--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shm_csr.py	Mon Dec 12 05:22:37 2016 -0500
@@ -0,0 +1,285 @@
+from __future__ import division
+from collections import defaultdict
+import re
+import argparse
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--input",
+					help="The '7_V-REGION-mutation-and-AA-change-table' and '10_V-REGION-mutation-hotspots' merged together, with an added 'best_match' annotation")
+parser.add_argument("--genes", help="The genes available in the 'best_match' column")
+parser.add_argument("--empty_region_filter", help="Where does the sequence start?", choices=['leader', 'FR1', 'CDR1', 'FR2'])
+parser.add_argument("--output", help="Output file")
+
+args = parser.parse_args()
+
+infile = args.input
+genes = str(args.genes).split(",")
+empty_region_filter = args.empty_region_filter
+outfile = args.output
+
+genedic = dict()
+
+mutationdic = dict()
+mutationMatcher = re.compile("^(.)(\d+).(.),?(.)?(\d+)?.?(.)?(.?.?.?.?.?)?")
+NAMatchResult = (None, None, None, None, None, None, '')
+linecount = 0
+
+IDIndex = 0
+best_matchIndex = 0
+fr1Index = 0
+cdr1Index = 0
+fr2Index = 0
+cdr2Index = 0
+fr3Index = 0
+first = True
+IDlist = []
+mutationList = []
+mutationListByID = {}
+cdr1LengthDic = {}
+cdr2LengthDic = {}
+
+with open(infile, 'r') as i:
+	for line in i:
+		if first:
+			linesplt = line.split("\t")
+			IDIndex = linesplt.index("Sequence.ID")
+			best_matchIndex = linesplt.index("best_match")
+			fr1Index = linesplt.index("FR1.IMGT")
+			cdr1Index = linesplt.index("CDR1.IMGT")
+			fr2Index = linesplt.index("FR2.IMGT")
+			cdr2Index = linesplt.index("CDR2.IMGT")
+			fr3Index = linesplt.index("FR3.IMGT")
+			cdr1LengthIndex = linesplt.index("CDR1.IMGT.length")
+			cdr2LengthIndex = linesplt.index("CDR2.IMGT.length")
+			first = False
+			continue
+		linecount += 1
+		linesplt = line.split("\t")
+		ID = linesplt[IDIndex]
+		genedic[ID] = linesplt[best_matchIndex]
+		try:
+			mutationdic[ID + "_FR1"] = [mutationMatcher.match(x).groups() for x in linesplt[fr1Index].split("|") if x] if (linesplt[fr1Index] != "NA" and empty_region_filter == "leader") else []
+			mutationdic[ID + "_CDR1"] = [mutationMatcher.match(x).groups() for x in linesplt[cdr1Index].split("|") if x] if (linesplt[cdr1Index] != "NA" and empty_region_filter in ["leader", "FR1"]) else []
+			mutationdic[ID + "_FR2"] = [mutationMatcher.match(x).groups() for x in linesplt[fr2Index].split("|") if x] if (linesplt[fr2Index] != "NA" and empty_region_filter in ["leader", "FR1", "CDR1"]) else []
+			mutationdic[ID + "_CDR2"] = [mutationMatcher.match(x).groups() for x in linesplt[cdr2Index].split("|") if x] if (linesplt[cdr2Index] != "NA") else []
+			mutationdic[ID + "_FR2-CDR2"] = mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"]
+			mutationdic[ID + "_FR3"] = [mutationMatcher.match(x).groups() for x in linesplt[fr3Index].split("|") if x] if linesplt[fr3Index] != "NA" else []
+		except Exception as e:
+			print "Something went wrong while processing this line:"
+			print linesplt
+			print linecount
+			print e
+		mutationList += mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
+		mutationListByID[ID] = mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
+
+		cdr1Length = linesplt[cdr1LengthIndex]
+		cdr2Length = linesplt[cdr2LengthIndex]
+
+		cdr1LengthDic[ID] = int(cdr1Length) if cdr1Length != "X" else 0
+		cdr2LengthDic[ID] = int(cdr2Length) if cdr2Length != "X" else 0
+		
+		IDlist += [ID]
+
+AALength = (int(max(mutationList, key=lambda i: int(i[4]) if i[4] else 0)[4]) + 1)  # [4] is the position of the AA mutation, None if silent
+if AALength < 60:
+	AALength = 64
+
+AA_mutation = [0] * AALength
+AA_mutation_dic = {"IGA": AA_mutation[:], "IGG": AA_mutation[:], "IGM": AA_mutation[:], "IGE": AA_mutation[:], "unm": AA_mutation[:], "all": AA_mutation[:]}
+AA_mutation_empty = AA_mutation[:]
+
+aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt"
+with open(aa_mutations_by_id_file, 'w') as o:
+	o.write("ID\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n")
+	for ID in mutationListByID.keys():
+		AA_mutation_for_ID = AA_mutation_empty[:]
+		for mutation in mutationListByID[ID]:
+			if mutation[4]:
+				AA_mutation_position = int(mutation[4])
+				AA_mutation[AA_mutation_position] += 1
+				AA_mutation_for_ID[AA_mutation_position] += 1
+				clss = genedic[ID][:3]
+				AA_mutation_dic[clss][AA_mutation_position] += 1
+		o.write(ID + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID[1:]]) + "\n")
+
+
+
+#absent AA stuff
+absentAACDR1Dic = defaultdict(list)
+absentAACDR1Dic[5] = range(29,36)
+absentAACDR1Dic[6] = range(29,35)
+absentAACDR1Dic[7] = range(30,35)
+absentAACDR1Dic[8] = range(30,34)
+absentAACDR1Dic[9] = range(31,34)
+absentAACDR1Dic[10] = range(31,33)
+absentAACDR1Dic[11] = [32]
+
+absentAACDR2Dic = defaultdict(list)
+absentAACDR2Dic[0] = range(55,65)
+absentAACDR2Dic[1] = range(56,65)
+absentAACDR2Dic[2] = range(56,64)
+absentAACDR2Dic[3] = range(57,64)
+absentAACDR2Dic[4] = range(57,63)
+absentAACDR2Dic[5] = range(58,63)
+absentAACDR2Dic[6] = range(58,62)
+absentAACDR2Dic[7] = range(59,62)
+absentAACDR2Dic[8] = range(59,61)
+absentAACDR2Dic[9] = [60]
+
+absentAA = [len(IDlist)] * (AALength-1)
+for k, cdr1Length in cdr1LengthDic.iteritems():
+	for c in absentAACDR1Dic[cdr1Length]:
+		absentAA[c] -= 1
+
+for k, cdr2Length in cdr2LengthDic.iteritems():
+	for c in absentAACDR2Dic[cdr2Length]:
+		absentAA[c] -= 1
+
+
+aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/absent_aa_id.txt"
+with open(aa_mutations_by_id_file, 'w') as o:
+	o.write("ID\tcdr1length\tcdr2length\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n")
+	for ID in IDlist:
+		absentAAbyID = [1] * (AALength-1)
+		cdr1Length = cdr1LengthDic[ID]
+		for c in absentAACDR1Dic[cdr1Length]:
+			absentAAbyID[c] -= 1
+
+		cdr2Length = cdr2LengthDic[ID]
+		for c in absentAACDR2Dic[cdr2Length]:
+			absentAAbyID[c] -= 1
+		o.write(ID + "\t" + str(cdr1Length) + "\t" + str(cdr2Length) + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in absentAAbyID]) + "\n")
+
+if linecount == 0:
+	print "No data, exiting"
+	with open(outfile, 'w') as o:
+		o.write("RGYW (%)," + ("0,0,0\n" * len(genes)))
+		o.write("WRCY (%)," + ("0,0,0\n" * len(genes)))
+		o.write("WA (%)," + ("0,0,0\n" * len(genes)))
+		o.write("TW (%)," + ("0,0,0\n" * len(genes)))
+	import sys
+
+	sys.exit()
+
+hotspotMatcher = re.compile("[actg]+,(\d+)-(\d+)\((.*)\)")
+RGYWCount = {}
+WRCYCount = {}
+WACount = {}
+TWCount = {}
+
+#IDIndex = 0
+ataIndex = 0
+tatIndex = 0
+aggctatIndex = 0
+atagcctIndex = 0
+first = True
+with open(infile, 'r') as i:
+	for line in i:
+		if first:
+			linesplt = line.split("\t")
+			ataIndex = linesplt.index("X.a.t.a")
+			tatIndex = linesplt.index("t.a.t.")
+			aggctatIndex = linesplt.index("X.a.g.g.c.t..a.t.")
+			atagcctIndex = linesplt.index("X.a.t..a.g.c.c.t.")
+			first = False
+			continue
+		linesplt = line.split("\t")
+		gene = linesplt[best_matchIndex]
+		ID = linesplt[IDIndex]
+		RGYW = [(int(x), int(y), z) for (x, y, z) in
+				[hotspotMatcher.match(x).groups() for x in linesplt[aggctatIndex].split("|") if x]]
+		WRCY = [(int(x), int(y), z) for (x, y, z) in
+				[hotspotMatcher.match(x).groups() for x in linesplt[atagcctIndex].split("|") if x]]
+		WA = [(int(x), int(y), z) for (x, y, z) in
+			  [hotspotMatcher.match(x).groups() for x in linesplt[ataIndex].split("|") if x]]
+		TW = [(int(x), int(y), z) for (x, y, z) in
+			  [hotspotMatcher.match(x).groups() for x in linesplt[tatIndex].split("|") if x]]
+		RGYWCount[ID], WRCYCount[ID], WACount[ID], TWCount[ID] = 0, 0, 0, 0
+
+		mutationList = mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
+		for mutation in mutationList:
+			frm, where, to, AAfrm, AAwhere, AAto, junk = mutation
+			mutation_in_RGYW = any([(start <= int(where) <= end) for (start, end, region) in RGYW])
+			mutation_in_WRCY = any([(start <= int(where) <= end) for (start, end, region) in WRCY])
+			mutation_in_WA = any([(start <= int(where) <= end) for (start, end, region) in WA])
+			mutation_in_TW = any([(start <= int(where) <= end) for (start, end, region) in TW])
+
+			in_how_many_motifs = sum([mutation_in_RGYW, mutation_in_WRCY, mutation_in_WA, mutation_in_TW])
+
+			if in_how_many_motifs > 0:
+				RGYWCount[ID] += (1.0 * int(mutation_in_RGYW)) / in_how_many_motifs
+				WRCYCount[ID] += (1.0 * int(mutation_in_WRCY)) / in_how_many_motifs
+				WACount[ID] += (1.0 * int(mutation_in_WA)) / in_how_many_motifs
+				TWCount[ID] += (1.0 * int(mutation_in_TW)) / in_how_many_motifs
+
+
+def mean(lst):
+	return (float(sum(lst)) / len(lst)) if len(lst) > 0 else 0.0
+
+
+def median(lst):
+	lst = sorted(lst)
+	l = len(lst)
+	if l == 0:
+		return 0
+	if l == 1:
+		return lst[0]
+		
+	l = int(l / 2)
+	
+	if len(lst) % 2 == 0:
+		return float(lst[l] + lst[(l - 1)]) / 2.0
+	else:
+		return lst[l]
+
+funcs = {"mean": mean, "median": median, "sum": sum}
+
+directory = outfile[:outfile.rfind("/") + 1]
+value = 0
+valuedic = dict()
+
+for fname in funcs.keys():
+	for gene in genes:
+		with open(directory + gene + "_" + fname + "_value.txt", 'r') as v:
+			valuedic[gene + "_" + fname] = float(v.readlines()[0].rstrip())
+	with open(directory + "all_" + fname + "_value.txt", 'r') as v:
+		valuedic["total_" + fname] = float(v.readlines()[0].rstrip())
+	
+
+def get_xyz(lst, gene, f, fname):
+	x = round(round(f(lst), 1))
+	y = valuedic[gene + "_" + fname]
+	z = str(round(x / float(y) * 100, 1)) if y != 0 else "0"
+	return (str(x), str(y), z)
+
+dic = {"RGYW": RGYWCount, "WRCY": WRCYCount, "WA": WACount, "TW": TWCount}
+arr = ["RGYW", "WRCY", "WA", "TW"]
+
+geneMatchers = {gene: re.compile("^" + gene + ".*") for gene in genes}
+
+for fname in funcs.keys():
+	func = funcs[fname]
+	foutfile = outfile[:outfile.rindex("/")] + "/hotspot_analysis_" + fname + ".txt"
+	with open(foutfile, 'w') as o:
+		for typ in arr:
+			o.write(typ + " (%)")
+			curr = dic[typ]
+			for gene in genes:
+				geneMatcher = geneMatchers[gene]
+				if valuedic[gene + "_" + fname] is 0:
+					o.write(",0,0,0")
+				else:
+					x, y, z = get_xyz([curr[x] for x in [y for y, z in genedic.iteritems() if geneMatcher.match(z)]], gene, func, fname)
+					o.write("," + x + "," + y + "," + z)
+			x, y, z = get_xyz([y for x, y in curr.iteritems() if not genedic[x].startswith("unmatched")], "total", func, fname)
+			#x, y, z = get_xyz([y for x, y in curr.iteritems()], "total", func, fname)
+			o.write("," + x + "," + y + "," + z + "\n")
+
+
+# for testing
+seq_motif_file = outfile[:outfile.rindex("/")] + "/motif_per_seq.txt"
+with open(seq_motif_file, 'w') as o:
+	o.write("ID\tRGYW\tWRCY\tWA\tTW\n")
+	for ID in IDlist:
+		#o.write(ID + "\t" + str(round(RGYWCount[ID], 2)) + "\t" + str(round(WRCYCount[ID], 2)) + "\t" + str(round(WACount[ID], 2)) + "\t" + str(round(TWCount[ID], 2)) + "\n")
+		o.write(ID + "\t" + str(RGYWCount[ID]) + "\t" + str(WRCYCount[ID]) + "\t" + str(WACount[ID]) + "\t" + str(TWCount[ID]) + "\n")