--- a/trips_create_new_organism/create_annotation_sqlite.py	Fri Feb 25 11:24:50 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,787 +0,0 @@
-# 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)))

--- a/trips_create_new_organism/create_annotation_sqlite.xml	Fri Feb 25 11:24:50 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-<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

--- a/trips_create_new_organism/create_annotation_sqlite_.xml	Fri Feb 25 11:24:50 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-<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>