--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trips_create_new_organism/create_annotation_sqlite.py	Fri Feb 25 11:24:50 2022 +0000
@@ -0,0 +1,787 @@
+# Python3 script which takes in an annotation file(gtf/gff3) and a transcriptomic fasta file
+# and produces an sqlite file which can be uploaded to Trips-Viz
+# All co-ordinates produced are 1 based
+# All start codon positions (including cds_start) should be at the first nucleotide of the codon
+# All stop codon positions (including cds_stop) should be at the last nucleotide of the codon
+import sys
+import re
+import sqlite3
+from intervaltree import Interval, IntervalTree
+import itertools
+
+
+
+#This should be a GTF or GFF3 file
+annotation_file = open(sys.argv[1],"r")
+#This needs to be the transcriptomic fasta file
+fasta_file = open(sys.argv[2],"r")
+#This value will be added used to create UTRs of this length, useful when looking at transcriptomes without annotated UTRs
+pseudo_utr_len = int(sys.argv[3])
+#An example of a transcript_id from the annotation file, e.g ENST000000123456
+user_transcript_id = sys.argv[4]
+#An example of a gene name from the annotation file
+user_gene_name = sys.argv[5]
+# Set to true if transcript version is included in transcript_id, e.g: ENST000000123456.1
+TRAN_VERSION = True
+
+
+
+delimiters = {"transcripts":{"before":[],"after":[],"annot_types": ["cds","utr"]},
+			  "genes":{"before":[],"after":['"'],"annot_types": ["lnc_rna"]}}
+
+punctuation = [";"," ","-",":","-",".","=","\t"]
+#Find delimiters in the annotation and fasta files using the user_transcript_id
+#and user_gene_name examples given by user.
+for line in annotation_file:
+	if user_transcript_id in line:
+		tabsplitline = line.split("\t")
+		annot_type = tabsplitline[2]
+		if annot_type not in delimiters["transcripts"]["annot_types"]:
+			delimiters["transcripts"]["annot_types"].append(annot_type.lower())
+		splitline = line.split(user_transcript_id)
+		before_delimiter = splitline[0]
+		for item in punctuation:
+			if item in before_delimiter:
+				if len(before_delimiter.split(item)[-1]) >= 5:
+					before_delimiter = before_delimiter.split(item)[-1]
+		after_delimiter = splitline[1][:2]
+		if before_delimiter not in delimiters["transcripts"]["before"] and len(before_delimiter) >= 5:
+			delimiters["transcripts"]["before"].append(before_delimiter)
+		if after_delimiter not in delimiters["transcripts"]["after"]:
+			delimiters["transcripts"]["after"].append(after_delimiter)
+	if user_gene_name in line:
+		tabsplitline = line.split("\t")
+		annot_type = tabsplitline[2]
+		if annot_type not in delimiters["genes"]["annot_types"]:
+			delimiters["genes"]["annot_types"].append(annot_type.lower())
+		splitline = line.split(user_gene_name)
+		before_delimiter = splitline[0]
+		for item in punctuation:
+			if item in before_delimiter:
+				if len(before_delimiter.split(item)[-1]) >= 5:
+					before_delimiter = before_delimiter.split(item)[-1]
+		after_delimiter = splitline[1][0]
+		if before_delimiter not in delimiters["genes"]["before"] and len(before_delimiter) >= 5:
+			delimiters["genes"]["before"].append(before_delimiter)
+		if after_delimiter not in delimiters["genes"]["after"]:
+			if after_delimiter in punctuation:
+				delimiters["genes"]["after"].append(after_delimiter)
+for line in fasta_file:
+	if user_transcript_id in line:
+		splitline = line.split(user_transcript_id)
+		before_delimiter = splitline[0]
+		for item in punctuation:
+			if item in before_delimiter:
+				if len(before_delimiter.split(item)[1]) >= 5:
+					before_delimiter = before_delimiter.split(item)[1]
+		after_delimiter = splitline[1][0]
+		if before_delimiter not in delimiters["transcripts"]["before"] and len(before_delimiter) >= 5:
+			delimiters["transcripts"]["before"].append(before_delimiter)
+		if after_delimiter not in delimiters["transcripts"]["after"]:
+			delimiters["transcripts"]["after"].append(after_delimiter)
+fasta_file.close()
+annotation_file.close()
+
+
+
+
+
+if delimiters["transcripts"]["before"] == []:
+	print ("ERROR: No transcript_id with the name {} could be found in the annotation file".format(user_transcript_id))
+	sys.exit()
+if delimiters["genes"]["before"] == []:
+	print ("ERROR: No gene with the name {} could be found in the annotation file".format(user_gene_name))
+	sys.exit()
+
+master_dict = {}
+coding_dict = {}
+notinfasta = open("notinfasta.csv","w")
+
+#Given a nucleotide sequence returns the positions of all start and stop codons.
+def get_start_stops(transcript_sequence):
+	transcript_sequence = transcript_sequence.upper()
+	start_codons = ['ATG']
+	stop_codons = ['TAA', 'TAG', 'TGA']
+	seq_frames = {'starts': [], 'stops': []}
+	for codons, positions in ((start_codons, 'starts'),(stop_codons, 'stops')):
+		if len(codons) > 1:
+			pat = re.compile('|'.join(codons))
+		else:
+			pat = re.compile(codons[0])
+		for m in re.finditer(pat, transcript_sequence):
+			# Increment position by 1, Frame 1 starts at position 1 not 0,
+			# if it's a stop codon add another 2 so it points to the last nuc of the codon
+			if positions == "starts":
+				start = m.start() + 1
+			else:
+				start = m.start() + 3
+			seq_frames[positions].append(start)
+	return seq_frames
+
+
+#parse fasta to get the nucleotide sequence of transcripts and the positions of start/stop codons.
+fasta_file = open(sys.argv[2],"r")
+read_fasta = fasta_file.read()
+split_fasta = read_fasta.split(">")
+for entry in split_fasta[1:]:
+	newline_split = entry.split("\n")
+	tran = newline_split[0]
+	for item in delimiters["transcripts"]["after"]:
+		if item in tran:
+			tran = tran.split(item)[0]
+	tran = tran.replace("-","_").replace("(","").replace(")","")
+	seq = ("".join(newline_split[1:]))
+	if "_PAR_Y" in tran:
+		tran += "_chrY"
+	elif "_PAR_X" in tran:
+		tran += "_chrX"
+	tran = tran.upper()
+	starts_stops = get_start_stops(seq)
+	if tran not in master_dict:
+		master_dict[tran] = {"utr":[], "cds":[], "exon":[],"start_codon":[],"stop_codon":[],"start_list":starts_stops["starts"],
+							"stop_list":starts_stops["stops"],"transcript":[], "strand":"" ,"gene_name":"","chrom":"","seq":seq,"cds_start":"NULL","cds_stop":"NULL",
+							"length":len(seq),"principal":0,"version":"NULL"}
+
+
+
+
+def to_ranges(iterable):
+	tup_list = []
+	iterable = sorted(set(iterable))
+	for key, group in itertools.groupby(enumerate(iterable),lambda t: t[1] - t[0]):
+		group = list(group)
+		tup_list.append((group[0][1], group[-1][1]))
+	return tup_list
+
+#parse annotation file to get chromsome, exon location and CDS info for each transcript
+def parse_gtf_file(annotation_file):
+	for line in annotation_file:
+		if line == "\n":
+			continue
+		if line[0] != '#':
+			splitline = (line.replace("\n","")).split("\t")
+			chrom = splitline[0]
+			try:
+				annot_type = splitline[2].lower()
+			except:
+				print ("ERROR tried to index to second item in splitline: ",splitline, line)
+				sys.exit()
+			#if annot_type not in ["cds", "utr", "exon", "transcript","five_prime_utr", "three_prime_utr","stop_codon","start_codon"]:
+			#	continue
+			if annot_type not in delimiters["transcripts"]["annot_types"] and annot_type not in delimiters["genes"]["annot_types"]:
+				continue
+			if annot_type == "five_prime_utr" or annot_type == "three_prime_utr":
+				annot_type = "utr"
+			strand = splitline[6]
+			if strand == "+":
+				start = int(splitline[3])
+				end = int(splitline[4])
+			else:
+				start = int(splitline[3])+1
+				end = int(splitline[4])+1
+			desc = splitline[8]
+			tran = desc
+			gene = desc
+			for item in delimiters["transcripts"]["before"]:
+				if item in tran:
+					tran = tran.split(item)[1]
+			for item in delimiters["transcripts"]["after"]:
+				if item in tran:
+					tran = tran.split(item)[0]
+			if "." in tran and TRAN_VERSION == True:
+				#print ("raw tran",tran)
+				tran = tran.split(".")
+				version = int(tran[-1].split("_")[0])
+				tran = tran[0]
+			else:
+				version = "NULL"
+			tran = tran.replace("-","_").replace(".","_")
+			tran = tran.replace("(","").replace(")","")
+			tran = tran.replace(" ","").replace("\t","")
+			tran = tran.upper()
+			tran = tran.replace("GENE_","").replace("ID_","")
+			#print ("tran",tran,version)
+			#if tran == "ENST00000316448":
+			#	print ("annot type",annot_type)
+			#	print ("appending exon to tran", start, end,line)
+
+			gene_found = False
+
+			if annot_type in delimiters["genes"]["annot_types"]:
+				for item in delimiters["genes"]["before"]:
+					if item in gene:
+						gene_found = True
+						gene = gene.split(item)[1]
+				for item in delimiters["genes"]["after"]:
+					if item in gene:
+						gene = gene.split(item)[0]
+				gene = gene.replace("'","''")
+				gene = gene.replace("GENE_","")
+				gene = gene.replace("ID_","")
+				gene = gene.upper()
+
+			if tran in master_dict:
+				if annot_type in master_dict[tran]:
+					master_dict[tran][annot_type].append((start, end))
+				master_dict[tran]["strand"] = strand
+				master_dict[tran]["chrom"] = chrom
+				master_dict[tran]["version"] = version
+				if gene_found == True:
+					master_dict[tran]["gene_name"] = gene
+			else:
+				notinfasta.write("{}\n".format(tran))
+
+annotation_file = open(sys.argv[1],"r")
+parse_gtf_file(annotation_file)
+
+
+#remove transcripts that were in fasta file but not in annotation_file
+notinannotation = []
+for tran in master_dict:
+	if master_dict[tran]["chrom"] == "":
+		#print ("tran {} has no chrom :(".format(tran))
+		notinannotation.append(tran)
+for tran in notinannotation:
+	del master_dict[tran]
+
+#Dictionary to store the coding status of a gene, if any transcript of this gene is coding, the value will be True
+coding_genes_dict = {}
+#parse master_dict to calculate length, cds_start/stop and exon junction positions
+for tran in master_dict:
+	try:
+		transeq = master_dict[tran]["seq"]
+	except Exception as e:
+		print ("not in fasta", tran)
+		notinfasta.write("{}\n".format(tran))
+		continue
+	exon_junctions = []
+	total_length = len(transeq)
+	three_len = 1
+	five_len = 1
+	strand = master_dict[tran]["strand"]
+	if master_dict[tran]["gene_name"] == "":
+		master_dict[tran]["gene_name"] = tran
+	gene = master_dict[tran]["gene_name"]
+	if gene not in coding_genes_dict:
+		coding_genes_dict[gene] = False
+
+	if master_dict[tran]["cds"] == []:
+		tran_type = "noncoding"
+		cds_start = 'NULL'
+		cds_stop = 'NULL'
+	else:
+		#get utr lengths from annotation
+		tran_type = "coding"
+		coding_genes_dict[gene] = True
+		sorted_exons = sorted(master_dict[tran]["exon"])
+		sorted_cds = sorted(master_dict[tran]["cds"])
+		min_cds = sorted_cds[0][0]
+		#Some annotation files do not have utr annotation types, so fix that here if thats the case
+		if master_dict[tran]["utr"] == []:
+			for exon_tup in master_dict[tran]["exon"]:
+				if exon_tup not in master_dict[tran]["cds"]:
+					# Now check if this overlaps with any of the CDS exons
+					overlap = False
+					for cds_tup in master_dict[tran]["cds"]:
+						if exon_tup[0] == cds_tup[0] and exon_tup[1] != cds_tup[1]:
+							master_dict[tran]["utr"].append((cds_tup[1],exon_tup[1]))
+							overlap = True
+						if exon_tup[0] != cds_tup[0] and exon_tup[1] == cds_tup[1]:
+							master_dict[tran]["utr"].append((exon_tup[0],cds_tup[0]))
+							overlap = True
+					if overlap == False:
+						master_dict[tran]["utr"].append(exon_tup)
+
+
+		'''
+		if tran == "NM_001258497":
+			print ("sorted cds",sorted_cds)
+			print ("min cds",min_cds)
+			print ("chrom",master_dict[tran]["chrom"])
+			print ("sorted exons", sorted_exons)
+			print ("utr",master_dict[tran]["utr"])
+			sys.exit()
+		'''
+		#if tran == "ENST00000381401":
+		#	print ("min cds,sorted utr",min_cds,sorted(master_dict[tran]["utr"]))
+		for tup in sorted(master_dict[tran]["utr"]):
+			#if tran == "ENST00000381401":
+			#	print ("tup", tup)
+			if tup[0] < min_cds:
+				five_len += (tup[1]-tup[0])+1
+				#if tran == "ENST00000381401":
+				#	print ("adding to fivelen")
+			elif tup[0] > min_cds:
+				three_len += (tup[1] - tup[0])+1
+				#if tran == "ENST00000381401":
+				#	print ("adding to three len")
+			else:
+				pass
+		if strand == "+":
+			if len(sorted_exons) > 1:
+				sorted_exons[0] = (sorted_exons[0][0]-pseudo_utr_len, sorted_exons[0][1])
+				sorted_exons[-1] = (sorted_exons[-1][0], sorted_exons[-1][1]+pseudo_utr_len)
+			else:
+				sorted_exons[0] = (sorted_exons[0][0]-pseudo_utr_len, sorted_exons[0][1]+pseudo_utr_len)
+			master_dict[tran]["exon"] = sorted_exons
+			cds_start = (five_len+pseudo_utr_len)
+			cds_stop = ((total_length - three_len)-pseudo_utr_len)+1
+		elif strand == "-":
+			if len(sorted_exons) > 1:
+				sorted_exons[0] = (sorted_exons[0][0]-pseudo_utr_len, sorted_exons[0][1])
+				sorted_exons[-1] = (sorted_exons[-1][0], sorted_exons[-1][1]+pseudo_utr_len)
+			else:
+				sorted_exons[0] = (sorted_exons[0][0]-pseudo_utr_len, sorted_exons[0][1]+pseudo_utr_len)
+			master_dict[tran]["exon"] = sorted_exons
+			cds_start = (three_len+pseudo_utr_len)
+			cds_stop  = ((total_length - (five_len))-pseudo_utr_len)+1
+			#if tran == "ENST00000381401":
+			#	print ("cds start, cds stop, five_len, three_len",cds_start,cds_stop,five_len,three_len)
+			#	#sys.exit()
+		else:
+			print ("strand is unknown: {}".format(strand))
+			sys.exit()
+
+	#get exon junctions, cds is easy just get end of each tuple except last, same for utr except for if same as cds start/stop
+	total_intronic = 0
+	try:
+		if strand == "+":
+			tx_start = min(sorted(master_dict[tran]["exon"]))[0]
+			prev_end = tx_start
+			for tup in sorted(master_dict[tran]["exon"])[:-1]:
+				total_intronic += tup[0]-prev_end
+				exon_junctions.append(((tup[1])-tx_start)-total_intronic)
+				prev_end = tup[1]
+		elif strand == "-":
+			tx_start = max(sorted(master_dict[tran]["exon"]))[-1]
+			prev_end = tx_start
+			for tup in (sorted(master_dict[tran]["exon"])[1:])[::-1]:
+				total_intronic += (tup[0]+1)-prev_end
+				exon_junctions.append(((tup[1])-tx_start)-total_intronic)
+				prev_end = tup[1]
+	except:
+		if strand == "+":
+			tx_start = min(sorted(master_dict[tran]["cds"]))[0]
+			prev_end = tx_start
+			for tup in sorted(master_dict[tran]["cds"])[:-1]:
+				total_intronic += tup[0]-prev_end
+				exon_junctions.append(((tup[1])-tx_start)-total_intronic)
+				prev_end = tup[1]
+		elif strand == "-":
+			tx_start = max(sorted(master_dict[tran]["cds"]))[-1]
+			prev_end = tx_start
+			for tup in (sorted(master_dict[tran]["cds"])[1:])[::-1]:
+				total_intronic += (tup[0]+1)-prev_end
+				exon_junctions.append(((tup[1])-tx_start)-total_intronic)
+				prev_end = tup[1]
+	if strand == "+" and cds_start != "NULL":
+		master_dict[tran]["cds_start"] = cds_start
+		master_dict[tran]["cds_stop"] = cds_stop
+	elif strand == "-" and cds_start != "NULL":
+		master_dict[tran]["cds_start"] = cds_start
+		master_dict[tran]["cds_stop"] = cds_stop
+	master_dict[tran]["strand"] = strand
+	master_dict[tran]["tran_type"] = tran_type
+	master_dict[tran]["exon_junctions"] = exon_junctions
+
+longest_tran_dict = {}
+for tran in master_dict:
+	try:
+		gene = master_dict[tran]["gene_name"]
+	except:
+		continue
+	if coding_genes_dict[gene] == True:
+		if "cds_start" in master_dict[tran]:
+			if master_dict[tran]["cds_stop"] != "NULL" and master_dict[tran]["cds_start"] != "NULL":
+				cds_length = master_dict[tran]["cds_stop"]- master_dict[tran]["cds_start"]
+				if gene not in longest_tran_dict:
+					longest_tran_dict[gene] = {"tran":tran,"length":cds_length}
+				else:
+					if cds_length > longest_tran_dict[gene]["length"]:
+						longest_tran_dict[gene] = {"tran":tran,"length":cds_length}
+					if cds_length == longest_tran_dict[gene]["length"]:
+						if master_dict[tran]["length"] > master_dict[longest_tran_dict[gene]["tran"]]["length"]:
+							longest_tran_dict[gene] = {"tran":tran,"length":cds_length}
+	else:
+		length = master_dict[tran]["length"]
+		if gene not in longest_tran_dict:
+			longest_tran_dict[gene] = {"tran":tran,"length":length}
+		elif length > longest_tran_dict[gene]["length"]:
+			longest_tran_dict[gene] = {"tran":tran,"length":length}
+
+
+
+
+
+for gene in longest_tran_dict:
+	longest_tran = longest_tran_dict[gene]["tran"]
+	master_dict[longest_tran]["principal"] = 1
+
+gene_sample = []
+for key in list(master_dict)[:10]:
+	try:
+		gene_sample.append(master_dict[key]["gene_name"])
+	except:
+		pass
+
+print ("Here is a sample of the transcript ids: {}".format(list(master_dict)[:10]))
+print ("Here is a sample of the gene names: {}".format(gene_sample))
+
+
+# Takes a transcript, transcriptomic position and a master_dict (see ribopipe scripts) and returns the genomic position, positions should be passed 1 at a time.
+def tran_to_genome(tran, start_pos, end_pos, master_dict):
+	pos_list = []
+	for i in range(start_pos,end_pos+1):
+		pos_list.append(i)
+	genomic_pos_list = []
+	if tran in master_dict:
+		transcript_info = master_dict[tran]
+	else:
+		return ("Null", [])
+
+	chrom = transcript_info["chrom"]
+	strand = transcript_info["strand"]
+	exons = transcript_info["exon"]
+	#print ("chrom,strand,exons",chrom,strand,exons)
+	for pos in pos_list:
+		#print ("pos",pos)
+		if strand == "+":
+			exon_start = 0
+			for tup in exons:
+				#print ("tup",tup)
+				exon_start = tup[0]
+				exonlen = tup[1] - tup[0]
+				if pos > exonlen:
+					pos = (pos - exonlen)-1
+				else:
+					break
+			#print ("appending exon_start-pos", exon_start, pos, exon_start+pos)
+			genomic_pos_list.append((exon_start+pos)-1)
+		elif strand == "-":
+			exon_start = 0
+			for tup in exons[::-1]:
+				#print ("tup",tup)
+				exon_start = tup[1]
+				exonlen = tup[1] - tup[0]
+				#print ("exonlen",exonlen)
+				if pos > exonlen:
+					#print ("pos is greater")
+					pos = (pos - exonlen)-1
+					#print ("new pos",pos)
+				else:
+					break
+			#print ("appending exon_start-pos", exon_start, pos, exon_start-pos)
+			genomic_pos_list.append((exon_start-pos)+1)
+	return (chrom, genomic_pos_list)
+
+
+
+
+orf_dict = {"uorf":{},
+	"ouorf":{},
+	"cds":{},
+	"nested":{},
+	"odorf":{},
+	"dorf":{},
+	"minusone":{},
+	"readthrough":{},
+	"plusone":{},
+	"noncoding":{},
+	"extension":{},
+	"inframe_stop":{}
+		}
+
+start_codons = ["ATG","GTG","CTG"]
+stop_codons = ["TAG","TAA","TGA"]
+
+
+# Keep track of the longest transcript for each noncoding gene, append this to transcript list later
+longest_noncoding = {}
+
+
+tran_count = 0
+# This section is used to gather all cds regions, convert them to genomic regions and store them in a dictionary to check against later (all transcript contribute to this not just those
+# in the transcript list)
+genomic_cds_dict = {}
+tree_dict = {}
+for transcript in master_dict:
+	#print (transcript, master_dict[transcript]["tran_type"])
+	tran_count += 1
+	if "seq" not in master_dict[transcript]:
+		continue
+	chrom = master_dict[transcript]["chrom"]
+	if chrom not in genomic_cds_dict:
+		genomic_cds_dict[chrom] = []
+	if "cds_start" in master_dict[transcript]:
+		cds_start = master_dict[transcript]["cds_start"]
+		cds_stop = master_dict[transcript]["cds_stop"]
+		if cds_start != "NULL":
+			cds_pos = []
+			for i in range(cds_start, cds_stop+1):
+				cds_pos.append(i)
+
+			for tup in master_dict[transcript]["cds"]:
+				if tup[0] != tup[1]:
+					if tup not in genomic_cds_dict[chrom]:
+						genomic_cds_dict[chrom].append(tup)
+
+print ("genomic cds dict built")
+print (list(genomic_cds_dict))
+for chrom in genomic_cds_dict:
+	tree_dict[chrom] = IntervalTree.from_tuples(genomic_cds_dict[chrom])
+
+#print (list(tree_dict))
+
+
+connection = sqlite3.connect("{}".format(sys.argv[6]))
+cursor = connection.cursor()
+cursor.execute("CREATE TABLE IF NOT EXISTS transcripts (transcript VARCHAR(50), gene VARCHAR(50), length INT(6), cds_start INT(6), cds_stop INT(6), sequence VARCHAR(50000), strand CHAR(1), stop_list VARCHAR(10000), start_list VARCHAR(10000), exon_junctions VARCHAR(1000), tran_type INT(1), gene_type INT(1), principal INT(1), version INT(2),gc INT(3),five_gc INT(3), cds_gc INT(3), three_gc INT(3), chrom VARCHAR(20));")
+cursor.execute("CREATE TABLE IF NOT EXISTS coding_regions (transcript VARCHAR(50), coding_start INT(6), coding_stop INT(6));")
+cursor.execute("CREATE TABLE IF NOT EXISTS exons (transcript VARCHAR(50), exon_start INT(6), exon_stop INT(6));")
+cursor.execute("CREATE TABLE IF NOT EXISTS uorf (transcript VARCHAR(300), start_codon VARCHAR(10), length INT(6), start INT(6), stop INT(6), sequence VARCHAR(50000), cds_coverage FLOAT(20));")
+cursor.execute("CREATE TABLE IF NOT EXISTS ouorf (transcript VARCHAR(300), start_codon VARCHAR(10), length INT(6), start INT(6), stop INT(6), sequence VARCHAR(50000), cds_coverage FLOAT(20));")
+cursor.execute("CREATE TABLE IF NOT EXISTS cds (transcript VARCHAR(300), start_codon VARCHAR(10), length INT(6), start INT(6), stop INT(6), sequence VARCHAR(50000), cds_coverage FLOAT(20));")
+cursor.execute("CREATE TABLE IF NOT EXISTS nested (transcript VARCHAR(300), start_codon VARCHAR(10), length INT(6), start INT(6), stop INT(6), sequence VARCHAR(50000), cds_coverage FLOAT(20));")
+cursor.execute("CREATE TABLE IF NOT EXISTS odorf (transcript VARCHAR(300), start_codon VARCHAR(10), length INT(6), start INT(6), stop INT(6), sequence VARCHAR(50000), cds_coverage FLOAT(20));")
+cursor.execute("CREATE TABLE IF NOT EXISTS dorf (transcript VARCHAR(300), start_codon VARCHAR(10), length INT(6), start INT(6), stop INT(6), sequence VARCHAR(50000), cds_coverage FLOAT(20));")
+cursor.execute("CREATE TABLE IF NOT EXISTS minusone(transcript VARCHAR(300), start_codon VARCHAR(10), length INT(6), start INT(6), stop INT(6), sequence VARCHAR(50000), cds_coverage FLOAT(20));")
+cursor.execute("CREATE TABLE IF NOT EXISTS readthrough (transcript VARCHAR(300), start_codon VARCHAR(10), length INT(6), start INT(6), stop INT(6), sequence VARCHAR(50000), cds_coverage FLOAT(20));")
+cursor.execute("CREATE TABLE IF NOT EXISTS plusone (transcript VARCHAR(300), start_codon VARCHAR(10), length INT(6), start INT(6), stop INT(6), sequence VARCHAR(50000), cds_coverage FLOAT(20));")
+cursor.execute("CREATE TABLE IF NOT EXISTS noncoding (transcript VARCHAR(300), start_codon VARCHAR(10), length INT(6), start INT(6), stop INT(6), sequence VARCHAR(50000), cds_coverage FLOAT(20));")
+cursor.execute("CREATE TABLE IF NOT EXISTS extension (transcript VARCHAR(300), start_codon VARCHAR(10), length INT(6), start INT(6), stop INT(6), sequence VARCHAR(50000), cds_coverage FLOAT(20));")
+cursor.execute("CREATE TABLE IF NOT EXISTS inframe_stop (transcript VARCHAR(300), start_codon VARCHAR(10), length INT(6), start INT(6), stop INT(6), sequence VARCHAR(50000), cds_coverage FLOAT(20));")
+connection.commit();
+
+
+print ("Finding ORFs")
+transcript_count = 0
+total_transcripts = len(list(master_dict))
+for transcript in master_dict:
+	#print ("transcript",transcript)
+	#if transcript != "ENST00000316448":
+	#	continue
+	transcript_count += 1
+	if transcript_count%100 == 0:
+		print ("Transcripts complete: {}/{}".format(transcript_count,total_transcripts))
+	if "seq" not in master_dict[transcript]:
+		print ("transcript {} has no sequence".format(transcript))
+		continue
+	seq = master_dict[transcript]["seq"]
+	cds_start = "NULL"
+	cds_stop = "NULL"
+	transcript_len = len(seq)
+	if "cds_start" in master_dict[transcript]:
+		cds_start = master_dict[transcript]["cds_start"]
+		cds_stop = master_dict[transcript]["cds_stop"]
+
+	#Find out what regions of this transcript overlap with any other coding regions
+	coding_positions = []
+	if cds_start != "NULL":
+		#If this is a coding transcript don't bother checking the CDS
+		for i in range(cds_start,cds_stop):
+			coding_positions.append(i)
+		#check 5' leader
+		chrom, pos_list = tran_to_genome(transcript, 0, cds_start, master_dict)
+		for i in range(0,cds_start):
+			genomic_pos = pos_list[i]
+			overlap = tree_dict[chrom][genomic_pos]
+			if len(overlap) != 0:
+				coding_positions.append(i)
+		#check 3' trailer
+		chrom, pos_list = tran_to_genome(transcript, cds_stop, transcript_len, master_dict)
+		for i in range(cds_stop,transcript_len+1):
+			#print ("i",i)
+			genomic_pos = pos_list[i-cds_stop]
+			#print ("genomic position",genomic_pos)
+			overlap = tree_dict[chrom][genomic_pos]
+			if len(overlap) != 0:
+				#print ("overlap not empty appending i",overlap)
+				coding_positions.append(i)
+	else:
+		#check entire transcript
+		chrom, pos_list = tran_to_genome(transcript, 0, transcript_len, master_dict)
+		for i in range(0,transcript_len):
+			genomic_pos = pos_list[i]
+			overlap = tree_dict[chrom][genomic_pos]
+			if len(overlap) != 0:
+				coding_positions.append(i)
+	coding_positions_tuple = to_ranges(coding_positions)
+	coding_dict[transcript] = coding_positions_tuple
+	coding_positions = set(coding_positions)
+	#if this is a coding transcript find the minusone, readhtrough, plusone co-ordinates
+	if cds_start != "NULL":
+		if pseudo_utr_len != 0:
+			cds_stop -= 3 # take 3 from stop so we can match it with orf_stop, do it here rather than above in case cds_stop is null
+		recoding_dict = {0:"minusone",1:"readthrough",2:"plusone"}
+		for addition in recoding_dict:
+			orftype = recoding_dict[addition]
+			for i in range(cds_stop+addition,transcript_len,3):
+				if seq[i:i+3] in stop_codons:
+					orf_seq = seq[cds_stop:i+3]
+					orf_start = cds_stop
+					orf_stop = i+2 # +2 so it refers to the end of the stop codon
+					start_codon = None
+					if orf_seq:
+						length = len(orf_seq)
+						orf_pos_list = []
+						#determine how many nucleotides in this orf overlap with an annotated coding region
+						cds_cov_count = 0.0
+						for position in range(orf_start,orf_stop):
+							orf_pos_list.append(position)
+						for pos in range(orf_start, orf_stop+1):
+							if pos in coding_positions:
+								cds_cov_count += 1
+						cds_cov = cds_cov_count/length
+						cursor.execute("INSERT INTO {} VALUES('{}','{}',{},{},{},'{}',{});".format(orftype, transcript, start_codon, length,orf_start,orf_stop,orf_seq,cds_cov))
+					break
+	for frame in [0,1,2]:
+		for i in range(frame,transcript_len,3):
+			if seq[i:i+3] in start_codons:
+				for x in range(i, transcript_len,3):
+					if seq[x:x+3] in stop_codons:
+						orf_seq = seq[i:x+3]
+						orf_start = i
+						orf_stop = x+2 # +2 so it refers to the end of the stop codon
+						start_codon = seq[i:i+3]
+						length = len(orf_seq)
+						orf_pos_list = []
+						#determine how many nucleotides in this orf overlap with an annotated coding region
+						cds_cov_count = 0.0
+						for pos in range(orf_start, orf_stop+1):
+							if pos in coding_positions:
+								cds_cov_count += 1
+						cds_cov = float(cds_cov_count)/float(length)
+						# Now determine orf type
+						if cds_start == "NULL":
+							orftype = "noncoding"
+						else:
+							#print ("cds start is not null :{}:".format(cds_start))
+							if orf_start == cds_start and orf_stop == cds_stop:
+								orftype = "cds"
+							elif orf_start < cds_start and orf_stop == cds_stop:
+								orftype = "extension"
+								#special case for extensions, we only take from the orf_start to the cds_start, and re-calculate cds coverage
+								orf_stop = cds_start
+								cds_cov_count = 0.0
+								for pos in range(orf_start, orf_stop+1):
+									if pos in coding_positions:
+										cds_cov_count += 1
+								cds_cov = float(cds_cov_count)/float(length)
+								orf_seq = seq[orf_start:cds_start]
+								length = len(orf_seq)
+							elif orf_start < cds_start and orf_stop <= cds_start:
+								orftype = "uorf"
+							elif orf_start < cds_start and orf_stop > cds_start:
+								orftype = "ouorf"
+							elif orf_start >= cds_start and orf_start <= cds_stop and orf_stop <= cds_stop:
+								if orf_stop == cds_stop:
+									break
+								orftype = "nested"
+							elif orf_start >= cds_start and orf_start <= cds_stop and orf_stop > cds_stop:
+								orftype = "odorf"
+							elif orf_start > cds_stop and orf_stop > cds_stop:
+								orftype = "dorf"
+							if orf_stop > cds_start and orf_stop < cds_stop:
+								if (orf_stop+1)%3 == cds_start%3:
+									orftype = "inframe_stop"
+									if transcript not in orf_dict:
+										orf_dict[orftype][transcript] = []
+						cursor.execute("INSERT INTO {} VALUES('{}','{}',{},{},{},'{}',{});".format(orftype, transcript, start_codon, length,orf_start,orf_stop,orf_seq,cds_cov))
+						break
+# Used to keep track of the codons at cds_start and cds_stop positions,
+# If there is an issue with the cds co-ordinates the starts and stops counts will
+# be much lower than the other count, start with 1 to prevent division by 0
+nuc_dict = {"stops":{"stops":1,"other":0}, "starts":{"starts":1,"other":0}}
+
+def calcgc(seq):
+	if seq == "":
+		return "NULL"
+	g_count = 0
+	c_count = 0
+	a_count = 0
+	t_count = 0
+	for char in seq:
+		if char == "A":
+			a_count += 1
+		if char == "T":
+			t_count += 1
+		if char == "G":
+			g_count += 1
+		if char == "C":
+			c_count += 1
+		gc = ((g_count+c_count)/float(len(seq)))*100
+	return round(gc,2)
+
+
+
+
+for transcript in master_dict:
+	#print ("transcripts", transcript)
+	length = master_dict[transcript]["length"]
+	cds_start = master_dict[transcript]["cds_start"]
+	cds_stop = master_dict[transcript]["cds_stop"]
+	seq = master_dict[transcript]["seq"]
+	strand = master_dict[transcript]["strand"]
+	chrom = master_dict[transcript]["chrom"]
+	gene = master_dict[transcript]["gene_name"]
+	gc = calcgc(seq)
+	five_gc = "NULL"
+	cds_gc = "NULL"
+	three_gc = "NULL"
+	if cds_start != "NULL":
+		five_gc = calcgc(seq[:cds_start])
+		cds_gc = calcgc(seq[cds_start:cds_stop])
+		three_gc = calcgc(seq[cds_stop:])
+		# check that the nucleotide cds_start points to is the first of the start codon
+		# take one becase cds_start is 1 based but python indexing is 0 based
+		start_nuc = seq[cds_start-1:cds_start+2]
+		#print ("start nuc",start_nuc)
+		if start_nuc == "ATG":
+			nuc_dict["starts"]["starts"] += 1
+		else:
+			nuc_dict["starts"]["other"] += 1
+		stop_nuc = seq[cds_stop-3:cds_stop]
+		#print ("stop_nuc",stop_nuc)
+		if stop_nuc in ["TAG","TAA","TGA"]:
+			nuc_dict["stops"]["stops"] += 1
+		else:
+			nuc_dict["stops"]["other"] += 1
+	tran_type = master_dict[transcript]["tran_type"]
+	if coding_genes_dict[gene] == True:
+		gene_type = 1
+	else:
+		gene_type = 0
+	#print ("tran type before",tran_type)
+	if tran_type == "coding":
+		tran_type = 1
+	else:
+		tran_type = 0
+	#print ("tran type after",tran_type)
+	start_list = str(master_dict[transcript]["start_list"]).replace(" ","").strip("[]")
+	stop_list = str(master_dict[transcript]["stop_list"]).replace(" ","").strip("[]")
+	exon_junctions = str(master_dict[transcript]["exon_junctions"]).replace(" ","").strip("[]")
+	principal = master_dict[transcript]["principal"]
+	version = master_dict[transcript]["version"]
+	#print (master_dict[transcript])
+	#print (tran_type)
+	#print (gene_type)
+	#print (principal)
+	#print (version)
+	#print ("INSERT INTO transcripts VALUES('{}','{}',{},{},{},'{}','{}','{}','{}','{}',{},{},{},{});".format(transcript, gene, length, cds_start, cds_stop, seq, strand,stop_list, start_list, exon_junctions, tran_type,gene_type,principal,version))
+	cursor.execute("INSERT INTO transcripts VALUES('{}','{}',{},{},{},'{}','{}','{}','{}','{}',{},{},{},{},{},{},{},{},'{}');".format(transcript, gene, length, cds_start, cds_stop, seq, strand,stop_list, start_list, exon_junctions, tran_type,gene_type,principal,version,gc,five_gc,cds_gc,three_gc,chrom))
+
+	for tup in master_dict[transcript]["exon"]:
+		cursor.execute("INSERT INTO exons VALUES('{}',{},{});".format(transcript,tup[0],tup[1]))
+	if transcript in coding_dict:
+		for tup in coding_dict[transcript]:
+			cursor.execute("INSERT INTO coding_regions VALUES('{}',{},{});".format(transcript,tup[0],tup[1]))
+
+connection.commit()
+connection.close()
+
+if (nuc_dict["starts"]["other"]/nuc_dict["starts"]["starts"]) > 0.05:
+	print ("Warning: {} transcripts do not have a an AUG at the CDS start position".format(nuc_dict["starts"]["other"]))
+if (nuc_dict["stops"]["other"]/nuc_dict["stops"]["stops"]) > 0.05:
+	print ("Warning: {} transcripts do not have a an stop codon at the CDS stop position".format(nuc_dict["stops"]["other"]))
+if len(notinannotation) >0:
+	print ("Warning: {} transcripts were in the fasta file, but not the annotation file, these will be discarded".format(len(notinannotation)))

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trips_create_new_organism/create_annotation_sqlite.xml	Fri Feb 25 11:24:50 2022 +0000
@@ -0,0 +1,84 @@
+<tool id="create_annotation_sqlite" name="create annotation in sqlite for trips-viz" version="0.1.0" python_template_version="3.5">
+    <requirements>
+		 <requirement type="package" version="3.0.2">intervaltree</requirement>
+		  <requirement type="package" version="3.37.0">sqlite</requirement>
+		  <requirement type="package" version="0.4.6">pysqlite3</requirement>
+		  <requirement type="package" version="3.1.0">python-intervaltree</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+	    python2 '$__tool_directory__/create_annotation_sqlite.py' $annotation $fasta $pseudo_utr_len $transcript $gene $output
+    ]]></command>
+    <inputs>
+     <param format="gtf,gff" name="annotation" type="data" label="GTF/GFF3 File"/>
+    <param format="fasta" name="fasta" type="data" label="Transcriptome FASTA file"/>
+    <param name="pseudo_utr_len" type="text" label="Pseudo UTR length"/>
+    <param name="transcript" type="text" label="Example transcript"/>
+    <param name="gene" type="text" label="Example gene"/>
+    </inputs>
+    <outputs>
+         <data format="sqlite" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="fa_gc_content_input.fa"/>
+            <output name="output" file="saccharomyces_cerevisiae.sqlite"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        **GTF/GFF3 File**
+
+GFF lines have nine required fields that must be tab-separated.
+The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats.
+
+Both transcript ids and gene names should be listed in the file.
+
+-----
+
+**Transcriptome FASTA file**
+
+A FASTA file with an entry for every transcript. The headers should be the transcript id's as they appear in the GTF/GFF3 file. 
+
+-----
+
+**Psuedo UTR length**
+An integer representing the length (in nucleotides) to be added to the 5' end and 3' end of every transcript with an annotated
+CDS. Useful for when an organism does not have any annotated UTR's, if it does use 0. If not 0, the extra nucleotides should
+already be present in the FASTA file. 
+
+-----
+
+**Example transcript**
+
+An example of a transcript id that appears in the FASTA/GTF/GFF3 file, e.g ENST00000123456
+
+-----
+
+**Example Gene**
+
+An example of a gene name as it appears in the GTF/GFF3 file, e.g BRCA1
+
+-----
+
+**Output**
+
+The output of the script can be downloaded and uploaded to Trips-viz_. by signing in and going to the uploads page, then selecting
+"Upload new transcriptome". When uploaded the new organism will appear on the home page of Trips-viz, or under the transcriptomes
+page if the organism name used is already present on Trips-viz.  
+
+
+
+.. _Trips-viz: http://trips.ucc.ie
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubTrips-Viz,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {Trips-Viz},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/skiniry/Trips-Viz},
+}</citation>
+    </citations>
+</tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trips_create_new_organism/create_annotation_sqlite_.xml	Fri Feb 25 11:24:50 2022 +0000
@@ -0,0 +1,71 @@
+<tool id="create_annotation_sqlite" name="Trips-viz:" version="0.1.0">
+  <description>create new organism</description>
+  <command interpreter="python">create_annotation_sqlite.py $annotation $fasta $pseudo_utr_len $transcript $gene $output</command>
+  <inputs>
+    <param format="gtf,gff" name="annotation" type="data" label="GTF/GFF3 File"/>
+    <param format="fasta" name="fasta" type="data" label="Transcriptome FASTA file"/>
+    <param name="pseudo_utr_len" type="text" label="Pseudo UTR length"/>
+    <param name="transcript" type="text" label="Example transcript"/>
+    <param name="gene" type="text" label="Example gene"/>
+  </inputs>
+
+  <outputs>
+    <data format="sqlite" name="output" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="fa_gc_content_input.fa"/>
+      <output name="output" file="saccharomyces_cerevisiae.sqlite"/>
+    </test>
+  </tests>
+
+  <help>
+
+**GTF/GFF3 File**
+
+GFF lines have nine required fields that must be tab-separated.
+The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats.
+
+Both transcript ids and gene names should be listed in the file.
+
+-----
+
+**Transcriptome FASTA file**
+
+A FASTA file with an entry for every transcript. The headers should be the transcript id's as they appear in the GTF/GFF3 file. 
+
+-----
+
+**Psuedo UTR length**
+An integer representing the length (in nucleotides) to be added to the 5' end and 3' end of every transcript with an annotated
+CDS. Useful for when an organism does not have any annotated UTR's, if it does use 0. If not 0, the extra nucleotides should
+already be present in the FASTA file. 
+
+-----
+
+**Example transcript**
+
+An example of a transcript id that appears in the FASTA/GTF/GFF3 file, e.g ENST00000123456
+
+-----
+
+**Example Gene**
+
+An example of a gene name as it appears in the GTF/GFF3 file, e.g BRCA1
+
+-----
+
+**Output**
+
+The output of the script can be downloaded and uploaded to Trips-viz_. by signing in and going to the uploads page, then selecting
+"Upload new transcriptome". When uploaded the new organism will appear on the home page of Trips-viz, or under the transcriptomes
+page if the organism name used is already present on Trips-viz.  
+
+
+
+.. _Trips-viz: http://trips.ucc.ie
+
+
+</help>
+</tool>