ORForise 1.4.3__py3-none-any.whl → 1.5.0__py3-none-any.whl

ORForise/Tools/Prokka/Prokka.py

@@ -10,31 +10,36 @@ except ImportError:
 
 def Prokka(*args):
     tool_pred = args[0]
-    genome = args[1]
+    dna_regions = args[1]
     types = args[2]
     prokkaORFs = collections.defaultdict(list)
-    genome_size = len(genome)
-    genome_rev = revCompIterative(genome)
-    with open(tool_pred, 'r') as prodigal_input:
-        for line in prodigal_input:
-            if '#' not in line:
-                line = line.split('\t')
-                if "prokka" not in line[1] and line[8].startswith('ID='):
-                    start = int(line[3])
-                    stop = int(line[4])
-                    strand = line[6]
-                    info = line[8]
-                    if '-' in strand:  # Reverse Compliment starts and stops adjusted
-                        r_start = genome_size - stop
-                        r_stop = genome_size - start
-                        startCodon = genome_rev[r_start:r_start + 3]
-                        stopCodon = genome_rev[r_stop - 2:r_stop + 1]
-                    elif '+' in strand:
-                        startCodon = genome[start - 1:start + 2]
-                        stopCodon = genome[stop - 3:stop]
-                    po = str(start) + ',' + str(stop)
-                    orf = [strand, startCodon, stopCodon, line[2], 'Prokka|'+info]
-                    prokkaORFs.update({po: orf})
+    for dna_region in dna_regions:
+        prokkaORFs[dna_region] = collections.OrderedDict()
+    for dna_region in dna_regions:
+        genome = dna_regions[dna_region][0]
+        genome_size = len(genome)
+        genome_rev = revCompIterative(genome)
+        with open(tool_pred, 'r') as prodigal_input:
+            for line in prodigal_input:
+                if '#' not in line:
+                    line = line.split('\t')
+                    if "prokka" not in line[1] and line[8].startswith('ID=') and dna_region in line[0] and "CDS" in line[2]:
+                        start = int(line[3])
+                        stop = int(line[4])
+                        strand = line[6]
+                        info = line[8]
+                        if '-' in strand:  # Reverse Compliment starts and stops adjusted
+                            r_start = genome_size - stop
+                            r_stop = genome_size - start
+                            startCodon = genome_rev[r_start:r_start + 3]
+                            stopCodon = genome_rev[r_stop - 2:r_stop + 1]
+                        elif '+' in strand:
+                            startCodon = genome[start - 1:start + 2]
+                            stopCodon = genome[stop - 3:stop]
+                        po = str(start) + ',' + str(stop)
+                        orf = [strand, startCodon, stopCodon, line[2], 'Prokka']
+                        prokkaORFs.update({po: orf})
 
-    prodigalORFs = sortORFs(prokkaORFs)
-    return prodigalORFs
+    for group in prokkaORFs:
+        prokkaORFs[group] = sortORFs(prokkaORFs[group])
+    return prokkaORFs

ORForise/Tools/StORF_Reporter/StORF_Reporter.py

@@ -8,30 +8,37 @@ except ImportError:
     from ORForise.utils import sortORFs
 
 
-def StORF_Reporter(tool_pred, genome):
-    storf_orfs = collections.OrderedDict()
-    genome_size = len(genome)
-    genome_rev = revCompIterative(genome)
-    with open(tool_pred, 'r') as storf_input:
-        for line in storf_input:
-            if not line.startswith('#') and not line.startswith('\n'):
-                line = line.split()
-                if 'StORF_Reporter' in line[1] or 'StoRF_Reporter' in line[1]  or 'StORF' in line[1] or 'StORF-Reporter' in line[1]: # need to harmonise this.
-                    start = int(line[3])
-                    stop = int(line[4])
-                    strand = line[6]
-                    info = line[8]
-                    if '-' in strand:  # Reverse Compliment starts and stops adjusted
-                        r_start = genome_size - stop
-                        r_stop = genome_size - start
-                        startCodon = genome_rev[r_start:r_start + 3]
-                        stopCodon = genome_rev[r_stop - 2:r_stop + 1]
-                    elif '+' in strand:
-                        startCodon = genome[start:start + 3]
-                        stopCodon = genome[stop - 3:stop]
-                    po = str(start) + ',' + str(stop)
-                    orf = [strand, startCodon, stopCodon, 'CDS', info] # StORF/Con-StORF or CDS??
-                    storf_orfs.update({po: orf})
+def StORF_Reporter(*args):
+    tool_pred = args[0]
+    dna_regions = args[1]
+    storf_ORFs = collections.OrderedDict()
+    for dna_region in dna_regions:
+        storf_ORFs[dna_region] = collections.OrderedDict()
+    for dna_region in dna_regions:
+        genome = dna_regions[dna_region][0]
+        genome_size = len(genome)
+        genome_rev = revCompIterative(genome)
+        with open(tool_pred, 'r') as storf_input:
+            for line in storf_input:
+                if not line.startswith('#') and not line.startswith('\n'):
+                    line = line.split()
+                    if 'StORF_Reporter' in line[1] or 'StoRF_Reporter' in line[1]  or 'StORF' in line[1] or 'StORF-Reporter' in line[1] and dna_region in line[0]: # need to harmonise this.
+                        start = int(line[3])
+                        stop = int(line[4])
+                        strand = line[6]
+                        info = line[8]
+                        if '-' in strand:  # Reverse Compliment starts and stops adjusted
+                            r_start = genome_size - stop
+                            r_stop = genome_size - start
+                            startCodon = genome_rev[r_start:r_start + 3]
+                            stopCodon = genome_rev[r_stop - 2:r_stop + 1]
+                        elif '+' in strand:
+                            startCodon = genome[start:start + 3]
+                            stopCodon = genome[stop - 3:stop]
+                        po = str(start) + ',' + str(stop)
+                        orf = [strand, startCodon, stopCodon, 'CDS', 'StORF-Reporter'] # StORF/Con-StORF or CDS??
+                        storf_ORFs.update({po: orf})
 
-    storf_orfs = sortORFs(storf_orfs)
-    return storf_orfs
+    for group in storf_ORFs:
+        storf_ORFs[group] = sortORFs(storf_ORFs[group])
+    return storf_ORFs

ORForise/Tools/TransDecoder/TransDecoder.py

@@ -8,28 +8,35 @@ except ImportError:
     from ORForise.utils import sortORFs
 
 
-def TransDecoder(tool_pred, genome):
+def TransDecoder(*args):
+    tool_pred = args[0]
+    dna_regions = args[1]
     transDecoder_ORFs = collections.OrderedDict()
-    genome_size = len(genome)
-    genome_rev = revCompIterative(genome)
-    with open(tool_pred, 'r') as transDecoder_Input:
-        for line in transDecoder_Input:
-            line = line.split()
-            if len(line) == 9 and "transdecoder" in line[1] and "CDS" in line[2]:
-                start = int(line[3])
-                stop = int(line[4])
-                strand = line[6]
-                if '-' in strand:  # Reverse Compliment starts and stops adjusted
-                    r_start = genome_size - stop
-                    r_stop = genome_size - start
-                    startCodon = genome_rev[r_start:r_start + 3]
-                    stopCodon = genome_rev[r_stop - 2:r_stop + 1]
-                elif '+' in strand:
-                    startCodon = genome[start - 1:start + 2]
-                    stopCodon = genome[stop - 3:stop]
-                po = str(start) + ',' + str(stop)
-                orf = [strand, startCodon, stopCodon, 'CDS']
-                transDecoder_ORFs.update({po: orf})
+    for dna_region in dna_regions:
+        transDecoder_ORFs[dna_region] = collections.OrderedDict()
+    for dna_region in dna_regions:
+        genome = dna_regions[dna_region][0]
+        genome_size = len(genome)
+        genome_rev = revCompIterative(genome)
+        with open(tool_pred, 'r') as transDecoder_Input:
+            for line in transDecoder_Input:
+                line = line.split()
+                if len(line) == 9 and "transdecoder" in line[1] and "CDS" in line[2] and dna_region in line[0]:
+                    start = int(line[3])
+                    stop = int(line[4])
+                    strand = line[6]
+                    if '-' in strand:  # Reverse Compliment starts and stops adjusted
+                        r_start = genome_size - stop
+                        r_stop = genome_size - start
+                        startCodon = genome_rev[r_start:r_start + 3]
+                        stopCodon = genome_rev[r_stop - 2:r_stop + 1]
+                    elif '+' in strand:
+                        startCodon = genome[start - 1:start + 2]
+                        stopCodon = genome[stop - 3:stop]
+                    po = str(start) + ',' + str(stop)
+                    orf = [strand, startCodon, stopCodon, 'CDS', 'TransDecoder']
+                    transDecoder_ORFs.update({po: orf})
 
-    transDecoder_ORFs = sortORFs(transDecoder_ORFs)
+    for group in transDecoder_ORFs:
+        transDecoder_ORFs[group] = sortORFs(transDecoder_ORFs[group])
     return transDecoder_ORFs

ORForise/utils.py

@@ -4,7 +4,7 @@ import collections
 # Constants
 SHORT_ORF_LENGTH = 300
 MIN_COVERAGE = 75
-ORForise_Version = 'v1.4.3'
+ORForise_Version = 'v1.5.0'
 
 
 def revCompIterative(watson):  # Gets Reverse Complement
@@ -28,4 +28,206 @@ def sortGenes(Genes):  # Will sort by given start position and then rearrange fo
         if detail[1] < prev_stop:
             Genes_Sorted[pos], Genes_Sorted[pos-1] = Genes_Sorted[pos-1], Genes_Sorted[pos]
         prev_stop = detail[1]
-    return Genes_Sorted
+    return Genes_Sorted
+
+
+def gff_load(options,gff_in,dna_regions):
+    count = 0
+    for line in gff_in:  # Get gene loci from GFF - ID=Gene will also classify Pseudogenes as genes
+        line_data = line.split('\t')
+        if line.startswith('\n') or line.startswith('#') or 'European Nucleotide Archive' in line:  # Not to crash on empty lines in GFF
+            continue
+        elif options.gene_ident[0] == 'ID=gene':
+            if line_data[0] in dna_regions and options.gene_ident[0] in line_data[8]:
+                start = int(line_data[3])
+                stop = int(line_data[4])
+                strand = line_data[6]
+                gene_details = [start,stop,strand]
+                dna_regions[line_data[0]][2].append({count:gene_details}) # This will add to list
+                count += 1
+        else:
+            try:
+                if line_data[2] == 'region':
+                    continue
+                elif line_data[0] in dna_regions:
+                    if any(gene_type in line_data[2] for gene_type in options.gene_ident): # line[2] for normal run
+                        start = int(line_data[3])
+                        stop = int(line_data[4])
+                        strand = line_data[6]
+                        gene_details = [start, stop, strand]
+                        if gene_details not in dna_regions[line_data[0]][2]:
+                            dna_regions[line_data[0]][2].append({count:gene_details}) # This will add to list
+                            count += 1
+            except IndexError:
+                continue
+    return dna_regions
+
+
+def fasta_load(fasta_in):
+    dna_regions = collections.OrderedDict()
+    first = True
+    if '>' in fasta_in.readline().rstrip():
+        fasta_in.seek(0)
+        #### Default for when presented with standard fasta file
+        for line in fasta_in:
+            line = line.strip()
+            if line.startswith('>') and first == False:  # Check if first seq in file
+                dna_region_length = len(seq)
+                dna_regions.update({dna_region_id: (seq, dna_region_length, list(), None)})
+                seq = ''
+                dna_region_id = line.split()[0].replace('>', '')
+            elif line.startswith('>'):
+                seq = ''
+                dna_region_id = line.split()[0].replace('>', '')
+            else:
+                seq += str(line)
+                first = False
+        dna_region_length = len(seq)
+        dna_regions.update({dna_region_id: (seq, dna_region_length, list(), None)})
+    elif '##' in  fasta_in.readline().rstrip(): # Clunky and may fall over
+        fasta_in.seek(0)
+        #### Called when presented with Prokka GFF file so must get fasta from inside it
+        ### Get to genome seq
+        at_FASTA = False
+        for line in fasta_in:  # Get gene loci from GFF - ID=Gene will also classify Pseudogenes as genes
+            if line.startswith('##FASTA'):  # Not to crash on empty lines in GFF
+                at_FASTA = True
+            elif at_FASTA == True:
+                line = line.strip()
+                if line.startswith('>') and first == False:  # Check if first seq in file
+                    dna_region_length = len(seq)
+                    dna_regions.update({dna_region_id: (seq, dna_region_length, list(), None)})
+                    seq = ''
+                    dna_region_id = line.split()[0].replace('>', '')
+                elif line.startswith('>'):
+                    seq = ''
+                    dna_region_id = line.split()[0].replace('>', '')
+                else:
+                    seq += str(line)
+                    first = False
+        dna_region_length = len(seq)
+        dna_regions.update({dna_region_id: (seq, dna_region_length, list(), None)})
+
+    return dna_regions
+
+
+def get_rep_metrics(result):
+    rep_metric_description = ('Percentage_of_Genes_Detected,Percentage_of_ORFs_that_Detected_a_Gene,'
+                              'Percent_Difference_of_All_ORFs,Median_Length_Difference,Percentage_of_Perfect_Matches,'
+                              'Median_Start_Difference_of_Matched_ORFs,Median_Stop_Difference_of_Matched_ORFs,'
+                              'Percentage_Difference_of_Matched_Overlapping_CDSs,Percent_Difference_of_Short-Matched-ORFs,'
+                              'Precision,Recall,False_Discovery_Rate')
+    rep_metrics = [result['rep_metrics']['Percentage_of_Genes_Detected'],
+                   result['rep_metrics']['Percentage_of_ORFs_that_Detected_a_Gene'],
+                   result['rep_metrics']['Percent_Difference_of_All_ORFs'],
+                   result['rep_metrics']['Median_Length_Difference'],
+                   result['rep_metrics']['Percentage_of_Perfect_Matches'],
+                   result['rep_metrics']['Median_Start_Difference_of_Matched_ORFs'],
+                   result['rep_metrics']['Median_Stop_Difference_of_Matched_ORFs'],
+                   result['rep_metrics']['Percentage_Difference_of_Matched_Overlapping_CDSs'],
+                   result['rep_metrics']['Percent_Difference_of_Short-Matched-ORFs'],
+                   result['rep_metrics']['Precision'],
+                   result['rep_metrics']['Recall'],
+                   result['rep_metrics']['False_Discovery_Rate']]
+    return rep_metric_description, rep_metrics
+
+
+def get_all_metrics(result):
+    all_metric_description = ('Number_of_ORFs,Percent_Difference_of_All_ORFs,Number_of_ORFs_that_Detected_a_Gene,'
+         'Percentage_of_ORFs_that_Detected_a_Gene,Number_of_Genes_Detected,Percentage_of_Genes_Detected,'
+         'Median_Length_of_All_ORFs,Median_Length_Difference,Minimum_Length_of_All_ORFs,Minimum_Length_Difference,'
+         'Maximum_Length_of_All_ORFs,Maximum_Length_Difference,Median_GC_content_of_All_ORFs,'
+         'Percent_Difference_of_All_ORFs_Median_GC,Median_GC_content_of_Matched_ORFs,'
+         'Percent_Difference_of_Matched_ORF_GC,Number_of_ORFs_which_Overlap_Another_ORF,'
+         'Percent_Difference_of_Overlapping_ORFs,Maximum_ORF_Overlap,Median_ORF_Overlap,'
+         'Number_of_Matched_ORFs_Overlapping_Another_ORF,Percentage_Difference_of_Matched_Overlapping_CDSs,'
+         'Maximum_Matched_ORF_Overlap,Median_Matched_ORF_Overlap,Number_of_Short-ORFs,Percent_Difference_of_Short-ORFs,'
+         'Number_of_Short-Matched-ORFs,Percent_Difference_of_Short-Matched-ORFs,Number_of_Perfect_Matches,'
+         'Percentage_of_Perfect_Matches,Number_of_Perfect_Starts,Percentage_of_Perfect_Starts,Number_of_Perfect_Stops,'
+         'Percentage_of_Perfect_Stops,Number_of_Out_of_Frame_ORFs,Number_of_Matched_ORFs_Extending_a_Coding_Region,'
+         'Percentage_of_Matched_ORFs_Extending_a_Coding_Region,Number_of_Matched_ORFs_Extending_Start_Region,'
+         'Percentage_of_Matched_ORFs_Extending_Start_Region,Number_of_Matched_ORFs_Extending_Stop_Region,'
+         'Percentage_of_Matched_ORFs_Extending_Stop_Region,Number_of_All_ORFs_on_Positive_Strand,'
+         'Percentage_of_All_ORFs_on_Positive_Strand,Number_of_All_ORFs_on_Negative_Strand,'
+         'Percentage_of_All_ORFs_on_Negative_Strand,Median_Start_Difference_of_Matched_ORFs,'
+         'Median_Stop_Difference_of_Matched_ORFs,ATG_Start_Percentage,GTG_Start_Percentage,TTG_Start_Percentage,'
+         'ATT_Start_Percentage,CTG_Start_Percentage,Other_Start_Codon_Percentage,TAG_Stop_Percentage,'
+         'TAA_Stop_Percentage,TGA_Stop_Percentage,Other_Stop_Codon_Percentage,True_Positive,False_Positive,'
+         'False_Negative,Precision,Recall,False_Discovery_Rate,Nucleotide_True_Positive,Nucleotide_False_Positive,'
+         'Nucleotide_True_Negative,Nucleotide_False_Negative,Nucleotide_Precision,Nucleotide_Recall,'
+         'Nucleotide_False_Discovery_Rate,ORF_Nucleotide_Coverage_of_Genome,Matched_ORF_Nucleotide_Coverage_of_Genome')
+    all_metrics = rep_metrics = [result['pred_metrics']['Number_of_ORFs'],
+                                    result['pred_metrics']['Percent_Difference_of_All_ORFs'],
+                                    result['pred_metrics']['Number_of_ORFs_that_Detected_a_Gene'],
+                                    result['pred_metrics']['Percentage_of_ORFs_that_Detected_a_Gene'],
+                                    result['pred_metrics']['Number_of_Genes_Detected'],
+                                    result['pred_metrics']['Percentage_of_Genes_Detected'],
+                                    result['pred_metrics']['Median_Length_of_All_ORFs'],
+                                    result['pred_metrics']['Median_Length_Difference'],
+                                    result['pred_metrics']['Minimum_Length_of_All_ORFs'],
+                                    result['pred_metrics']['Minimum_Length_Difference'],
+                                    result['pred_metrics']['Maximum_Length_of_All_ORFs'],
+                                    result['pred_metrics']['Maximum_Length_Difference'],
+                                    result['pred_metrics']['Median_GC_content_of_All_ORFs'],
+                                    result['pred_metrics']['Percent_Difference_of_All_ORFs_Median_GC'],
+                                    result['pred_metrics']['Median_GC_content_of_Matched_ORFs'],
+                                    result['pred_metrics']['Percent_Difference_of_Matched_ORF_GC'],
+                                    result['pred_metrics']['Number_of_ORFs_which_Overlap_Another_ORF'],
+                                    result['pred_metrics']['Percent_Difference_of_Overlapping_ORFs'],
+                                    result['pred_metrics']['Maximum_ORF_Overlap'],
+                                    result['pred_metrics']['Median_ORF_Overlap'],
+                                    result['pred_metrics']['Number_of_Matched_ORFs_Overlapping_Another_ORF'],
+                                    result['pred_metrics']['Percentage_Difference_of_Matched_Overlapping_CDSs'],
+                                    result['pred_metrics']['Maximum_Matched_ORF_Overlap'],
+                                    result['pred_metrics']['Median_Matched_ORF_Overlap'],
+                                    result['pred_metrics']['Number_of_Short-ORFs'],
+                                    result['pred_metrics']['Percent_Difference_of_Short-ORFs'],
+                                    result['pred_metrics']['Number_of_Short-Matched-ORFs'],
+                                    result['pred_metrics']['Percent_Difference_of_Short-Matched-ORFs'],
+                                    result['pred_metrics']['Number_of_Perfect_Matches'],
+                                    result['pred_metrics']['Percentage_of_Perfect_Matches'],
+                                    result['pred_metrics']['Number_of_Perfect_Starts'],
+                                    result['pred_metrics']['Percentage_of_Perfect_Starts'],
+                                    result['pred_metrics']['Number_of_Perfect_Stops'],
+                                    result['pred_metrics']['Percentage_of_Perfect_Stops'],
+                                    result['pred_metrics']['Number_of_Out_of_Frame_ORFs'],
+                                    result['pred_metrics']['Number_of_Matched_ORFs_Extending_a_Coding_Region'],
+                                    result['pred_metrics']['Percentage_of_Matched_ORFs_Extending_a_Coding_Region'],
+                                    result['pred_metrics']['Number_of_Matched_ORFs_Extending_Start_Region'],
+                                    result['pred_metrics']['Percentage_of_Matched_ORFs_Extending_Start_Region'],
+                                    result['pred_metrics']['Number_of_Matched_ORFs_Extending_Stop_Region'],
+                                    result['pred_metrics']['Percentage_of_Matched_ORFs_Extending_Stop_Region'],
+                                    result['pred_metrics']['Number_of_All_ORFs_on_Positive_Strand'],
+                                    result['pred_metrics']['Percentage_of_All_ORFs_on_Positive_Strand'],
+                                    result['pred_metrics']['Number_of_All_ORFs_on_Negative_Strand'],
+                                    result['pred_metrics']['Percentage_of_All_ORFs_on_Negative_Strand'],
+                                    result['pred_metrics']['Median_Start_Difference_of_Matched_ORFs'],
+                                    result['pred_metrics']['Median_Stop_Difference_of_Matched_ORFs'],
+                                    result['pred_metrics']['ATG_Start_Percentage'],
+                                    result['pred_metrics']['GTG_Start_Percentage'],
+                                    result['pred_metrics']['TTG_Start_Percentage'],
+                                    result['pred_metrics']['ATT_Start_Percentage'],
+                                    result['pred_metrics']['CTG_Start_Percentage'],
+                                    result['pred_metrics']['Other_Start_Codon_Percentage'],
+                                    result['pred_metrics']['TAG_Stop_Percentage'],
+                                    result['pred_metrics']['TAA_Stop_Percentage'],
+                                    result['pred_metrics']['TGA_Stop_Percentage'],
+                                    result['pred_metrics']['Other_Stop_Codon_Percentage'],
+                                    result['pred_metrics']['True_Positive'],
+                                    result['pred_metrics']['False_Positive'],
+                                    result['pred_metrics']['False_Negative'],
+                                    result['pred_metrics']['Precision'],
+                                    result['pred_metrics']['Recall'],
+                                    result['pred_metrics']['False_Discovery_Rate'],
+                                    result['pred_metrics']['Nucleotide_True_Positive'],
+                                    result['pred_metrics']['Nucleotide_False_Positive'],
+                                    result['pred_metrics']['Nucleotide_True_Negative'],
+                                    result['pred_metrics']['Nucleotide_False_Negative'],
+                                    result['pred_metrics']['Nucleotide_Precision'],
+                                    result['pred_metrics']['Nucleotide_Recall'],
+                                    result['pred_metrics']['Nucleotide_False_Discovery_Rate'],
+                                    result['pred_metrics']['ORF_Nucleotide_Coverage_of_Genome'],
+                                    result['pred_metrics']['Matched_ORF_Nucleotide_Coverage_of_Genome']]
+
+
+    return all_metric_description, all_metrics

{orforise-1.4.3.dist-info → orforise-1.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ORForise
-Version: 1.4.3
+Version: 1.5.0
 Summary: ORForise - Platform for analysing and comparing Prokaryote CoDing Sequence (CDS) Gene Predictions.
 Home-page: https://github.com/NickJD/ORForise
 Author: Nicholas Dimonaco
@@ -63,7 +63,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: Annotation_Compare.py [-h] -dna GENOME_DNA -ref REFERENCE_ANNOTATION -t TOOL -tp TOOL_PREDICTION
                              [-rt REFERENCE_TOOL] [-o OUTNAME] [-v {True,False}]
 
-ORForise v1.4.3: Annotatione-Compare Run Parameters.
+ORForise v1.5.0: Annotatione-Compare Run Parameters.
 
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -113,7 +113,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: Aggregate_Compare.py [-h] -dna GENOME_DNA -t TOOLS -tp TOOL_PREDICTIONS -ref REFERENCE_ANNOTATION
                             [-rt REFERENCE_TOOL] [-o OUTNAME] [-v {True,False}]
 
-ORForise v1.4.3: Aggregate-Compare Run Parameters.
+ORForise v1.5.0: Aggregate-Compare Run Parameters.
 
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -267,7 +267,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: GFF_Adder.py [-h] -dna GENOME_DNA -ref REFERENCE_ANNOTATION -at ADDITIONAL_TOOL -add ADDITIONAL_ANNOTATION -o
                     OUTPUT_FILE [-rt REFERENCE_TOOL] [-gi GENE_IDENT] [-gene_ident GENE_IDENT] [-olap OVERLAP]
 
-ORForise v1.4.3: GFF-Adder Run Parameters.
+ORForise v1.5.0: GFF-Adder Run Parameters.
 
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on
@@ -329,7 +329,7 @@ Please report any issues to: https://github.com/NickJD/ORForise/issues
 usage: GFF_Intersector.py [-h] -dna GENOME_DNA -ref REFERENCE_ANNOTATION -at ADDITIONAL_TOOL -add
                           ADDITIONAL_ANNOTATION -o OUTPUT_FILE [-rt REFERENCE_TOOL] [-gi GENE_IDENT] [-cov COVERAGE]
 
-ORForise v1.4.3: GFF-Intersector Run Parameters.
+ORForise v1.5.0: GFF-Intersector Run Parameters.
 
 Required Arguments:
   -dna GENOME_DNA       Genome DNA file (.fa) which both annotations are based on

{orforise-1.4.3.dist-info → orforise-1.5.0.dist-info}/RECORD

@@ -1,56 +1,56 @@
-ORForise/Aggregate_Compare.py,sha256=cY0PdA_SnywPcqwPomXmEHaZ6OUDS9k_QeLtXnewjiA,10648
-ORForise/Annotation_Compare.py,sha256=6y_RiJg0q9g4Bcwy8Lxi5gSDkMLwm6uYJG2evxnKAhU,10228
-ORForise/Comparator.py,sha256=kGRn7_CYKULI5xV7IH2RpRIP0xpj_OfPxO4iGdLBnKQ,45081
+ORForise/Aggregate_Compare.py,sha256=WzP34E4YqkOBXlE9obZfPf3Sp1Gwl40WPqE7PsGntqk,22977
+ORForise/Annotation_Compare.py,sha256=4o2bXOaIJ7gpwAfso5efDpu9GhUf36okVoSZT4KFbQU,18482
+ORForise/Comparator.py,sha256=SJRbTFqn9fLm3sFfhT2J6fhxnPb_JzU7zAA75LLyHZU,47189
 ORForise/GFF_Adder.py,sha256=-BlF6DQWcbhyYT88M0ZkoaWA2YDDxsby-7jksfeJN1Q,14057
 ORForise/GFF_Intersector.py,sha256=EcDKyJr_47066kma2CguMf3uwzB2tYomPDFjmoX8IoU,9900
 ORForise/StORForise.py,sha256=2QU6q3wPK6iqtyKg2jEVwFTB4bSymyc-mSpk7T8yNaY,5431
 ORForise/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/utils.py,sha256=39OeKjNTRkyoEqxsTCrcwucbrkKOq3CTd6wEm1p7MOA,1099
+ORForise/utils.py,sha256=9HJk3Yx4ohrulEDI_ZriLFCVLmisY-Gx1xF1uNDqnnY,15548
 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
-ORForise/ORForise_Analysis/genome_Metrics.py,sha256=qsv9VNaeb6Z2-k7hmlNxXEGCzghHnxnYY-H718bMjhs,10085
+ORForise/ORForise_Analysis/genome_Metrics.py,sha256=Vra7X6AVJoBvjT6EAO819dPpqAOnWMlwSkWhwTVWNZk,10417
 ORForise/ORForise_Analysis/hypothetical_gene_predictions.py,sha256=6SRNrNKUOHOnwsP96s1nI25oCj2oY4_2NcONO0EXj0c,3479
 ORForise/ORForise_Analysis/missed_Gene_Metrics.py,sha256=ir54WJ_UpY_1UQd9kz67tTDwZvt7NSb20Yz0yVKVX3w,10890
 ORForise/ORForise_Analysis/parital_Match_Analysis.py,sha256=a-f5MejmQftgrCUDtWV69Tp-UOYyJlgM77zf4v-MEVY,9515
 ORForise/ORForise_Analysis/result_File_Analysis.py,sha256=ZHKW6sRW45NEExBqLVDnxpBPwsZyGTU-vm1TjawFsgY,9886
 ORForise/ORForise_Analysis/start_Codon_Substitution.py,sha256=x_I7EGR0KqV3uos_UEJI79JKnuhjwqD-1XlJ0SR82uA,6114
 ORForise/Tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/Augustus/Augustus.py,sha256=eeRiSWXCKKehLx2Nlktlfc-bnsqiWhLV5pvY_KVq8NI,1323
+ORForise/Tools/Augustus/Augustus.py,sha256=rEZ3h3eHrCfMFDorXxF5h0j4Wr5vTHG_rrQ-1sOiRFs,1717
 ORForise/Tools/Augustus/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/Balrog/Balrog.py,sha256=DRHl9ZHft5NJ38O0WXHSGqAQRwVXxrTzo7O-0-AP4wA,1387
+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=mOjHQBJAVyav0HkpRvFmZtCCkeH4KhnBIeB934bOVNs,1323
+ORForise/Tools/EasyGene/EasyGene.py,sha256=_1gGRYulpnhgB2xL7ZsnkXF4U8O9XgC0XQTZq7XubC4,1752
 ORForise/Tools/EasyGene/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/FGENESB/FGENESB.py,sha256=TCvsGzfZ41tKkgF6TaBFpsuZBrueSygmoBco7d6o8-8,1480
+ORForise/Tools/FGENESB/FGENESB.py,sha256=3Jxe2DzUTG77wllSJpN__c_4cdl_gcj2idLXNMkv1Cs,1871
 ORForise/Tools/FGENESB/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/FragGeneScan/FragGeneScan.py,sha256=l3lqIxRUEx7lIV8Odhm6NsTgfHTrriYXcFoA4WW-E-E,1376
+ORForise/Tools/FragGeneScan/FragGeneScan.py,sha256=ofywMVF-FBM4s3FPwoWsJKQUX0T_iTCqlTXaeOxHw4g,1770
 ORForise/Tools/FragGeneScan/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/GFF/GFF.py,sha256=RF-PtryGTV0Lgz6sT7L5idVEwCF_MP0prIcfaUYCoAQ,2806
+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=9WQNSdlhQOpHQ4zcxncrTb2Lt6tiUB8Y0FBoyGxG_Yc,1723
+ORForise/Tools/GLIMMER_3/GLIMMER_3.py,sha256=McFulHAHV4e3ROVmTn0JSz-r0TTqiEor0MsemsIkSjc,2124
 ORForise/Tools/GLIMMER_3/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/GeneMark/GeneMark.py,sha256=l2Fptz4o-EFbZvFalGS4RNBcitJcElq3xQ4LPIrbAQ4,5374
+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=FEp-Kp-pMvY-GiZMj0gI2kQEnHAHaR3njnq8rJJBxVo,1346
+ORForise/Tools/GeneMark_HA/GeneMark_HA.py,sha256=nfMEAszBEZw4zhhW3VtZt6yqJprXkydVAR1a3RrAm1k,1737
 ORForise/Tools/GeneMark_HA/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/GeneMark_HMM/GeneMark_HMM.py,sha256=sfW87XhLbkpJas0Ao7u0YM5DKVPEQyFmIN-exW3XshU,1359
+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=gU5lomUseYlUIl3iAy0NQUqAju4tnUntf5ScP4aoRfk,1334
+ORForise/Tools/GeneMark_S/GeneMark_S.py,sha256=56FQ-u-uvZFN41Ii0tGCUuBWsZaPaxvigbuOVg_4QCw,1722
 ORForise/Tools/GeneMark_S/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/GeneMark_S_2/GeneMark_S_2.py,sha256=EclP7u5Q7jGtmFJs2u7DLU_4dW8-LPcADAeOyAXPJ-U,1468
+ORForise/Tools/GeneMark_S_2/GeneMark_S_2.py,sha256=OxYt_jsH1j61we45O3y-gf-nwnKm1JFUK2b9q1W9rVE,1799
 ORForise/Tools/GeneMark_S_2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/MetaGene/MetaGene.py,sha256=N821p7fbPlDTHsDw8_Riqm2P2ZUqeGb85rhu66xZbFQ,1334
+ORForise/Tools/MetaGene/MetaGene.py,sha256=sQ5tj-yWEKh4BDI3Hiw8KYSZv6fyN0DpZbp4BpYnBwY,1716
 ORForise/Tools/MetaGene/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/MetaGeneAnnotator/MetaGeneAnnotator.py,sha256=NJIk_8JK4P2Z2FgMWgIHEGE0K-kbJi5T1e4B_Z2oceQ,1469
+ORForise/Tools/MetaGeneAnnotator/MetaGeneAnnotator.py,sha256=pfQgzwwBz54kVsLWH7GkZ85XCZ9rqj4gYfPdX8O3zWg,1882
 ORForise/Tools/MetaGeneAnnotator/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/MetaGeneMark/MetaGeneMark.py,sha256=vIJxIBmfxMKut19nQWBc_C94V9oKDa6Eu4vEKnDrVf0,1452
+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=8-MJrEbhSL4sbNjI1JEUZ1jm5PRz9OUBdlyD8qsSLjI,1427
+ORForise/Tools/Prodigal/Prodigal.py,sha256=y8bnh9_A4DmTJAsKqD_1S_d9ak56ZXsnUiFhrGudNcw,1758
 ORForise/Tools/Prodigal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ORForise/Tools/Prokka/Prokka.py,sha256=akq0lu2TbOqLt-GI27a0Zbh8yfJIVAHBi07FtCfCAcY,1537
+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=mljwJO1iNy1HxcuqHAqH5ODDuLomw9HcRwOEJDScNQc,1609
+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
@@ -58,11 +58,11 @@ ORForise/Tools/StORF_Undetected/Completely_Undetected/Completey_Undetected.py,sh
 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/TransDecoder/TransDecoder.py,sha256=utnL52il6BGbbBxoizYPnY1qwBGeslYDCa5xU9RGWPg,1384
+ORForise/Tools/TransDecoder/TransDecoder.py,sha256=YlYxxicuP8xjwNkAKbHOdfaurvOHH0whYxaiB6B2kjs,1778
 ORForise/Tools/TransDecoder/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-orforise-1.4.3.dist-info/licenses/LICENSE,sha256=eAL1bBUjSMCdvudcn9E3sbujCBCa839cqXxauONDbSU,32476
-orforise-1.4.3.dist-info/METADATA,sha256=7JZBTCxggexbQcUsHTNdZBKUQ1laUnINv0vIGq_6k0k,36479
-orforise-1.4.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-orforise-1.4.3.dist-info/entry_points.txt,sha256=ss2cbLmljRmLIeZ3t48p_06NuQuRiKeA11IOUYg_uiY,246
-orforise-1.4.3.dist-info/top_level.txt,sha256=7kmFicUFY65FJmioc0cpZtXVz93V7KSKvZVWpGz5Hyk,9
-orforise-1.4.3.dist-info/RECORD,,
+orforise-1.5.0.dist-info/licenses/LICENSE,sha256=eAL1bBUjSMCdvudcn9E3sbujCBCa839cqXxauONDbSU,32476
+orforise-1.5.0.dist-info/METADATA,sha256=6H1gu2ry-qd8jkhbc90F5aJTAFF48K1jCRzOEeTW7QI,36479
+orforise-1.5.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+orforise-1.5.0.dist-info/entry_points.txt,sha256=VXYTkaTIjYu4LhZjhRyCezsg7n9bNeG7W2l4FTwCopE,474
+orforise-1.5.0.dist-info/top_level.txt,sha256=7kmFicUFY65FJmioc0cpZtXVz93V7KSKvZVWpGz5Hyk,9
+orforise-1.5.0.dist-info/RECORD,,

{orforise-1.4.3.dist-info → orforise-1.5.0.dist-info}/entry_points.txt

@@ -4,3 +4,8 @@ Annotation-Compare = ORForise.Annotation_Compare:main
 GFF-Adder = ORForise.GFF_Adder:main
 GFF-Intersector = ORForise.GFF_Intersector:main
 StORForise = ORForise.StORForise:main
+aggregate-compare = ORForise.Aggregate_Compare:main
+annotation-compare = ORForise.Annotation_Compare:main
+gff-adder = ORForise.GFF_Adder:main
+gff-intersector = ORForise.GFF_Intersector:main
+storforise = ORForise.StORForise:main