant_input):
+    proteins = read_maxquant(maxquant_input).proteins
+    output_file = open("prey.txt",'w')
+    for a in proteins:
+        a = a.replace("\n","") # remove \n for input into function
+        a = a.replace("\r","") # ditto for \r
+        seq = get_info(a).seqlength
+        GN = get_info(a).genename
+        if seq != 'NA':
+            output_file.write(a+"\t"+str(seq)+ "\t" + str(GN) + "\n")
+    output_file.close()
+def no_error_inter(maxquant_input): # remake inter file without protein errors from Uniprot
+    err = readtab("error proteins.txt")
+    bait = readtab(baitfile)
+    data = read_maxquant(maxquant_input).data
+    header = read_maxquant(maxquant_input).header
+    header = [i.replace(r"\"", "") for i in header]
+    header = [i.replace(r"Intensity.", r"") for i in header]
+    header = [i.replace(r".", r"-") for i in header]
+    print header
+    bait_index = []
+    for i in bait:
+        bait_index.append(header.index(i[0]))
+    proteins = read_maxquant(maxquant_input).proteins
+    errors = []
+    for e in err:
+        errors.append(e[0])
+    with open('inter.txt', 'w') as y:
+        l = 0; a = 0
+        for bb in bait:
+            for lst in data:
+                if proteins[a] not in errors:
+                    y.write(header[bait_index[l]] + '\t' + bb[1] + '\t' + proteins[a] + '\t' + lst[bait_index[l]] + '\n')
+                a+=1
+                if a == len(proteins):
+                    l += 1; a = 0
+def bait_check(bait, maxquant_input): # check that bait names share header titles
+    bait_in = readtab(bait)
+    header = read_maxquant(maxquant_input).header
+    for i in bait_in:
+        if i[0] not in header:
+            sys.exit("Bait must share header titles with maxquant output")
+
+if __name__ == '__main__':
+    main(infile, make_bait)