# HG changeset patch
# User triasteran
# Date 1645788290 0
# Node ID c5a566609a25b4a6f78e274f929b3939d6658837
Uploaded
diff -r 000000000000 -r c5a566609a25 trips_create_new_organism/create_annotation_sqlite.py
--- /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)))
diff -r 000000000000 -r c5a566609a25 trips_create_new_organism/create_annotation_sqlite.xml
--- /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 @@
+
+
+ intervaltree
+ sqlite
+ pysqlite3
+ python-intervaltree
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+@misc{githubTrips-Viz,
+ author = {LastTODO, FirstTODO},
+ year = {TODO},
+ title = {Trips-Viz},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/skiniry/Trips-Viz},
+}
+
+
\ No newline at end of file
diff -r 000000000000 -r c5a566609a25 trips_create_new_organism/create_annotation_sqlite_.xml
--- /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 @@
+
+ create new organism
+ create_annotation_sqlite.py $annotation $fasta $pseudo_utr_len $transcript $gene $output
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**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
+
+
+
+