# HG changeset patch # User abims-sbr # Date 1606760446 0 # Node ID 294f5ba287468ae47592ac6309878d8b70223ebb "planemo upload for repository https://github.com/abims-sbr/tools-abims/tools/gffalign commit d8aa0e49353e78e5fd772498a1fcf591e2744f99" diff -r 000000000000 -r 294f5ba28746 GFFalign.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GFFalign.py Mon Nov 30 18:20:46 2020 +0000 @@ -0,0 +1,337 @@ +#!/usr/bin/python3 + +import argparse +import os +import gffutils +from Bio import SeqIO + + +class GeneComp: + # This cass aims to discover the position of the genes in the alignment + # and to extract informations on the genes characteristics + + def __init__(self, ccgene, qstart, qend, otgene, dstart, dend, extract, tol, gattr, output=None): + # d* / ot* are the db result, q* / cc the query + # gene are the gene from maf-tab file + # start, end are the coordinates ''' + self.otbeg = int(otgene.start) - dstart + self.otend = int(otgene.end) - dstart + self.ccbeg = int(ccgene.start) - qstart + self.ccend = int(ccgene.end) - qstart + self.tol = tol # how much tolerance in nucleotides + self.ccname = ccgene.chrom + self.otname = otgene.chrom + self.q_outstart = qstart+self.otbeg + self.q_outend = qstart+self.otend + self.genelist = [] + self.qstart = qstart + if extract: + self.fastafile = extract[0] + self.fastaout = extract[1] + self.output = output + self.out = "" + self.gattr = f"New_annotation='{gattr}'" + + def is_equal(self): + if (self.otbeg - self.tol) <= self.ccbeg <= (self.otbeg + self.tol) and (self.otend - self.tol) <= self.ccend <= (self.otend + self.tol): + self.out = f"{self.ccname}\tprediction\tgene\t{self.q_outstart}\t{self.q_outend}\t.\t{self.qstart}\t.\tID={self.ccname};{self.gattr};Note=confirmed" + return self.out + + def is_shorter(self): + if (self.otbeg + self.tol) < self.ccbeg and (self.otend - self.tol) > self.ccend: + self.out = f"{self.ccname}\tprediction\tgene\t{self.q_outstart}\t{self.q_outend}\t.\t{self.qstart}\t.\tID={self.ccname};{self.gattr};Note=shorter" + return self.out + elif (self.otbeg - self.tol) <= self.ccbeg <= (self.otbeg + self.tol) and (self.otend - self.tol) > self.ccend: + self.out = f"{self.ccname}\tprediction\tgene\t{self.q_outstart}\t{self.q_outend}\t.\t{self.qstart}\t.\tID={self.ccname};{self.gattr};Note=shorter_right" + return self.out + elif (self.otbeg + self.tol) < self.ccbeg and (self.otend - self.tol) <= self.ccend <= (self.otend + self.tol): + self.out = f"{self.ccname}\tprediction\tgene\t{self.q_outstart}\t{self.q_outend}\t.\t{self.qstart}\t.\tID={self.ccname};{self.gattr};Note=shorter_left" + return self.out + + def is_longer(self): + if (self.otbeg - self.tol) > self.ccbeg and (self.otend + self.tol) < self.ccend: + self.out = f"{self.ccname}\tprediction\tgene\t{self.q_outstart}\t{self.q_outend}\t.\t{self.qstart}\t.\tID={self.ccname};{self.gattr};Note=longer" + return self.out + elif (self.otbeg - self.tol) <= self.ccbeg <= (self.otbeg + self.tol) and (self.otend + self.tol) < self.ccend: + self.out = f"{self.ccname}\tprediction\tgene\t{self.q_outstart}\t{self.q_outend}\t.\t{self.qstart}\t.\tID={self.ccname};{self.gattr};Note=longer_right" + return self.out + elif (self.otbeg - self.tol) > self.ccbeg and (self.otend - self.tol) <= self.ccend <= (self.otend + self.tol): + self.out = f"{self.ccname}\tprediction\tgene\t{self.q_outstart}\t{self.q_outend}\t.\t{self.qstart}\t.\tID={self.ccname};{self.gattr};Note=longer_left" + return self.out + + def is_offset(self): + if (self.otbeg + self.tol) < self.ccbeg < (self.otend - self.tol) and (self.otend + self.tol) < self.ccend: + self.out = f"{self.ccname}\tprediction\tgene\t{self.q_outstart}\t{self.q_outend}\t.\t{self.qstart}\t.\tID={self.ccname};{self.gattr};Note=offset_right" + return self.out + if (self.otbeg - self.tol) > self.ccbeg and (self.otbeg - self.tol) < self.ccend < self.otend + self.tol: + self.out = f"{self.ccname}\tprediction\tgene\t{self.q_outstart}\t{self.q_outend}\t.\t{self.qstart}\t.\tID={self.ccname};{self.gattr};Note=offset_left" + return self.out + + def is_different(self): + if self.otbeg - self.tol > self.ccend or self.otend + self.tol < self.otbeg: + self.out = f"{self.ccname}\tprediction\tgene\t{self.q_outstart}\t{self.q_outend}\t.\t{self.qstart}\t.\tID={self.ccname};{self.gattr};Note=new" + return self.out + + def extract_fasta(self): + with open(self.fastaout,"a") as fileout: + with open(self.fastafile) as filefasta: + for record in SeqIO.parse(filefasta,"fasta"): + if record.id == self.ccname: + fileout.write(f">{self.ccname}_{self.q_outstart}:{self.q_outend}\n{record.seq[self.q_outstart:self.q_outend]}\n") + + # def extract_stout(self): + # with open(self.fastafile) as filefasta: + # for record in SeqIO.parse(filefasta,"fasta"): + # if record.id == self.ccname: + # print(f">{self.ccname}_{self.q_outstart}:{self.q_outend}\n{record.seq[self.q_outstart:self.q_outend]}") + + + #def __str__(self): + # return f"{self.ccname}\t{self.q_outstart}\t{self.q_outend}" + + + def fout(self): + try: + if self.__class__.fout.called: + with open(self.output,"a") as fileout: + fileout.write(self.out+"\n") + except AttributeError: + try: + if os.path.isfile(self.output): + os.remove(self.output) + with open(self.output,"a") as fileout: + #fileout.write("##gff-version 3\n") + fileout.write(f"##gff-version 3\n{self.out}\n") + self.__class__.fout.called = True + self.__class__.fout(self) + except TypeError: + pass + + +def diff_gene(query_genes, target_genes, dstart, dend, qstart, qend, query_db): + # are the two genes the same? + if args.extract: + extract = args.extract + else: + extract = None + + if args.tollerance: + tol = args.tollerance + else: + tol = 30 + + + for otgene in target_genes: + # gattr is a variable created to store the the annotation of the target gene. + # It will be use to suggest a functional annotation + gattr = str(otgene).split("\t")[-1] + for ccgene in query_genes: + algene = GeneComp(ccgene, qstart, qend, otgene, dstart, dend, extract, tol, gattr) + if "new" in args.verbosity or "all" in args.verbosity: + if algene.is_different(): + algene_out = algene.is_different() + algene_name = algene_out.split("\t")[0] + algene_start = int(algene_out.split("\t")[3]) + algene_end = int(algene_out.split("\t")[4]) + #print(al_name, al_start, al_end) + #print(list(target_db.region(region=(al_name, al_start, al_end), completely_within=True))) + if not list(query_db.region(region=(algene_name, algene_start, algene_end), completely_within=False)): + if args.output: + algene.output=args.output + algene.fout() + else: + print(algene.is_different()) + if args.extract: + algene.extract_fasta() + + if "shorter" in args.verbosity or "all" in args.verbosity: + if algene.is_shorter(): + if args.output: + algene.output=args.output + algene.fout() + else: + print(algene.is_shorter()) + if args.extract: + algene.extract_fasta() + if "longer" in args.verbosity or "all" in args.verbosity: + if algene.is_longer(): + if args.output: + algene.output=args.output + algene.fout() + else: + print(algene.is_longer()) + if args.extract: + algene.extract_fasta() + if "offset" in args.verbosity or "all" in args.verbosity: + if algene.is_offset(): + if args.output: + algene.output=args.output + algene.fout() + else: + print(algene.is_offset()) + if args.extract: + algene.extract_fasta() + if "confirmed" in args.verbosity: + if algene.is_equal(): + if args.output: + algene.output=args.output + algene.fout() + else: + print(algene.is_equal()) + if args.extract: + algene.extract_fasta() + + +def gff_gene_check(GffName, db_name, memory=0): + # The IDs on the GFFs must be unique. Moreover, because only the gene + # information are needed, all the other information must be removed + # from the GFFs. + tempgff="" + for line in open(GffName): + if line[0] != "#": + if line.split()[2] == "gene": + tempgff+=line + + else: + tempgff+=line + + if memory: + # Write the db in memory and return it as variable so it can be used + # as subclass of _DBCreator + dbout = gffutils.create_db(tempgff, ":memory:", from_string=True) + return dbout + else: + gffutils.create_db(tempgff, db_name, from_string=True) + +def check_strand(start,leng,strand): + if strand == "+": + end = start+leng + else: + end = start-leng + start,end = end,start + return(start,end) + +def check_position(line, query_db,target_db): + # check if there is a gene in the aligned area + # lets' start with the coordinatescharacteristics + elsp = line.split('\t') + dname = elsp[1] + dstart = int(elsp[2]) + dlen = int(elsp[3]) + dstrand = elsp[4] + qname = elsp[6] + qstart = int(elsp[7]) + qlen = int(elsp[8]) + qstrand = elsp[9] + + # check the strand, if - reverse the start and the end + qstart,qend = check_strand(qstart,qlen,qstrand) + dstart,dend = check_strand(dstart,dlen,dstrand) + + #counter + d_counter = 0 + + # lists of gene within the coordinates + target_genes = [ gene for gene in list(target_db.region(region=(dname, dstart, dend), completely_within=True))] + query_genes = [ gene for gene in list(query_db.region(region=(qname, qstart, qend), completely_within=True))] + + if len(target_genes): + # and len(query_genes): +###### +# PER PROVARE HO TOLTO QUESTO, DA CONTROLLARE +###### + #if len(target_genes) >= len(query_genes): # the number of genes in the aligned area must be bigger in the target (?) + diff_gene(query_genes, target_genes, dstart, dend, qstart, qend, query_db) + + + if d_counter>=1: + return(d_counter) + else: + return(0) + + +def main(args): + fcounter = 0 + # import the GFF library and create (has to be done only once) + # the GFF databases + target_db = query_db = None + db_query_name=args.queryGff + "_db" + db_target_name=args.targetGff + "_db" + + if args.force_database: + # remove the database if required by user + os.remove(db_query_name) + os.remove(db_target_name) + + if args.use_query_database: + # use the db passed by the user + query_db = gffutils.FeatureDB(args.use_query_database) + else: + #create the db + #gffutils.create_db(args.queryGff, db_query_name) + qdbout = gff_gene_check(args.queryGff, db_query_name, args.memory) + + if args.memory: + query_db = gffutils.FeatureDB(qdbout.dbfn) + else: + query_db = gffutils.FeatureDB(db_query_name) + # except ValueError: + # print("Please check your GFF file") + # except: + # raise Exception(f"It seems you already have a db called {db_query_name}. Use the -qu if you want to use it or delete the") + + + if args.use_target_database: + target_db = gffutils.FeatureDB(args.use_target_database) + else: + tdbout = gff_gene_check(args.targetGff, db_target_name, args.memory) + if args.memory: + target_db = gffutils.FeatureDB(tdbout.dbfn) + else: + target_db = gffutils.FeatureDB(db_target_name) + # except ValueError: + # print("Please check your GFF file")if "all" in args.verbosity: + # except: + # raise Exception(f"It seems you already have a db called {db_target_name}. Use the -du if you want to use it or delete the") + + # put the content of the DB in objects + with open(args.aln) as maftab: + for line in maftab: + if line[0] != "#": + fcounter += check_position(line, query_db, target_db) + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description = '''Tool to extract genes coordinates from a whole genome alignent. + This script needs an alignement in TAB format and two gff files''') + parser.add_argument('aln', help='alignment file in TAB format. The suggested way to obtain it is to run Last and\ + than convert the file from MAF to TAB with maf-convert') + parser.add_argument('queryGff', + help='''Gff file of the query organism. The gene IDs in the GFF must be unique.''') + parser.add_argument('targetGff', + help='''Gff file of the "target" organism. The gene IDs in the GFF must be unique.''') + parser.add_argument("-uq", "--use-query-database", + help='''Use this parament if you already have a query gffutils formatted database or + if it\'s not the first time you run this script''', type=str) + parser.add_argument("-ut", "--use-target-database", + help='''Use this parament if you already have a target gffutils formatted database or + if it\'s not the first time you run this script''', type=str) + parser.add_argument("-fd", "--force-database", help="delete old gffutils databases and create new ones", action='store_true') + parser.add_argument("-m", "--memory", help='''create an in-memory database. This option can't be used with the other DB options. + probably usefull in Galaxy integration''', action='store_true' ) + parser.add_argument("-e", "--extract", + help='''Extract the fasta sequence of the new suggested gene. It takes two argument: the fasta file + of the genome and the name of the output file. This will slow down the process A LOT.''', nargs=2, type=str) + #parser.add_argument("-es", "--extract_stout", help='Like -e but it will print the result in the standard output. FASTER than -e. It need the fasta file', type=str) + parser.add_argument("-o", "--output", help='Name of the output file. Default output is stout', type=str) + parser.add_argument("-t", "--tollerance", help='Interval, in nucleotide, within a gene is considered in the same position. Default 30', default=30, type=int) + parser.add_argument("-v", "--verbosity", + help='''Output options. If not specify the software shows only the genes that are in the exact position of the + genes in the target. It\'s possible to show annotated genes that are in aligned regions but that have different lengths or in slightly + different positions. It's possible to select multiple, space separated, values.''', + choices=["all","shorter", "longer", "offset", "new", "confirmed"], nargs='*', default='new', type=str) + #metavar=('all','shorter','longer','shifted','new'), + #action='append', + #choices=["all","shorter", "longer", "shifted", "new"], default="new") + parser.add_argument('--version', action='version', version='0.1.0') + args = parser.parse_args() + main(args) \ No newline at end of file diff -r 000000000000 -r 294f5ba28746 GFFalign.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GFFalign.xml Mon Nov 30 18:20:46 2020 +0000 @@ -0,0 +1,73 @@ + + + biopython + gffutils + + '$output_file' + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + options['extract_fasta'] == 'true' + + + + + + + + + + + + + + + + + @manual{title="https://github.com/eosc-life/D4_marine_eukaryote_genomics_portal", url="https://github.com/eosc-life/D4_marine_eukaryote_genomics_portal"} + + diff -r 000000000000 -r 294f5ba28746 test-data/genome_aln.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_aln.tab Mon Nov 30 18:20:46 2020 +0000 @@ -0,0 +1,3 @@ +9920 NW_012219049.1 513841 4747 + 2725244 scaffold7 968452 4684 - 3903238 150,9:0,13,0:17,6,0:1,11,0:1,13,0:13,17,7:0,5,1:0,12,0:3,13,6:0,7,0:1,24,4:0,10,11:0,121,0:3,107,0:3,28,0:11,18,0:5,27,0:1,6,15:0,112,2:0,9,5:0,50,0:1,31,1:0,23,4:0,6,0:3,10,0:4,23,3:0,6,7:0,14,0:5,9,0:1,12,0:18,18,0:8,7,2:0,17,1:0,23,0:4,9,0:14,5,12:0,20,1:0,71,5:0,114,0:3,44,22:0,78,6:0,11,0:3,29,0:3,45,0:18,14,0:1,17,0:11,6,0:1,29,0:30,45,11:0,17,4:0,35,1:0,5,0:8,35,0:12,5,3:0,87,1:0,24,0:16,5,0:9,7,0:10,8,8:0,13,3:0,23,2:0,14,0:6,25,12:0,19,1:0,20,9:0,6,8:0,174,0:5,53,0:1,136,2:0,58,0:4,34,7:0,23,5:0,38,0:2,29,4:0,7,4:0,12,23:0,6,0:7,5,0:18,32,0:4,14,4:0,9,4:0,76,0:2,40,0:2,21,0:10,10,8:0,11,2:0,5,12:0,32,0:1,85,0:1,47,2:0,124,1:0,6,2:0,17,8:0,49,9:0,8,1:0,122,1:0,60,32:0,37,10:0,28,2:0,11,0:3,9,7:0,33,9:0,3,0:14,31,0:3,42,5:0,15,0:13,19,0:4,56,9:0,69,0:4,81,1:0,48,0:23,5,2:0,37,5:0,27,0:2,34,1:0,25,0:5,33,0:6,105,5:0,5,5:0,33,0:3,30,0:4,15,0:3,7,0:2,33,76:0,18,1:0,188,3:0,7,0:2,18 mismap=1e-10 +11428 NW_012217743.1 12365405 6678 + 13053552 scaffold21 1062549 6820 + 2391267 12,4:0,28,4:0,16,4:0,53,3:0,9,4:0,21,0:2,3,6:0,7,1:0,11,0:3,24,3:0,32,4:0,25,0:2,18,0:2,53,6:0,2,0:1,23,2:0,16,0:3,8,10:0,18,5:0,86,2:0,13,0:1,36,0:12,32,6:0,50,6:0,13,1:0,30,2:0,5,3:0,27,7:0,22,7:0,6,0:5,110,0:1,3,8:0,19,0:1,24,0:4,5,1:0,59,4:0,31,1:0,4,4:0,3,0:3,31,0:1,41,0:11,18,20:0,52,0:2,12,2:0,10,0:3,76,1:0,14,2:0,16,1:0,327,6:0,78,0:24,101,3:0,890,0:43,11,4:0,16,6:0,68,0:3,29,2:0,138,4:0,9,3:0,30,3:0,25,1:0,16,0:6,20,0:2,31,0:11,33,2:0,31,0:17,12,5:0,4,0:10,7,1:0,22,5:0,17,0:1,50,5:0,12,0:4,19,2:0,54,0:1,10,0:3,8,0:4,27,2:0,20,10:0,88,0:8,87,2:0,16,4:0,85,0:36,23,0:5,38,0:6,3,11:0,15,3:0,75,0:11,3,3:0,7,9:0,9,0:5,16,6:0,10,6:0,2,0:5,12,1:0,37,2:0,28,4:0,14,10:0,11,0:33,14,0:3,53,4:0,85,0:35,12,0:8,19,3:0,36,0:6,6,0:8,27,0:1,8,10:0,34,0:15,22,10:0,8,0:10,5,0:5,6,34:0,17,30:0,15,2:0,10,7:0,41,8:0,134,6:0,19,3:0,37,4:0,126,0:9,4,0:8,15,0:4,5,7:0,13,0:7,13,4:0,13,0:15,8,2:0,17,2:0,25,4:0,10,0:5,179,17:0,13,7:0,17,0:18,11,0:1,20,13:0,9,0:11,6,0:25,17,0:1,14,0:1,35,1:0,10,0:5,9,0:5,12,0:43,13,1:0,148,0:9,35,0:5,15,0:4,7,9:0,15,0:2,97,0:2,27,0:1,10,11:0,76,0:18,13,0:27,13,0:16,11,1:0,5,0:25,29,0:3,7,0:13,20,14:0,50,0:21,24,0:1,9,5:0,7,2:0,33,1:0,18,16:0,10,16:0,16,0:5,12,21:0,5,1:0,19,3:0,41,21:0,24,0:3,22,0:7,133,5:0,20 mismap=1e-10 +19504 NW_012222569.1 351588 5843 + 2417895 scaffold27 2112341 5893 - 2121867 16,8:0,108,0:13,5,0:10,26,6:0,13,0:5,33,0:2,23,0:5,10,0:5,27,3:0,29,0:2,10,1:0,12,0:5,16,0:9,19,0:4,5,13:0,11,0:1,28,4:0,11,4:0,27,14:0,50,6:0,12,0:7,6,0:15,10,8:0,86,0:20,20,4:0,60,0:2,16,0:2,34,0:1,37,0:1,166,0:1,56,1:0,114,0:31,63,2:0,16,0:5,6,0:5,15,0:10,14,10:0,38,0:29,9,0:5,10,14:0,17,9:0,17,0:7,27,18:0,24,1:0,9,16:0,33,0:1,6,1:0,14,0:1,15,5:0,16,0:61,40,11:0,6,0:1,44,3:0,111,8:0,11,2:0,10,9:0,37,0:2,12,1:0,44,9:0,49,1:0,26,1:0,35,3:0,31,1:0,19,1:0,28,2:0,17,5:0,150,1:0,161,1:0,4,1:0,40,0:1,131,1:0,43,0:5,12,0:6,43,1:0,875,6:0,369,6:0,421,3:0,931,3:0,16,0:3,375,3:0,43,6:0,8,0:4,19 mismap=1e-10 diff -r 000000000000 -r 294f5ba28746 test-data/output.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.gff Mon Nov 30 18:20:46 2020 +0000 @@ -0,0 +1,3 @@ +scaffold7 prediction gene 967081 968380 . 963768 . ID=scaffold7;New_annotation='ID=gene2900;Dbxref=GeneID:105913423;Name=LOC105913423;gbkey=Gene;gene=LOC105913423;gene_biotype=lncRNA';Note=new +scaffold21 prediction gene 1066913 1069210 . 1062549 . ID=scaffold21;New_annotation='ID=gene518;Dbxref=GeneID:105888784;Name=LOC105888784;gbkey=Gene;gene=LOC105888784;gene_biotype=protein_coding';Note=new +scaffold27 prediction gene 2109210 2112138 . 2106448 . ID=scaffold27;New_annotation='ID=gene19467;Dbxref=GeneID:105906405;Name=tshz2;gbkey=Gene;gene=tshz2;gene_biotype=protein_coding';Note=new diff -r 000000000000 -r 294f5ba28746 test-data/query.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/query.gff Mon Nov 30 18:20:46 2020 +0000 @@ -0,0 +1,126 @@ +scaffold7 maker gene 964712 966103 . - . ID=maker-scaffold7-exonerate_protein2genome-gene-9.10;Name=maker-scaffold7-exonerate_protein2genome-gene-9.10 +scaffold21 maker gene 219 1692 . + . ID=maker-scaffold21-exonerate_protein2genome-gene-0.0;Name=maker-scaffold21-exonerate_protein2genome-gene-0.0 +scaffold21 maker gene 9272 18338 . + . ID=maker-scaffold21-exonerate_protein2genome-gene-0.2;Name=maker-scaffold21-exonerate_protein2genome-gene-0.2 +scaffold21 maker gene 33298 36449 . + . ID=maker-scaffold21-exonerate_protein2genome-gene-0.4;Name=maker-scaffold21-exonerate_protein2genome-gene-0.4 +scaffold21 maker gene 2813 9288 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-0.5;Name=maker-scaffold21-exonerate_protein2genome-gene-0.5 +scaffold21 maker gene 24374 25243 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-0.8;Name=maker-scaffold21-exonerate_protein2genome-gene-0.8 +scaffold21 maker gene 144980 149321 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-1.0;Name=maker-scaffold21-exonerate_protein2genome-gene-1.0 +scaffold21 maker gene 217208 225190 . + . ID=maker-scaffold21-exonerate_protein2genome-gene-2.0;Name=maker-scaffold21-exonerate_protein2genome-gene-2.0 +scaffold21 maker gene 271640 278603 . + . ID=maker-scaffold21-exonerate_protein2genome-gene-2.9;Name=maker-scaffold21-exonerate_protein2genome-gene-2.9 +scaffold21 maker gene 281443 283476 . - . ID=maker-scaffold21-augustus-gene-2.9;Name=maker-scaffold21-augustus-gene-2.9;Dbxref=Coils:Coil,InterPro:IPR008386,PANTHER:PTHR12427,Pfam:PF05680;Note=Similar to ATP5ME: ATP synthase subunit e%2C mitochondrial (Bos taurus OX%3D9913);Ontology_term=GO:0000276,GO:0015078,GO:0015986 +scaffold21 maker gene 244209 248333 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-2.18;Name=maker-scaffold21-exonerate_protein2genome-gene-2.18 +scaffold21 maker gene 250981 253254 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-2.20;Name=maker-scaffold21-exonerate_protein2genome-gene-2.20 +scaffold21 maker gene 261621 262807 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-2.24;Name=maker-scaffold21-exonerate_protein2genome-gene-2.24 +scaffold21 maker gene 284698 285297 . + . ID=maker-scaffold21-exonerate_protein2genome-gene-2.14;Name=maker-scaffold21-exonerate_protein2genome-gene-2.14 +scaffold21 maker gene 298319 304580 . + . ID=maker-scaffold21-augustus-gene-3.10;Name=maker-scaffold21-augustus-gene-3.10;Dbxref=Gene3D:G3DSA:3.20.20.80,InterPro:IPR005199,InterPro:IPR017853,PANTHER:PTHR14363,PANTHER:PTHR14363:SF10,Pfam:PF03662,SUPERFAMILY:SSF51445;Note=Similar to HPSE: Heparanase (Homo sapiens OX%3D9606);Ontology_term=GO:0016020,GO:0016798 +scaffold21 maker gene 306866 318341 . + . ID=augustus-scaffold21-processed-gene-3.1;Name=augustus-scaffold21-processed-gene-3.1;Dbxref=Gene3D:G3DSA:1.20.5.490,InterPro:IPR024864,InterPro:IPR025712,PANTHER:PTHR13000,PANTHER:PTHR13000:SF0,Pfam:PF13874;Note=Similar to NUP54: Nucleoporin p54 (Homo sapiens OX%3D9606);Ontology_term=GO:0005643 +scaffold21 maker gene 338744 340636 . + . ID=maker-scaffold21-exonerate_protein2genome-gene-3.7;Name=maker-scaffold21-exonerate_protein2genome-gene-3.7 +scaffold21 maker gene 375900 382676 . + . ID=maker-scaffold21-exonerate_protein2genome-gene-3.9;Name=maker-scaffold21-exonerate_protein2genome-gene-3.9 +scaffold21 maker gene 304743 306373 . - . ID=maker-scaffold21-augustus-gene-3.12;Name=maker-scaffold21-augustus-gene-3.12;Dbxref=Gene3D:G3DSA:1.10.238.10,InterPro:IPR002048,InterPro:IPR011992,InterPro:IPR018247,MobiDBLite:mobidb-lite,PANTHER:PTHR23049,PANTHER:PTHR23049:SF8,Pfam:PF13405,ProSitePatterns:PS00018,ProSiteProfiles:PS50222,SMART:SM00054,SUPERFAMILY:SSF47473;Note=Similar to MYL5: Myosin light chain 5 (Felis catus OX%3D9685);Ontology_term=GO:0005509 +scaffold21 maker gene 319222 319661 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-3.14;Name=maker-scaffold21-exonerate_protein2genome-gene-3.14 +scaffold21 maker gene 342986 343267 . + . ID=maker-scaffold21-exonerate_protein2genome-gene-3.8;Name=maker-scaffold21-exonerate_protein2genome-gene-3.8 +scaffold21 maker gene 468193 474238 . + . ID=maker-scaffold21-augustus-gene-4.7;Name=maker-scaffold21-augustus-gene-4.7;Dbxref=CDD:cd03580,Gene3D:G3DSA:1.10.2000.10,Gene3D:G3DSA:2.40.50.120,InterPro:IPR001134,InterPro:IPR008993,InterPro:IPR015526,InterPro:IPR018933,InterPro:IPR020067,InterPro:IPR026559,InterPro:IPR036790,PANTHER:PTHR11309,PANTHER:PTHR11309:SF87,Pfam:PF01392,Pfam:PF01759,ProSiteProfiles:PS50038,ProSiteProfiles:PS50189,SMART:SM00063,SMART:SM00643,SUPERFAMILY:SSF50242,SUPERFAMILY:SSF63501;Note=Similar to Sfrp1: Secreted frizzled-related protein 1 (Mus musculus OX%3D10090);Ontology_term=GO:0005515 +scaffold21 maker gene 458084 464076 . - . ID=maker-scaffold21-augustus-gene-4.12;Name=maker-scaffold21-augustus-gene-4.12;Dbxref=Coils:Coil,InterPro:IPR019383,PANTHER:PTHR13254,PANTHER:PTHR13254:SF1,Pfam:PF10256;Note=Similar to GOLGA7: Golgin subfamily A member 7 (Homo sapiens OX%3D9606) +scaffold21 maker gene 423091 435097 . - . ID=maker-scaffold21-augustus-gene-4.10;Name=maker-scaffold21-augustus-gene-4.10;Dbxref=CDD:cd14735,Gene3D:G3DSA:1.25.40.420,Gene3D:G3DSA:2.120.10.80,Gene3D:G3DSA:3.30.710.10,InterPro:IPR000210,InterPro:IPR006652,InterPro:IPR011333,InterPro:IPR011705,InterPro:IPR015915,InterPro:IPR017096,InterPro:IPR030605,MobiDBLite:mobidb-lite,PANTHER:PTHR24412,PANTHER:PTHR24412:SF403,PIRSF:PIRSF037037,PRINTS:PR00501,Pfam:PF00651,Pfam:PF01344,Pfam:PF07707,ProSiteProfiles:PS50097,SMART:SM00225,SMART:SM00612,SMART:SM00875,SUPERFAMILY:SSF117281,SUPERFAMILY:SSF54695;Note=Similar to KLHL8: Kelch-like protein 8 (Homo sapiens OX%3D9606);Ontology_term=GO:0005515,GO:0016567,GO:0031463 +scaffold21 maker gene 386839 388958 . - . ID=maker-scaffold21-augustus-gene-4.8;Name=maker-scaffold21-augustus-gene-4.8;Dbxref=Gene3D:G3DSA:3.10.100.10,InterPro:IPR001304,InterPro:IPR016186,InterPro:IPR016187,InterPro:IPR018378,PANTHER:PTHR22803,PANTHER:PTHR22803:SF89,Pfam:PF00059,ProSitePatterns:PS00615,ProSiteProfiles:PS50041,SUPERFAMILY:SSF56436;Note=Similar to MRC1: Macrophage mannose receptor 1 (Homo sapiens OX%3D9606) +scaffold21 maker gene 452419 452901 . - . ID=maker-scaffold21-augustus-gene-4.11;Name=maker-scaffold21-augustus-gene-4.11;Note=Similar to SDAD1: Protein SDA1 homolog (Homo sapiens OX%3D9606) +scaffold21 maker gene 390939 391459 . - . ID=maker-scaffold21-augustus-gene-4.9;Name=maker-scaffold21-augustus-gene-4.9;Dbxref=CDD:cd00037,Gene3D:G3DSA:3.10.100.10,InterPro:IPR001304,InterPro:IPR016186,InterPro:IPR016187,PANTHER:PTHR22803,PANTHER:PTHR22803:SF89,Pfam:PF00059,ProSiteProfiles:PS50041,SMART:SM00034,SUPERFAMILY:SSF56436;Note=Similar to Fcer2: Low affinity immunoglobulin epsilon Fc receptor (Mus musculus OX%3D10090) +scaffold21 maker gene 392366 398239 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-4.4;Name=maker-scaffold21-exonerate_protein2genome-gene-4.4 +scaffold21 maker gene 442645 445385 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-4.20;Name=maker-scaffold21-exonerate_protein2genome-gene-4.20 +scaffold21 maker gene 454285 456766 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-4.25;Name=maker-scaffold21-exonerate_protein2genome-gene-4.25 +scaffold21 maker gene 566694 572975 . + . ID=maker-scaffold21-augustus-gene-5.15;Name=maker-scaffold21-augustus-gene-5.15;Dbxref=CDD:cd15329,Gene3D:G3DSA:1.20.1070.10,InterPro:IPR000276,InterPro:IPR001069,InterPro:IPR017452,PANTHER:PTHR24247,PANTHER:PTHR24247:SF88,PRINTS:PR00237,PRINTS:PR00652,Pfam:PF00001,ProSiteProfiles:PS50262,SUPERFAMILY:SSF81321;Note=Similar to Htr7: 5-hydroxytryptamine receptor 7 (Mus musculus OX%3D10090);Ontology_term=GO:0004930,GO:0004993,GO:0006939,GO:0007186,GO:0007268,GO:0007623,GO:0016021,GO:0042310 +scaffold21 maker gene 825856 827239 . - . ID=maker-scaffold21-augustus-gene-8.14;Name=maker-scaffold21-augustus-gene-8.14;Dbxref=Gene3D:G3DSA:3.40.50.1460,InterPro:IPR001309,InterPro:IPR002138,InterPro:IPR015471,InterPro:IPR015917,InterPro:IPR029030,MobiDBLite:mobidb-lite,PANTHER:PTHR10454,PANTHER:PTHR10454:SF31,PRINTS:PR00376,Pfam:PF00656,ProSiteProfiles:PS50207,ProSiteProfiles:PS50208,SMART:SM00115,SUPERFAMILY:SSF52129;Note=Similar to Casp7: Caspase-7 (Mus musculus OX%3D10090);Ontology_term=GO:0004197,GO:0006508,GO:0008234 +scaffold21 maker gene 834708 836367 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-8.18;Name=maker-scaffold21-exonerate_protein2genome-gene-8.18 +scaffold21 maker gene 861308 862096 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-8.20;Name=maker-scaffold21-exonerate_protein2genome-gene-8.20 +scaffold21 maker gene 890972 899157 . + . ID=augustus-scaffold21-processed-gene-9.3;Name=augustus-scaffold21-processed-gene-9.3;Dbxref=CDD:cd00924,Gene3D:G3DSA:2.60.11.10,InterPro:IPR002124,InterPro:IPR036972,PANTHER:PTHR10122,PANTHER:PTHR10122:SF4,Pfam:PF01215,ProDom:PD007270,ProSiteProfiles:PS51359,SUPERFAMILY:SSF57802;Note=Similar to COX5B: Cytochrome c oxidase subunit 5B%2C mitochondrial (Vulpes vulpes OX%3D9627);Ontology_term=GO:0004129,GO:0005740 +scaffold21 maker gene 926337 932981 . + . ID=maker-scaffold21-augustus-gene-9.1;Name=maker-scaffold21-augustus-gene-9.1;Dbxref=CDD:cd00012,Gene3D:G3DSA:3.30.420.40,Gene3D:G3DSA:3.90.640.10,InterPro:IPR004000,InterPro:IPR004001,InterPro:IPR020902,InterPro:IPR029909,PANTHER:PTHR11937,PANTHER:PTHR11937:SF195,PRINTS:PR00190,Pfam:PF00022,ProSitePatterns:PS00432,ProSitePatterns:PS01132,SMART:SM00268,SUPERFAMILY:SSF53067;Note=Similar to Actr1b: Beta-centractin (Mus musculus OX%3D10090);Ontology_term=GO:0005869 +scaffold21 maker gene 938048 942296 . + . ID=maker-scaffold21-exonerate_protein2genome-gene-9.11;Name=maker-scaffold21-exonerate_protein2genome-gene-9.11 +scaffold21 maker gene 977259 981092 . + . ID=maker-scaffold21-exonerate_protein2genome-gene-9.16;Name=maker-scaffold21-exonerate_protein2genome-gene-9.16 +scaffold21 maker gene 921431 924431 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-9.22;Name=maker-scaffold21-exonerate_protein2genome-gene-9.22 +scaffold21 maker gene 908085 909206 . + . ID=maker-scaffold21-exonerate_protein2genome-gene-9.3;Name=maker-scaffold21-exonerate_protein2genome-gene-9.3 +scaffold21 maker gene 919938 920906 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-9.20;Name=maker-scaffold21-exonerate_protein2genome-gene-9.20 +scaffold21 maker gene 996275 998398 . + . ID=maker-scaffold21-augustus-gene-10.9;Name=maker-scaffold21-augustus-gene-10.9;Note=Similar to RHOBTB2: Rho-related BTB domain-containing protein 2 (Homo sapiens OX%3D9606) +scaffold21 maker gene 994118 995287 . + . ID=maker-scaffold21-augustus-gene-10.8;Name=maker-scaffold21-augustus-gene-10.8;Dbxref=Gene3D:G3DSA:3.30.710.10,InterPro:IPR011333,PANTHER:PTHR24072,PANTHER:PTHR24072:SF137,SUPERFAMILY:SSF54695;Note=Similar to RHOBTB2: Rho-related BTB domain-containing protein 2 (Homo sapiens OX%3D9606) +scaffold21 maker gene 988098 990151 . - . ID=maker-scaffold21-augustus-gene-10.10;Name=maker-scaffold21-augustus-gene-10.10;Dbxref=InterPro:IPR004978,PANTHER:PTHR11245,PANTHER:PTHR11245:SF7,Pfam:PF03298;Note=Similar to stc: Stanniocalcin (Oncorhynchus kisutch OX%3D8019);Ontology_term=GO:0005179,GO:0005576 +scaffold21 maker gene 999806 1006534 . - . ID=maker-scaffold21-augustus-gene-10.11;Name=maker-scaffold21-augustus-gene-10.11;Dbxref=CDD:cd00038,CDD:cd05572,Coils:Coil,Gene3D:G3DSA:1.10.510.10,Gene3D:G3DSA:2.60.120.10,Gene3D:G3DSA:3.30.200.20,InterPro:IPR000595,InterPro:IPR000719,InterPro:IPR000961,InterPro:IPR002374,InterPro:IPR008271,InterPro:IPR011009,InterPro:IPR014710,InterPro:IPR017441,InterPro:IPR018488,InterPro:IPR018490,InterPro:IPR035014,MobiDBLite:mobidb-lite,PANTHER:PTHR24353,PANTHER:PTHR24353:SF68,PRINTS:PR00104,Pfam:PF00027,Pfam:PF00069,ProSitePatterns:PS00107,ProSitePatterns:PS00108,ProSitePatterns:PS00888,ProSitePatterns:PS00889,ProSiteProfiles:PS50011,ProSiteProfiles:PS50042,ProSiteProfiles:PS51285,SMART:SM00100,SMART:SM00133,SMART:SM00220,SUPERFAMILY:SSF51206,SUPERFAMILY:SSF56112;Note=Similar to PRKG1: cGMP-dependent protein kinase 1 (Bos taurus OX%3D9913);Ontology_term=GO:0004672,GO:0004674,GO:0004692,GO:0005524,GO:0006468 +scaffold21 maker gene 1017091 1024394 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-10.25;Name=maker-scaffold21-exonerate_protein2genome-gene-10.25 +scaffold21 maker gene 1063842 1065209 . - . ID=maker-scaffold21-exonerate_protein2genome-gene-10.33;Name=maker-scaffold21-exonerate_protein2genome-gene-10.33 +scaffold21 maker gene 1013571 1014220 . + . ID=maker-scaffold21-exonerate_protein2genome-gene-10.3;Name=maker-scaffold21-exonerate_protein2genome-gene-10.3 +scaffold27 maker gene 78964 84532 . + . ID=maker-scaffold27-augustus-gene-0.6;Name=maker-scaffold27-augustus-gene-0.6;Dbxref=Coils:Coil,Gene3D:G3DSA:1.10.287.370,InterPro:IPR002777,InterPro:IPR009053,InterPro:IPR016661,PANTHER:PTHR21100,PIRSF:PIRSF016477,Pfam:PF01920,SUPERFAMILY:SSF46579;Note=Similar to PFDN4: Prefoldin subunit 4 (Homo sapiens OX%3D9606);Ontology_term=GO:0006457,GO:0016272,GO:0051082 +scaffold27 maker gene 48231 52047 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-0.4;Name=maker-scaffold27-exonerate_protein2genome-gene-0.4 +scaffold27 maker gene 61378 65183 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-0.6;Name=maker-scaffold27-exonerate_protein2genome-gene-0.6 +scaffold27 maker gene 3695 6685 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-0.0;Name=maker-scaffold27-exonerate_protein2genome-gene-0.0 +scaffold27 maker gene 148461 162196 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-1.6;Name=maker-scaffold27-exonerate_protein2genome-gene-1.6 +scaffold27 maker gene 102125 102751 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-1.2;Name=maker-scaffold27-exonerate_protein2genome-gene-1.2 +scaffold27 maker gene 113040 113444 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-1.3;Name=maker-scaffold27-exonerate_protein2genome-gene-1.3 +scaffold27 maker gene 141043 141363 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-1.4;Name=maker-scaffold27-exonerate_protein2genome-gene-1.4 +scaffold27 maker gene 134273 134461 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-1.5;Name=maker-scaffold27-exonerate_protein2genome-gene-1.5 +scaffold27 maker gene 199903 200492 . - . ID=maker-scaffold27-augustus-gene-2.0;Name=maker-scaffold27-augustus-gene-2.0;Dbxref=Gene3D:G3DSA:1.10.10.60,PANTHER:PTHR11211,PANTHER:PTHR11211:SF12;Note=Similar to irx5: Iroquois-class homeodomain protein irx-5 (Xenopus laevis OX%3D8355) +scaffold27 maker gene 379798 388445 . + . ID=maker-scaffold27-augustus-gene-3.0;Name=maker-scaffold27-augustus-gene-3.0;Dbxref=CDD:cd04278,Gene3D:G3DSA:2.60.40.10,Gene3D:G3DSA:3.40.390.10,InterPro:IPR001818,InterPro:IPR006026,InterPro:IPR007110,InterPro:IPR013783,InterPro:IPR021190,InterPro:IPR024079,InterPro:IPR028687,InterPro:IPR033739,InterPro:IPR036179,PANTHER:PTHR10201,PANTHER:PTHR10201:SF7,PRINTS:PR00138,Pfam:PF00413,ProSiteProfiles:PS50835,SMART:SM00235,SUPERFAMILY:SSF48726,SUPERFAMILY:SSF55486;Note=Similar to MMP23: Matrix metalloproteinase-23 (Bos taurus OX%3D9913);Ontology_term=GO:0004222,GO:0006508,GO:0008237,GO:0008270,GO:0031012 +scaffold27 maker gene 348162 352549 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-3.0;Name=maker-scaffold27-exonerate_protein2genome-gene-3.0 +scaffold27 maker gene 354599 366178 . - . ID=maker-scaffold27-augustus-gene-3.2;Name=maker-scaffold27-augustus-gene-3.2;Dbxref=CDD:cd14735,Gene3D:G3DSA:1.25.40.420,Gene3D:G3DSA:2.120.10.80,Gene3D:G3DSA:3.30.710.10,InterPro:IPR000210,InterPro:IPR006652,InterPro:IPR011333,InterPro:IPR011705,InterPro:IPR015915,InterPro:IPR017096,PANTHER:PTHR24412,PANTHER:PTHR24412:SF255,PIRSF:PIRSF037037,Pfam:PF00651,Pfam:PF01344,Pfam:PF07707,Pfam:PF13964,ProSiteProfiles:PS50097,SMART:SM00225,SMART:SM00612,SMART:SM00875,SUPERFAMILY:SSF117281,SUPERFAMILY:SSF54695;Note=Similar to klhl21: Kelch-like protein 21 (Danio rerio OX%3D7955);Ontology_term=GO:0005515 +scaffold27 maker gene 301455 310534 . - . ID=maker-scaffold27-augustus-gene-3.1;Name=maker-scaffold27-augustus-gene-3.1;Dbxref=CDD:cd00160,CDD:cd13244,Coils:Coil,Gene3D:G3DSA:1.20.900.10,Gene3D:G3DSA:2.30.29.30,InterPro:IPR000219,InterPro:IPR001849,InterPro:IPR011993,InterPro:IPR035899,MobiDBLite:mobidb-lite,PANTHER:PTHR13217,PANTHER:PTHR13217:SF9,Pfam:PF00621,ProSiteProfiles:PS50003,ProSiteProfiles:PS50010,SMART:SM00233,SMART:SM00325,SUPERFAMILY:SSF48065,SUPERFAMILY:SSF50729;Note=Similar to PLEKHG5: Pleckstrin homology domain-containing family G member 5 (Homo sapiens OX%3D9606);Ontology_term=GO:0005089,GO:0035023 +scaffold27 maker gene 274578 275266 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-3.10;Name=maker-scaffold27-exonerate_protein2genome-gene-3.10 +scaffold27 maker gene 331767 344451 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-3.16;Name=maker-scaffold27-exonerate_protein2genome-gene-3.16 +scaffold27 maker gene 370682 373215 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-3.23;Name=maker-scaffold27-exonerate_protein2genome-gene-3.23 +scaffold27 maker gene 353502 353825 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-3.19;Name=maker-scaffold27-exonerate_protein2genome-gene-3.19 +scaffold27 maker gene 412780 416126 . + . ID=maker-scaffold27-augustus-gene-4.7;Name=maker-scaffold27-augustus-gene-4.7;Dbxref=InterPro:IPR003112,PANTHER:PTHR23192,PANTHER:PTHR23192:SF49,Pfam:PF02191,ProSiteProfiles:PS51132,SMART:SM00284;Note=Similar to olfml3b: Olfactomedin-like protein 3B (Danio rerio OX%3D7955) +scaffold27 maker gene 398701 403728 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-4.7;Name=maker-scaffold27-exonerate_protein2genome-gene-4.7 +scaffold27 maker gene 417814 426306 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-4.8;Name=maker-scaffold27-exonerate_protein2genome-gene-4.8 +scaffold27 maker gene 434315 434716 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-4.11;Name=maker-scaffold27-exonerate_protein2genome-gene-4.11 +scaffold27 maker gene 569785 573302 . + . ID=augustus-scaffold27-processed-gene-5.20;Name=augustus-scaffold27-processed-gene-5.20;Dbxref=CDD:cd00063,Gene3D:G3DSA:2.60.40.10,InterPro:IPR003961,InterPro:IPR013783,InterPro:IPR026966,InterPro:IPR036116,MobiDBLite:mobidb-lite,PANTHER:PTHR43951,PANTHER:PTHR43951:SF2,Pfam:PF00041,Pfam:PF13882,ProSiteProfiles:PS50853,SMART:SM00060,SUPERFAMILY:SSF49265;Note=Similar to nadl1.1: Neural cell adhesion molecule L1.1 (Fragment) (Danio rerio OX%3D7955);Ontology_term=GO:0005515 +scaffold27 maker gene 500500 510440 . + . ID=maker-scaffold27-augustus-gene-5.4;Name=maker-scaffold27-augustus-gene-5.4;Dbxref=InterPro:IPR011685,PANTHER:PTHR14009,PANTHER:PTHR14009:SF13,Pfam:PF07766;Note=Similar to letmd1: LETM1 domain-containing protein 1 (Xenopus tropicalis OX%3D8364) +scaffold27 maker gene 475732 483996 . + . ID=maker-scaffold27-augustus-gene-5.3;Name=maker-scaffold27-augustus-gene-5.3;Dbxref=InterPro:IPR013662,InterPro:IPR015925,MobiDBLite:mobidb-lite,PANTHER:PTHR13715,PANTHER:PTHR13715:SF51,Pfam:PF08454;Note=Similar to ITPR3: Inositol 1%2C4%2C5-trisphosphate receptor type 3 (Homo sapiens OX%3D9606);Ontology_term=GO:0006816 +scaffold27 maker gene 467681 469205 . + . ID=maker-scaffold27-augustus-gene-5.2;Name=maker-scaffold27-augustus-gene-5.2;Dbxref=Coils:Coil,InterPro:IPR015925,PANTHER:PTHR13715,PANTHER:PTHR13715:SF51;Note=Similar to Itpr3: Inositol 1%2C4%2C5-trisphosphate receptor type 3 (Mus musculus OX%3D10090);Ontology_term=GO:0006816 +scaffold27 maker gene 460622 463709 . + . ID=maker-scaffold27-augustus-gene-5.1;Name=maker-scaffold27-augustus-gene-5.1;Dbxref=Coils:Coil,Gene3D:G3DSA:1.25.10.30,Gene3D:G3DSA:2.80.10.50,InterPro:IPR000699,InterPro:IPR015925,InterPro:IPR016093,InterPro:IPR035910,InterPro:IPR036300,PANTHER:PTHR13715,PANTHER:PTHR13715:SF51,Pfam:PF01365,Pfam:PF02815,SUPERFAMILY:SSF100909,SUPERFAMILY:SSF82109;Note=Similar to Itpr3: Inositol 1%2C4%2C5-trisphosphate receptor type 3 (Mus musculus OX%3D10090);Ontology_term=GO:0005262,GO:0006816,GO:0016020,GO:0070588 +scaffold27 maker gene 489952 495692 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-5.5;Name=maker-scaffold27-exonerate_protein2genome-gene-5.5 +scaffold27 maker gene 524406 524795 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-5.12;Name=maker-scaffold27-exonerate_protein2genome-gene-5.12 +scaffold27 maker gene 576979 593059 . + . ID=augustus-scaffold27-processed-gene-6.0;Name=augustus-scaffold27-processed-gene-6.0;Dbxref=CDD:cd03275,Coils:Coil,Gene3D:G3DSA:1.20.1060.20,Gene3D:G3DSA:3.30.70.1620,Gene3D:G3DSA:3.40.50.300,InterPro:IPR003395,InterPro:IPR010935,InterPro:IPR024704,InterPro:IPR027417,InterPro:IPR029683,InterPro:IPR036277,PANTHER:PTHR18937,PANTHER:PTHR18937:SF170,PIRSF:PIRSF005719,Pfam:PF02463,Pfam:PF06470,SMART:SM00968,SUPERFAMILY:SSF52540,SUPERFAMILY:SSF75553;Note=Similar to Smc1a: Structural maintenance of chromosomes protein 1A (Mus musculus OX%3D10090);Ontology_term=GO:0003682,GO:0005515,GO:0005524,GO:0005694,GO:0006281,GO:0007064,GO:0008278,GO:0051276 +scaffold27 maker gene 647681 651875 . + . ID=maker-scaffold27-augustus-gene-6.16;Name=maker-scaffold27-augustus-gene-6.16;Dbxref=CDD:cd07989,InterPro:IPR000872,InterPro:IPR002123,PANTHER:PTHR12497,PANTHER:PTHR12497:SF0,PRINTS:PR00979,Pfam:PF01553,SMART:SM00563,SUPERFAMILY:SSF69593;Note=Similar to TAZ: Tafazzin (Macaca mulatta OX%3D9544);Ontology_term=GO:0006644,GO:0008152,GO:0016746 +scaffold27 maker gene 601548 610645 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-6.5;Name=maker-scaffold27-exonerate_protein2genome-gene-6.5 +scaffold27 maker gene 621607 628922 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-6.12;Name=maker-scaffold27-exonerate_protein2genome-gene-6.12 +scaffold27 maker gene 640384 647146 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-6.17;Name=maker-scaffold27-exonerate_protein2genome-gene-6.17 +scaffold27 maker gene 653498 659083 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-6.28;Name=maker-scaffold27-exonerate_protein2genome-gene-6.28 +scaffold27 maker gene 662664 663493 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-6.29;Name=maker-scaffold27-exonerate_protein2genome-gene-6.29 +scaffold27 maker gene 670398 673271 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-6.30;Name=maker-scaffold27-exonerate_protein2genome-gene-6.30 +scaffold27 maker gene 615010 619770 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-6.31;Name=maker-scaffold27-exonerate_protein2genome-gene-6.31 +scaffold27 maker gene 634567 636892 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-6.33;Name=maker-scaffold27-exonerate_protein2genome-gene-6.33 +scaffold27 maker gene 785928 788634 . + . ID=maker-scaffold27-augustus-gene-7.3;Name=maker-scaffold27-augustus-gene-7.3;Dbxref=Gene3D:G3DSA:4.10.60.10,InterPro:IPR001878,InterPro:IPR036875,PANTHER:PTHR23002,PANTHER:PTHR23002:SF53,Pfam:PF00098,ProSiteProfiles:PS50158,SMART:SM00343,SUPERFAMILY:SSF57756;Note=Similar to CNBP: Cellular nucleic acid-binding protein (Bos taurus OX%3D9913);Ontology_term=GO:0003676,GO:0008270 +scaffold27 maker gene 752288 763459 . + . ID=maker-scaffold27-augustus-gene-7.2;Name=maker-scaffold27-augustus-gene-7.2;Dbxref=Coils:Coil,Gene3D:G3DSA:3.30.1490.20,Gene3D:G3DSA:3.30.470.20,Gene3D:G3DSA:3.40.50.20,InterPro:IPR001359,InterPro:IPR013815,InterPro:IPR016185,InterPro:IPR020897,InterPro:IPR020898,MobiDBLite:mobidb-lite,PANTHER:PTHR10841,PANTHER:PTHR10841:SF23,PRINTS:PR01368,Pfam:PF02078,Pfam:PF02750,SUPERFAMILY:SSF52440,SUPERFAMILY:SSF56059;Note=Similar to SYN1: Synapsin-1 (Bos taurus OX%3D9913);Ontology_term=GO:0005524,GO:0007269,GO:0008021 +scaffold27 maker gene 712784 722276 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-7.0;Name=maker-scaffold27-exonerate_protein2genome-gene-7.0 +scaffold27 maker gene 984863 985075 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-9.0;Name=maker-scaffold27-exonerate_protein2genome-gene-9.0 +scaffold27 maker gene 1138838 1140970 . + . ID=maker-scaffold27-augustus-gene-11.7;Name=maker-scaffold27-augustus-gene-11.7;Dbxref=Gene3D:G3DSA:4.10.75.10,InterPro:IPR008197,InterPro:IPR036645,PANTHER:PTHR19441,PANTHER:PTHR19441:SF42,PRINTS:PR00003,Pfam:PF00095,ProSiteProfiles:PS51390,SMART:SM00217,SUPERFAMILY:SSF57256;Note=Similar to WAP: Whey acidic protein (Macropus eugenii OX%3D9315);Ontology_term=GO:0005576,GO:0030414 +scaffold27 maker gene 1160062 1174007 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-11.4;Name=maker-scaffold27-exonerate_protein2genome-gene-11.4 +scaffold27 maker gene 1090337 1094397 . - . ID=maker-scaffold27-augustus-gene-11.9;Name=maker-scaffold27-augustus-gene-11.9;Dbxref=InterPro:IPR006838,PANTHER:PTHR10989,Pfam:PF04750;Note=Similar to AIG1: Androgen-induced gene 1 protein (Homo sapiens OX%3D9606);Ontology_term=GO:0016021 +scaffold27 maker gene 1110751 1127672 . - . ID=maker-scaffold27-augustus-gene-11.10;Name=maker-scaffold27-augustus-gene-11.10;Dbxref=CDD:cd09582,Gene3D:G3DSA:1.10.150.50,Gene3D:G3DSA:1.10.510.10,Gene3D:G3DSA:2.30.30.140,Gene3D:G3DSA:3.30.200.20,InterPro:IPR000719,InterPro:IPR000961,InterPro:IPR001660,InterPro:IPR002515,InterPro:IPR004092,InterPro:IPR008271,InterPro:IPR011009,InterPro:IPR013761,InterPro:IPR017892,InterPro:IPR036060,MobiDBLite:mobidb-lite,PANTHER:PTHR12247,PANTHER:PTHR12247:SF69,Pfam:PF00069,Pfam:PF00433,Pfam:PF00536,Pfam:PF01530,Pfam:PF02820,ProSitePatterns:PS00108,ProSiteProfiles:PS50011,ProSiteProfiles:PS50105,ProSiteProfiles:PS51079,ProSiteProfiles:PS51285,ProSiteProfiles:PS51802,SMART:SM00133,SMART:SM00220,SMART:SM00454,SMART:SM00561,SUPERFAMILY:SSF103637,SUPERFAMILY:SSF47769,SUPERFAMILY:SSF56112,SUPERFAMILY:SSF63748;Note=Similar to L3MBTL1: Lethal(3)malignant brain tumor-like protein 1 (Gallus gallus OX%3D9031);Ontology_term=GO:0003700,GO:0004672,GO:0004674,GO:0005515,GO:0005524,GO:0005634,GO:0006355,GO:0006468,GO:0008270 +scaffold27 maker gene 1174728 1189139 . - . ID=maker-scaffold27-augustus-gene-11.11;Name=maker-scaffold27-augustus-gene-11.11;Dbxref=Coils:Coil,InterPro:IPR024832,InterPro:IPR024835,MobiDBLite:mobidb-lite,PANTHER:PTHR15607,PANTHER:PTHR15607:SF12;Note=Similar to SYCP2: Synaptonemal complex protein 2 (Homo sapiens OX%3D9606) +scaffold27 maker gene 1085420 1086617 . - . ID=maker-scaffold27-augustus-gene-11.8;Name=maker-scaffold27-augustus-gene-11.8;Dbxref=InterPro:IPR029021,PANTHER:PTHR23339,PANTHER:PTHR23339:SF94,SUPERFAMILY:SSF52799;Note=Similar to ptpdc1: Protein tyrosine phosphatase domain-containing protein 1 (Danio rerio OX%3D7955) +scaffold27 maker gene 1080839 1085054 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-11.12;Name=maker-scaffold27-exonerate_protein2genome-gene-11.12 +scaffold27 maker gene 1096041 1099266 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-11.16;Name=maker-scaffold27-exonerate_protein2genome-gene-11.16 +scaffold27 maker gene 1102298 1109092 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-11.18;Name=maker-scaffold27-exonerate_protein2genome-gene-11.18 +scaffold27 maker gene 1129337 1132836 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-11.29;Name=maker-scaffold27-exonerate_protein2genome-gene-11.29 +scaffold27 maker gene 1142492 1148133 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-11.39;Name=maker-scaffold27-exonerate_protein2genome-gene-11.39 +scaffold27 maker gene 1208941 1212725 . + . ID=maker-scaffold27-augustus-gene-12.0;Name=maker-scaffold27-augustus-gene-12.0;Dbxref=InterPro:IPR029266,MobiDBLite:mobidb-lite,PANTHER:PTHR22145,PANTHER:PTHR22145:SF2,Pfam:PF15344;Note=Similar to FAM217B: Protein FAM217B (Homo sapiens OX%3D9606) +scaffold27 maker gene 1262942 1272995 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-12.3;Name=maker-scaffold27-exonerate_protein2genome-gene-12.3 +scaffold27 maker gene 1206565 1208726 . - . ID=maker-scaffold27-exonerate_est2genome-gene-12.3;Name=maker-scaffold27-exonerate_est2genome-gene-12.3;Dbxref=Gene3D:G3DSA:2.60.40.2440,InterPro:IPR005036,InterPro:IPR038175,MobiDBLite:mobidb-lite,PANTHER:PTHR12307,PANTHER:PTHR12307:SF4,Pfam:PF03370,ProSiteProfiles:PS51159;Note=Similar to PPP1R3D: Protein phosphatase 1 regulatory subunit 3D (Homo sapiens OX%3D9606);Ontology_term=GO:0005515 +scaffold27 maker gene 1213029 1217507 . - . ID=maker-scaffold27-augustus-gene-12.1;Name=maker-scaffold27-augustus-gene-12.1;Dbxref=Gene3D:G3DSA:3.30.1490.20,Gene3D:G3DSA:3.30.470.20,InterPro:IPR004344,InterPro:IPR013815,InterPro:IPR027751,PANTHER:PTHR12241,PANTHER:PTHR12241:SF39,Pfam:PF03133,ProSiteProfiles:PS51221,SUPERFAMILY:SSF56059;Note=Similar to TTLL9: Probable tubulin polyglutamylase TTLL9 (Homo sapiens OX%3D9606);Ontology_term=GO:0005524,GO:0006464 +scaffold27 maker gene 1198032 1202479 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-12.5;Name=maker-scaffold27-exonerate_protein2genome-gene-12.5 +scaffold27 maker gene 1226155 1230783 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-12.15;Name=maker-scaffold27-exonerate_protein2genome-gene-12.15 +scaffold27 maker gene 1430214 1446282 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-14.0;Name=maker-scaffold27-exonerate_protein2genome-gene-14.0 +scaffold27 maker gene 1447513 1451570 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-14.1;Name=maker-scaffold27-exonerate_protein2genome-gene-14.1 +scaffold27 maker gene 1865048 1865963 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-18.3;Name=maker-scaffold27-exonerate_protein2genome-gene-18.3 +scaffold27 maker gene 1841075 1845788 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-18.4;Name=maker-scaffold27-exonerate_protein2genome-gene-18.4 +scaffold27 maker gene 1867030 1868428 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-18.5;Name=maker-scaffold27-exonerate_protein2genome-gene-18.5 +scaffold27 maker gene 1874552 1880976 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-18.6;Name=maker-scaffold27-exonerate_protein2genome-gene-18.6 +scaffold27 maker gene 1893574 1898072 . + . ID=maker-scaffold27-augustus-gene-19.10;Name=maker-scaffold27-augustus-gene-19.10;Dbxref=InterPro:IPR019402,InterPro:IPR032990,PANTHER:PTHR21324,PANTHER:PTHR21324:SF10,Pfam:PF10277;Note=Similar to Dram2: DNA damage-regulated autophagy modulator protein 2 (Mus musculus OX%3D10090);Ontology_term=GO:0007601,GO:0010506 +scaffold27 maker gene 1947919 1954646 . + . ID=maker-scaffold27-augustus-gene-19.11;Name=maker-scaffold27-augustus-gene-19.11;Dbxref=Gene3D:G3DSA:1.20.1740.10,InterPro:IPR002293,MobiDBLite:mobidb-lite,PANTHER:PTHR11785,PANTHER:PTHR11785:SF315,PIRSF:PIRSF006060,Pfam:PF13520;Note=Similar to SLC7A5: Large neutral amino acids transporter small subunit 1 (Homo sapiens OX%3D9606);Ontology_term=GO:0016020,GO:0022857,GO:0055085 +scaffold27 maker gene 1884564 1890230 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-19.0;Name=maker-scaffold27-exonerate_protein2genome-gene-19.0 +scaffold27 maker gene 1899996 1916044 . - . ID=maker-scaffold27-augustus-gene-19.12;Name=maker-scaffold27-augustus-gene-19.12;Dbxref=Coils:Coil,Gene3D:G3DSA:3.30.450.200,Gene3D:G3DSA:3.40.50.11500,InterPro:IPR001194,InterPro:IPR005112,InterPro:IPR005113,InterPro:IPR037516,MobiDBLite:mobidb-lite,PANTHER:PTHR15288,PANTHER:PTHR15288:SF2,Pfam:PF02141,Pfam:PF03455,Pfam:PF03456,ProSiteProfiles:PS50211,SMART:SM00799,SMART:SM00800,SMART:SM00801;Note=Similar to DENND2D: DENN domain-containing protein 2D (Homo sapiens OX%3D9606) +scaffold27 maker gene 1932427 1935356 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-19.24;Name=maker-scaffold27-exonerate_protein2genome-gene-19.24 +scaffold27 maker gene 1960006 1967447 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-19.26;Name=maker-scaffold27-exonerate_protein2genome-gene-19.26 +scaffold27 maker gene 2089385 2093369 . + . ID=maker-scaffold27-augustus-gene-20.12;Name=maker-scaffold27-augustus-gene-20.12;Dbxref=CDD:cd00170,Gene3D:G3DSA:1.10.8.20,Gene3D:G3DSA:1.20.5.1200,Gene3D:G3DSA:3.40.525.10,InterPro:IPR001251,InterPro:IPR011074,InterPro:IPR036273,InterPro:IPR036865,PANTHER:PTHR10174,PANTHER:PTHR10174:SF130,PRINTS:PR00180,Pfam:PF00650,Pfam:PF03765,ProSiteProfiles:PS50191,SMART:SM00516,SMART:SM01100,SUPERFAMILY:SSF46938,SUPERFAMILY:SSF52087;Note=Similar to TTPAL: Alpha-tocopherol transfer protein-like (Pongo abelii OX%3D9601) +scaffold27 maker gene 2026933 2030798 . + . ID=augustus-scaffold27-processed-gene-20.1;Name=augustus-scaffold27-processed-gene-20.1;Dbxref=Coils:Coil,Gene3D:G3DSA:1.20.1050.10,Gene3D:G3DSA:3.40.30.10,InterPro:IPR010987,InterPro:IPR034336,InterPro:IPR036282,PANTHER:PTHR44188,PANTHER:PTHR44188:SF2,Pfam:PF13410,ProSiteProfiles:PS50405,SUPERFAMILY:SSF47616;Note=Similar to GDAP1L1: Ganglioside-induced differentiation-associated protein 1-like 1 (Homo sapiens OX%3D9606) +scaffold27 maker gene 2095740 2102605 . + . ID=maker-scaffold27-augustus-gene-20.13;Name=maker-scaffold27-augustus-gene-20.13;Note=Protein of unknown function +scaffold27 maker gene 2020036 2025103 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-20.2;Name=maker-scaffold27-exonerate_protein2genome-gene-20.2 +scaffold27 maker gene 2106469 2107842 . + . ID=maker-scaffold27-exonerate_protein2genome-gene-20.5;Name=maker-scaffold27-exonerate_protein2genome-gene-20.5 +scaffold27 maker gene 2033474 2034742 . - . ID=maker-scaffold27-exonerate_protein2genome-gene-20.7;Name=maker-scaffold27-exonerate_protein2genome-gene-20.7 diff -r 000000000000 -r 294f5ba28746 test-data/target.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/target.gff Mon Nov 30 18:20:46 2020 +0000 @@ -0,0 +1,3 @@ +NW_012219049.1 Gnomon gene 517154 518453 . + . ID=gene2900;Dbxref=GeneID:105913423;Name=LOC105913423;gbkey=Gene;gene=LOC105913423;gene_biotype=lncRNA +NW_012217743.1 Gnomon gene 12369769 12372066 . - . ID=gene518;Dbxref=GeneID:105888784;Name=LOC105888784;gbkey=Gene;gene=LOC105888784;gene_biotype=protein_coding +NW_012222569.1 Gnomon gene 354350 357278 . - . ID=gene19467;Dbxref=GeneID:105906405;Name=tshz2;gbkey=Gene;gene=tshz2;gene_biotype=protein_coding