ORForise 1.6.0__py3-none-any.whl → 1.6.1__py3-none-any.whl

{orforise-1.6.0.dist-info → orforise-1.6.1.dist-info}/RECORD

@@ -1,12 +1,22 @@
-ORForise/Aggregate_Compare.py,sha256=WzP34E4YqkOBXlE9obZfPf3Sp1Gwl40WPqE7PsGntqk,22977
-ORForise/Annotation_Compare.py,sha256=sMyfeMSp_bOJrv-yfp-5gNeiYkYrw1MD2V_6ZKHiCCE,18528
+ORForise/Aggregate_Compare.py,sha256=kf9O_W3520To9yi2zUtmNmDfWZ2oIGr9rfdpbzg699o,22767
+ORForise/Annotation_Compare.py,sha256=5IbaZX9OCkeP90tDYXLqV20KTsuNCHST1-eqbWjuid8,18436
+ORForise/Annotation_Intersector.py,sha256=8nXMCdEifpLAowtTfD1zUibwpOaS4Y3fRkji_3umfVo,34458
 ORForise/Comparator.py,sha256=hvoLppG4tq7iBrIJMmm-ckIpRoLYEryTRQrASNWAjs0,48062
-ORForise/Convert_To_GFF.py,sha256=FMrERozEsRPW4BMglyIjc6NXpKIb7FFo4X78IrepNX4,5981
-ORForise/GFF_Adder.py,sha256=-BlF6DQWcbhyYT88M0ZkoaWA2YDDxsby-7jksfeJN1Q,14057
-ORForise/GFF_Intersector.py,sha256=EcDKyJr_47066kma2CguMf3uwzB2tYomPDFjmoX8IoU,9900
-ORForise/StORForise.py,sha256=2QU6q3wPK6iqtyKg2jEVwFTB4bSymyc-mSpk7T8yNaY,5431
+ORForise/Convert_To_GFF.py,sha256=V1tg-qT6m7uKFgNNNVPK-bYjFTnSdREJd7y92wrGnvM,5889
+ORForise/GFF_Adder.py,sha256=n-AF-JQv6sL46qJEY761EoG4tG5yzqr30r2Zk0v-DMg,28537
+ORForise/List_Tools.py,sha256=6WxP_j6tLWpJ4-obcgM5pEL__C8eWx0rJnsMHY1jWtM,1666
+ORForise/StORForise.py,sha256=jXa-QmN3tIkN5qiqJcFufIY5VuxwU1k99vppGPWIOa4,5627
 ORForise/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/utils.py,sha256=05pc8q02lzwJG06ndUE5tIVdIkYi3uieiiS919oN0Eg,15548
+ORForise/utils.py,sha256=sEDOATM5v50g9sKbBf2QinaCnGel7EtnKiR-UebtTwQ,15751
+ORForise/Aux/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+ORForise/Aux/StORF_Undetected/StORF_Undetected.py,sha256=B7f9AxXD6j2ip4QtuOi7pwtfBCxkexE0XiDCJrKSX5U,1318
+ORForise/Aux/StORF_Undetected/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+ORForise/Aux/StORF_Undetected/Completely_Undetected/Completey_Undetected.py,sha256=PjCtqenheuofqTaWpfJa7VCiMK0s-9kMnOlGIBl9f7k,1860
+ORForise/Aux/StORF_Undetected/Completely_Undetected/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+ORForise/Aux/StORF_Undetected/unvitiated_Genes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+ORForise/Aux/StORF_Undetected/unvitiated_Genes/unvitiated_Missed_Genes.py,sha256=notWaFx7AG8BZjBhnGuSyitxa1cRK_7rygOPp9keGfM,1863
+ORForise/Aux/TabToGFF/TabToGFF.py,sha256=i9PnODPdIcsLBiCIntiq_3Z8_WeajB8ZE--DeLdRf24,5168
+ORForise/Aux/TabToGFF/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/ORForise_Analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/ORForise_Analysis/cds_checker.py,sha256=x838-PDd8HxZ3uhfW7wPzaJdiVwomNaYOZzMe-09f_0,2643
 ORForise/ORForise_Analysis/gene_Lenghts.py,sha256=eDmJqVjBJYkBMuLr4s4XDA-E-fv0eEITpWAPySOynow,939
@@ -21,7 +31,7 @@ ORForise/Tools/Augustus/Augustus.py,sha256=rEZ3h3eHrCfMFDorXxF5h0j4Wr5vTHG_rrQ-1
 ORForise/Tools/Augustus/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/Tools/Balrog/Balrog.py,sha256=wrxQe7Df-iYUq3IQvX8A9GzDy5qR9rt5LHkDnDUngKc,1768
 ORForise/Tools/Balrog/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/EasyGene/EasyGene.py,sha256=_1gGRYulpnhgB2xL7ZsnkXF4U8O9XgC0XQTZq7XubC4,1752
+ORForise/Tools/EasyGene/EasyGene.py,sha256=FCvcmL6w_ytefSNvWfWXIG6h0BKObPtTcCp0iGUSdH0,2330
 ORForise/Tools/EasyGene/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/Tools/FGENESB/FGENESB.py,sha256=3Jxe2DzUTG77wllSJpN__c_4cdl_gcj2idLXNMkv1Cs,1871
 ORForise/Tools/FGENESB/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -29,12 +39,12 @@ ORForise/Tools/FragGeneScan/FragGeneScan.py,sha256=ofywMVF-FBM4s3FPwoWsJKQUX0T_i
 ORForise/Tools/FragGeneScan/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/Tools/GFF/GFF.py,sha256=Z9xPCWNXrmRVvBR9_PNlajQz8ZYFHvOdXwCskXR1XhI,3219
 ORForise/Tools/GFF/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/GLIMMER_3/GLIMMER_3.py,sha256=McFulHAHV4e3ROVmTn0JSz-r0TTqiEor0MsemsIkSjc,2124
-ORForise/Tools/GLIMMER_3/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+ORForise/Tools/GLIMMER3/GLIMMER3.py,sha256=AP5FttPNsGBKrkvT-1EXO66P1LfHELj9rCo3lNWoqQk,2122
+ORForise/Tools/GLIMMER3/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/Tools/GeneMark/GeneMark.py,sha256=SeovWnoLy7Ktkc37TXLjWWUmmgEMvip7j2XIe5fiYaA,5815
 ORForise/Tools/GeneMark/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/GeneMark_HA/GeneMark_HA.py,sha256=nfMEAszBEZw4zhhW3VtZt6yqJprXkydVAR1a3RrAm1k,1737
-ORForise/Tools/GeneMark_HA/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+ORForise/Tools/GeneMarkHA/GeneMarkHA.py,sha256=FUBYsscSR9Uc1dM5kXKWtu-HJ1s2Dmn2cBapAT0t308,1736
+ORForise/Tools/GeneMarkHA/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/Tools/GeneMark_HMM/GeneMark_HMM.py,sha256=HK1SWj-M_9AWngMkkWOXQf6sr__kvON8ZL_wYRTMEzk,1753
 ORForise/Tools/GeneMark_HMM/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/Tools/GeneMark_S/GeneMark_S.py,sha256=56FQ-u-uvZFN41Ii0tGCUuBWsZaPaxvigbuOVg_4QCw,1722
@@ -47,25 +57,17 @@ ORForise/Tools/MetaGeneAnnotator/MetaGeneAnnotator.py,sha256=pfQgzwwBz54kVsLWH7G
 ORForise/Tools/MetaGeneAnnotator/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/Tools/MetaGeneMark/MetaGeneMark.py,sha256=_JMGtHvuX-qM-PSFI6EV91Jm86DWluukwGq7lFFCCSo,1848
 ORForise/Tools/MetaGeneMark/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/Prodigal/Prodigal.py,sha256=y8bnh9_A4DmTJAsKqD_1S_d9ak56ZXsnUiFhrGudNcw,1758
+ORForise/Tools/Prodigal/Prodigal.py,sha256=DwcZmYI0MSrBj180Yj_S-jq3lIYbVUMrf0PQpjsUSx8,2324
 ORForise/Tools/Prodigal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/Tools/Prokka/Prokka.py,sha256=-wKNDcZTbnUpqeqlc7VvXcC0KnwMZ4BduWAlH1p8ULU,1887
 ORForise/Tools/Prokka/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/Tools/StORF_Reporter/StORF_Reporter.py,sha256=areqA94r6nU3GOodnl4QzQbnkMd1XRve0SWn11XoOec,1993
 ORForise/Tools/StORF_Reporter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/StORF_Undetected/StORF_Undetected.py,sha256=B7f9AxXD6j2ip4QtuOi7pwtfBCxkexE0XiDCJrKSX5U,1318
-ORForise/Tools/StORF_Undetected/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/StORF_Undetected/Completely_Undetected/Completey_Undetected.py,sha256=PjCtqenheuofqTaWpfJa7VCiMK0s-9kMnOlGIBl9f7k,1860
-ORForise/Tools/StORF_Undetected/Completely_Undetected/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/StORF_Undetected/unvitiated_Genes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/StORF_Undetected/unvitiated_Genes/unvitiated_Missed_Genes.py,sha256=notWaFx7AG8BZjBhnGuSyitxa1cRK_7rygOPp9keGfM,1863
-ORForise/Tools/TabToGFF/TabToGFF.py,sha256=i9PnODPdIcsLBiCIntiq_3Z8_WeajB8ZE--DeLdRf24,5168
-ORForise/Tools/TabToGFF/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ORForise/Tools/TransDecoder/TransDecoder.py,sha256=YlYxxicuP8xjwNkAKbHOdfaurvOHH0whYxaiB6B2kjs,1778
 ORForise/Tools/TransDecoder/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-orforise-1.6.0.dist-info/licenses/LICENSE,sha256=eAL1bBUjSMCdvudcn9E3sbujCBCa839cqXxauONDbSU,32476
-orforise-1.6.0.dist-info/METADATA,sha256=GxlEILI_VbuQQtNyTAtEkrKXYRWi83Zb6yGTTTTkmsY,72816
-orforise-1.6.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-orforise-1.6.0.dist-info/entry_points.txt,sha256=FHQMpAIg2IUIQmgdI8A1QWDglVkyEasIAbUFupzL__Y,566
-orforise-1.6.0.dist-info/top_level.txt,sha256=7kmFicUFY65FJmioc0cpZtXVz93V7KSKvZVWpGz5Hyk,9
-orforise-1.6.0.dist-info/RECORD,,
+orforise-1.6.1.dist-info/licenses/LICENSE,sha256=eAL1bBUjSMCdvudcn9E3sbujCBCa839cqXxauONDbSU,32476
+orforise-1.6.1.dist-info/METADATA,sha256=swyauHPeW5wTZ72-k4BM_xUSwwBvsGrZHUKA_VyEGjc,59554
+orforise-1.6.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+orforise-1.6.1.dist-info/entry_points.txt,sha256=_HaBzKQFXCkxHIIgBH_XIOng92-GWJ5FC29LmNaSpR0,670
+orforise-1.6.1.dist-info/top_level.txt,sha256=7kmFicUFY65FJmioc0cpZtXVz93V7KSKvZVWpGz5Hyk,9
+orforise-1.6.1.dist-info/RECORD,,

{orforise-1.6.0.dist-info → orforise-1.6.1.dist-info}/entry_points.txt

@@ -1,13 +1,15 @@
 [console_scripts]
 Aggregate-Compare = ORForise.Aggregate_Compare:main
 Annotation-Compare = ORForise.Annotation_Compare:main
+Annotation-Intersector = ORForise.Annotation_Intersector:main
 Convert-To-GFF = ORForise.Convert_To_GFF:main
 GFF-Adder = ORForise.GFF_Adder:main
-GFF-Intersector = ORForise.GFF_Intersector:main
+List-Tools = ORForise.List_Tools:main
 StORForise = ORForise.StORForise:main
 aggregate-compare = ORForise.Aggregate_Compare:main
 annotation-compare = ORForise.Annotation_Compare:main
+annotation-intersector = ORForise.Annotation_Intersector:main
 convert-to-gff = ORForise.Convert_To_GFF:main
 gff-adder = ORForise.GFF_Adder:main
-gff-intersector = ORForise.GFF_Intersector:main
+list-tools = ORForise.List_Tools:main
 storforise = ORForise.StORForise:main

ORForise/GFF_Intersector.py

@@ -1,192 +0,0 @@
-from importlib import import_module
-import argparse
-import collections
-from datetime import date
-import sys
-try:
-    from utils import *
-except ImportError:
-    from .utils import *
-
-################################
-
-
-def gff_writer(genome_ID, genome_DNA,reference_annotation, reference_tool, ref_gene_set, additional_annotation, additional_tool, genes_To_Keep, output_file):
-    write_out = open(output_file, 'w')
-    write_out.write("##gff-version\t3\n#\tGFF-Intersector\n#\tRun Date:" + str(date.today()) + '\n')
-    write_out.write("##Genome DNA File:" + genome_DNA + '\n')
-    write_out.write("##Original File: " + reference_annotation + "\n##Intersecting File: " + additional_annotation + '\n')
-    for pos, data in genes_To_Keep.items():
-        pos_ = pos.split(',')
-        start = pos_[0]
-        stop = pos_[-1]
-        strand = data[0]
-        ref = reference_annotation.split('/')[-1].split('.')[0]
-        data[4] = data[4].replace('\n', '').replace('ID=','')
-        data[5] = data[5].replace('\n', '').replace('ID=','')
-        entry = (
-                    genome_ID + '\t' + ref + '\t' + data[2] + '\t' + start + '\t' + stop + '\t.\t' + strand + '\t.\tID=Original_Annotation=' + data[4] + ';Additional_Annotation=' + data[5] + ';Coverage=' + str(
-                data[1]) + '\n')
-        write_out.write(entry)
-
-
-def comparator(options):  # Only works for single contig genome
-    genome_seq = ""
-    with open(options.genome_DNA, 'r') as genome_fasta:
-        for line in genome_fasta:
-            line = line.replace("\n", "")
-            if not line.startswith('>'):
-                genome_seq += str(line)
-            else:
-                genome_ID = line.split()[0].replace('>', '')
-    ###########################################
-    if not options.reference_tool:  # IF using Ensembl for comparison
-        ref_genes = collections.OrderedDict()  # Order is important
-        count = 0
-        with open(options.reference_annotation, 'r') as genome_gff:
-            for line in genome_gff:
-                line = line.split('\t')
-                try:
-                    if 'CDS' in options.gene_ident and len(options.gene_ident) == 1:
-                        if "CDS" in line[2] and len(line) == 9:
-                            start = int(line[3])
-                            stop = int(line[4])
-                            strand = line[6]
-                            pos = str(start) + ',' + str(stop)
-                            info = line[8]
-                            ref_genes.update({pos: [strand, 'ref', 'CDS',info]})
-                            count += 1
-                    else:
-                        gene_types = options.gene_ident.split(',')
-                        if any(gene_type in line[2] for gene_type in gene_types):  # line[2] for normalrun
-                            start = int(line[3])
-                            stop = int(line[4])
-                            strand = line[6]
-                            pos = str(start) + ',' + str(stop)
-                            info = line[8]
-                            ref_genes.update(
-                                {pos: [strand, 'ref', line[2],info]})  # Report what type of gene/rRNA etc we have here
-                            count += 1
-                except IndexError:
-                    continue
-    else:  # IF using a tool as reference
-        try:
-            reference_tool_ = import_module('Tools.' + options.reference_tool + '.' + options.reference_tool,
-                                             package='my_current_pkg')
-        except ModuleNotFoundError:
-            try:
-                reference_tool_ = import_module('ORForise.Tools.' + options.reference_tool + '.' + options.reference_tool,
-                                             package='my_current_pkg')
-            except ModuleNotFoundError:
-                sys.exit("Tool not available")
-        reference_tool_ = getattr(reference_tool_, options.reference_tool)
-        ############ Reformatting tool output for ref_genes
-        ref_genes = reference_tool_(options.reference_annotation, genome_seq)
-    ref_gene_set = list(ref_genes.keys())
-    ############################## Get Add'l
-    try:
-        additional_tool_ = import_module('Tools.' + options.additional_tool + '.' + options.additional_tool,
-                                        package='my_current_pkg')
-    except ModuleNotFoundError:
-        try:
-            additional_tool_ = import_module('ORForise.Tools.' + options.additional_tool + '.' + options.additional_tool,
-                                            package='my_current_pkg')
-        except ModuleNotFoundError:
-            sys.exit("Tool not available")
-    additional_tool_ = getattr(additional_tool_, options.additional_tool)
-    additional_orfs = additional_tool_(options.additional_annotation,genome_seq,options.gene_ident)
-    ##############################
-
-
-    genes_To_Keep = collections.OrderedDict()
-
-    if options.coverage == 100:
-        for orf, data in additional_orfs.items():
-            o_Start = int(orf.split(',')[0])
-            o_Stop = int(orf.split(',')[1])
-            o_Strand = data[0]
-            additional_type = data[3]
-            additional_info = data[4]
-            try:
-                ref_type = ref_genes[str(o_Start) + ',' + str(o_Stop)][2]
-                ref_info = ref_genes[str(o_Start) + ',' + str(o_Stop)][3]
-            except KeyError:
-                continue
-            #try:
-                #if ref_genes[str(o_Start) + ',' + str(o_Stop)][2] == "CDS" : # Make sure 100% match and is also CDS
-            if additional_type == ref_type:
-                genes_To_Keep.update({str(o_Start) + ',' + str(o_Stop): [o_Strand, options.coverage,additional_type,ref_type,additional_info,ref_info]})  # o_ and g_ would be the same here
-            #except KeyError:
-            #    continue
-    else:
-        for orf, data in additional_orfs.items():  # Currently allows ORF to be bigger than Gene
-            o_Start = int(orf.split(',')[0])
-            o_Stop = int(orf.split(',')[1])
-            o_Strand = data[0]
-            orf_Set = set(range(int(o_Start), int(o_Stop) + 1))
-            for gene, r_data in ref_genes.items():  # Very ineffecient
-                g_Start = int(gene.split(',')[0])
-                g_Stop = int(gene.split(',')[1])
-                g_Strand = r_data[0]
-                gene_Set = set(range(int(g_Start), int(g_Stop) + 1))
-                overlap = len(orf_Set.intersection(gene_Set))
-                cov = 100 * float(overlap) / float(len(gene_Set))
-
-                additional_type = data[3]
-                additional_info = data[4]
-                ref_type = r_data[2]
-                ref_info = r_data[3]
-
-                if abs(o_Stop - g_Stop) % 3 == 0 and o_Strand == g_Strand and cov >= options.coverage:
-                    if additional_type == ref_type:
-                        genes_To_Keep.update({str(g_Start) + ',' + str(g_Stop): [g_Strand, int(cov),additional_type,ref_type,additional_info,ref_info]})
-                if g_Start > o_Stop:
-                    break
-    #########################################################
-    #### Currently, only CDSs are filtered
-    # for gene, g_data in ref_genes.items():  # Very ineffecient
-    #     if "CDS" not in g_data[2]:
-    #         g_Start = int(gene.split(',')[0])
-    #         g_Stop = int(gene.split(',')[1])
-    #         g_Strand = g_data[0]
-    #         genes_To_Keep.update({str(g_Start) + ',' + str(g_Stop): [g_Strand, "N/A",g_data[2]]})
-    genes_To_Keep = sortORFs(genes_To_Keep)
-    gff_writer(genome_ID, options.genome_DNA, options.reference_annotation, options.reference_tool, ref_gene_set, options.additional_annotation, options.additional_tool, genes_To_Keep, options.output_file)
-
-def main():
-    print("Thank you for using ORForise\nPlease report any issues to: https://github.com/NickJD/ORForise/issues\n#####")
-
-    parser = argparse.ArgumentParser(description='ORForise ' + ORForise_Version + ': GFF-Intersector Run Parameters.')
-    parser._action_groups.pop()
-
-    required = parser.add_argument_group('Required Arguments')
-    required.add_argument('-dna', dest='genome_DNA', required=True, help='Genome DNA file (.fa) which both annotations '
-                                                                    'are based on')
-    required.add_argument('-ref', dest='reference_annotation', required=True,
-                        help='Which reference annotation file to use as reference?')
-    required.add_argument('-at', dest='additional_tool', required=True,
-                        help='Which format to use for additional annotation?')
-    required.add_argument('-add', dest='additional_annotation', required=True,
-                        help='Which annotation file to add to reference annotation?')
-    required.add_argument('-o', dest='output_file', required=True,
-                        help='Output filename')
-
-    optional = parser.add_argument_group('Optional Arguments')
-    optional.add_argument('-rt', dest='reference_tool', required=False,
-                        help='Which tool format to use as reference? - If not provided, will default to the '
-                             'standard GFF format and will only look for "CDS" features')
-    optional.add_argument('-gi', dest='gene_ident', default='CDS', required=False,
-                        help='Identifier used for extraction of "genic" regions from reference annotation '
-                             '"CDS,rRNA,tRNA": Default for is "CDS" ')
-    optional.add_argument('-cov', dest='coverage', default=100, type=int, required=False,
-                        help='Percentage coverage of reference annotation needed to confirm intersection'
-                             ' - Default: 100 == exact match')
-
-    options = parser.parse_args()
-    comparator(options)
-
-
-
-if __name__ == "__main__":
-    main()
-    print("Complete")