Mercurial > repos > cpt > cpt_lipop_conversion
changeset 0:adde21b6bdb3 draft
Uploaded
| author | cpt |
|---|---|
| date | Fri, 13 May 2022 05:18:31 +0000 |
| parents | |
| children | 95be3ae33abc |
| files | cpt_lipop_conv/cpt-macros.xml cpt_lipop_conv/gff3.py cpt_lipop_conv/lipoP_to_gff3.py cpt_lipop_conv/lipoP_to_gff3.xml cpt_lipop_conv/macros.xml cpt_lipop_conv/test-data/LipoToGFF_In.gff3 cpt_lipop_conv/test-data/LipoToGFF_In.txt cpt_lipop_conv/test-data/LipoToGFF_Out.gff3 |
| diffstat | 8 files changed, 1360 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_lipop_conv/cpt-macros.xml Fri May 13 05:18:31 2022 +0000 @@ -0,0 +1,115 @@ +<?xml version="1.0"?> +<macros> + <xml name="gff_requirements"> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package" version="1.65">biopython</requirement> + <requirement type="package" version="2.12.1">requests</requirement> + <yield/> + </requirements> + <version_command> + <![CDATA[ + cd $__tool_directory__ && git rev-parse HEAD + ]]> + </version_command> + </xml> + <xml name="citation/mijalisrasche"> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex">@unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-crr"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Ross}, + title = {CPT Galaxy Tools}, + year = {2020-}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-2020"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Criscione}, + title = {CPT Galaxy Tools}, + year = {2019-2021}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-2020-AJC-solo"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Criscione}, + title = {CPT Galaxy Tools}, + year = {2019-2021}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-clm"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Maughmer}, + title = {CPT Galaxy Tools}, + year = {2017-2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="sl-citations-clm"> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Maughmer}, + title = {CPT Galaxy Tools}, + year = {2017-2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_lipop_conv/gff3.py Fri May 13 05:18:31 2022 +0000 @@ -0,0 +1,346 @@ +import copy +import logging + +log = logging.getLogger() +log.setLevel(logging.WARN) + + +def feature_lambda( + feature_list, + test, + test_kwargs, + subfeatures=True, + parent=None, + invert=False, + recurse=True, +): + """Recursively search through features, testing each with a test function, yielding matches. + + GFF3 is a hierachical data structure, so we need to be able to recursively + search through features. E.g. if you're looking for a feature with + ID='bob.42', you can't just do a simple list comprehension with a test + case. You don't know how deeply burried bob.42 will be in the feature tree. This is where feature_lambda steps in. + + :type feature_list: list + :param feature_list: an iterable of features + + :type test: function reference + :param test: a closure with the method signature (feature, **kwargs) where + the kwargs are those passed in the next argument. This + function should return True or False, True if the feature is + to be yielded as part of the main feature_lambda function, or + False if it is to be ignored. This function CAN mutate the + features passed to it (think "apply"). + + :type test_kwargs: dictionary + :param test_kwargs: kwargs to pass to your closure when it is called. + + :type subfeatures: boolean + :param subfeatures: when a feature is matched, should just that feature be + yielded to the caller, or should the entire sub_feature + tree for that feature be included? subfeatures=True is + useful in cases such as searching for a gene feature, + and wanting to know what RBS/Shine_Dalgarno_sequences + are in the sub_feature tree (which can be accomplished + with two feature_lambda calls). subfeatures=False is + useful in cases when you want to process (and possibly + return) the entire feature tree, such as applying a + qualifier to every single feature. + + :type invert: boolean + :param invert: Negate/invert the result of the filter. + + :rtype: yielded list + :return: Yields a list of matching features. + """ + # Either the top level set of [features] or the subfeature attribute + for feature in feature_list: + feature._parent = parent + if not parent: + # Set to self so we cannot go above root. + feature._parent = feature + test_result = test(feature, **test_kwargs) + # if (not invert and test_result) or (invert and not test_result): + if invert ^ test_result: + if not subfeatures: + feature_copy = copy.deepcopy(feature) + feature_copy.sub_features = list() + yield feature_copy + else: + yield feature + + if recurse and hasattr(feature, "sub_features"): + for x in feature_lambda( + feature.sub_features, + test, + test_kwargs, + subfeatures=subfeatures, + parent=feature, + invert=invert, + recurse=recurse, + ): + yield x + + +def fetchParent(feature): + if not hasattr(feature, "_parent") or feature._parent is None: + return feature + else: + return fetchParent(feature._parent) + + +def feature_test_true(feature, **kwargs): + return True + + +def feature_test_type(feature, **kwargs): + if "type" in kwargs: + return str(feature.type).upper() == str(kwargs["type"]).upper() + elif "types" in kwargs: + for x in kwargs["types"]: + if str(feature.type).upper() == str(x).upper(): + return True + return False + raise Exception("Incorrect feature_test_type call, need type or types") + + +def feature_test_qual_value(feature, **kwargs): + """Test qualifier values. + + For every feature, check that at least one value in + feature.quailfiers(kwargs['qualifier']) is in kwargs['attribute_list'] + """ + if isinstance(kwargs["qualifier"], list): + for qualifier in kwargs["qualifier"]: + for attribute_value in feature.qualifiers.get(qualifier, []): + if attribute_value in kwargs["attribute_list"]: + return True + else: + for attribute_value in feature.qualifiers.get(kwargs["qualifier"], []): + if attribute_value in kwargs["attribute_list"]: + return True + return False + + +def feature_test_location(feature, **kwargs): + if "strand" in kwargs: + if feature.location.strand != kwargs["strand"]: + return False + + return feature.location.start <= kwargs["loc"] <= feature.location.end + + +def feature_test_quals(feature, **kwargs): + """ + Example:: + + a = Feature(qualifiers={'Note': ['Some notes', 'Aasdf']}) + + # Check if a contains a Note + feature_test_quals(a, {'Note': None}) # Returns True + feature_test_quals(a, {'Product': None}) # Returns False + + # Check if a contains a note with specific value + feature_test_quals(a, {'Note': ['ome']}) # Returns True + + # Check if a contains a note with specific value + feature_test_quals(a, {'Note': ['other']}) # Returns False + """ + for key in kwargs: + if key not in feature.qualifiers: + return False + + # Key is present, no value specified + if kwargs[key] is None: + return True + + # Otherwise there is a key value we're looking for. + # so we make a list of matches + matches = [] + # And check all of the feature qualifier valuse + for value in feature.qualifiers[key]: + # For that kwargs[key] value + for x in kwargs[key]: + matches.append(x in value) + + # If none matched, then we return false. + if not any(matches): + return False + + return True + + +def feature_test_contains(feature, **kwargs): + if "index" in kwargs: + return feature.location.start < kwargs["index"] < feature.location.end + elif "range" in kwargs: + return ( + feature.location.start < kwargs["range"]["start"] < feature.location.end + and feature.location.start < kwargs["range"]["end"] < feature.location.end + ) + else: + raise RuntimeError("Must use index or range keyword") + + +def get_id(feature=None, parent_prefix=None): + result = "" + if parent_prefix is not None: + result += parent_prefix + "|" + if "locus_tag" in feature.qualifiers: + result += feature.qualifiers["locus_tag"][0] + elif "gene" in feature.qualifiers: + result += feature.qualifiers["gene"][0] + elif "Gene" in feature.qualifiers: + result += feature.qualifiers["Gene"][0] + elif "product" in feature.qualifiers: + result += feature.qualifiers["product"][0] + elif "Product" in feature.qualifiers: + result += feature.qualifiers["Product"][0] + elif "Name" in feature.qualifiers: + result += feature.qualifiers["Name"][0] + else: + return feature.id + # Leaving in case bad things happen. + # result += '%s_%s_%s_%s' % ( + # feature.id, + # feature.location.start, + # feature.location.end, + # feature.location.strand + # ) + return result + + +def get_gff3_id(gene): + return gene.qualifiers.get("Name", [gene.id])[0] + + +def ensure_location_in_bounds(start=0, end=0, parent_length=0): + # This prevents frameshift errors + while start < 0: + start += 3 + while end < 0: + end += 3 + while start > parent_length: + start -= 3 + while end > parent_length: + end -= 3 + return (start, end) + + +def coding_genes(feature_list): + for x in genes(feature_list): + if ( + len( + list( + feature_lambda( + x.sub_features, + feature_test_type, + {"type": "CDS"}, + subfeatures=False, + ) + ) + ) + > 0 + ): + yield x + + +def genes(feature_list, feature_type="gene", sort=False): + """ + Simple filter to extract gene features from the feature set. + """ + + if not sort: + for x in feature_lambda( + feature_list, feature_test_type, {"type": feature_type}, subfeatures=True + ): + yield x + else: + data = list(genes(feature_list, feature_type=feature_type, sort=False)) + data = sorted(data, key=lambda feature: feature.location.start) + for x in data: + yield x + + +def wa_unified_product_name(feature): + """ + Try and figure out a name. We gave conflicting instructions, so + this isn't as trivial as it should be. Sometimes it will be in + 'product' or 'Product', othertimes in 'Name' + """ + # Manually applied tags. + protein_product = feature.qualifiers.get( + "product", feature.qualifiers.get("Product", [None]) + )[0] + + # If neither of those are available ... + if protein_product is None: + # And there's a name... + if "Name" in feature.qualifiers: + if not is_uuid(feature.qualifiers["Name"][0]): + protein_product = feature.qualifiers["Name"][0] + + return protein_product + + +def is_uuid(name): + return name.count("-") == 4 and len(name) == 36 + + +def get_rbs_from(gene): + # Normal RBS annotation types + rbs_rbs = list( + feature_lambda( + gene.sub_features, feature_test_type, {"type": "RBS"}, subfeatures=False + ) + ) + rbs_sds = list( + feature_lambda( + gene.sub_features, + feature_test_type, + {"type": "Shine_Dalgarno_sequence"}, + subfeatures=False, + ) + ) + # Fraking apollo + apollo_exons = list( + feature_lambda( + gene.sub_features, feature_test_type, {"type": "exon"}, subfeatures=False + ) + ) + apollo_exons = [x for x in apollo_exons if len(x) < 10] + # These are more NCBI's style + regulatory_elements = list( + feature_lambda( + gene.sub_features, + feature_test_type, + {"type": "regulatory"}, + subfeatures=False, + ) + ) + rbs_regulatory = list( + feature_lambda( + regulatory_elements, + feature_test_quals, + {"regulatory_class": ["ribosome_binding_site"]}, + subfeatures=False, + ) + ) + # Here's hoping you find just one ;) + return rbs_rbs + rbs_sds + rbs_regulatory + apollo_exons + + +def nice_name(record): + """ + get the real name rather than NCBI IDs and so on. If fails, will return record.id + """ + name = record.id + likely_parental_contig = list(genes(record.features, feature_type="contig")) + if len(likely_parental_contig) == 1: + name = likely_parental_contig[0].qualifiers.get("organism", [name])[0] + return name + + +def fsort(it): + for i in sorted(it, key=lambda x: int(x.location.start)): + yield i
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_lipop_conv/lipoP_to_gff3.py Fri May 13 05:18:31 2022 +0000 @@ -0,0 +1,110 @@ +#!/usr/bin/env python +import sys +import copy +import argparse +from CPT_GFFParser import gffParse, gffWrite, gffSeqFeature +from Bio.Seq import Seq +from Bio.SeqRecord import SeqRecord +from Bio.SeqFeature import FeatureLocation +from gff3 import feature_lambda, feature_test_type, get_id + + +def lipoP_gff(lipoIn, gff3In, jBrowseOut, filterSP2): + + orgIDs = {} + orgID = "" + + # Take and parse the txt output into a sequence of records + # Dict of X records, with the ID as key and an array Y of each cleavage site as the value, + for row in lipoIn: + if row.startswith("#"): + orgID = "" + continue + + rowElem = row.split("\t") + + orgID = rowElem[0] + + if filterSP2: + if rowElem[2] == "CleavII": + if not (orgID in orgIDs.keys()): + orgIDs[orgID] = [] + orgIDs[orgID].append(int(rowElem[3])) # , int(rowElem[4]))) + else: + if rowElem[2] in "CleavII": + if not (orgID in orgIDs.keys()): + orgIDs[orgID] = [] + orgIDs[orgID].append(int(rowElem[3])) # , int(rowElem[4]))) + + + # Rebase + for gff in gffParse(gff3In): + keepSeq = [] + for xRec in gff.features: + cdss = list( + feature_lambda( + xRec.sub_features, + feature_test_type, + {"type": "CDS"}, + subfeatures=False, + ) + ) + findCleave = "" + cdsOff = 0 + for cds in cdss: + if cds.id in orgIDs: + findCleave = cds.id + break + cdsOff += 1 + if findCleave == "": + if not jBrowseOut: + keepSeq.append(xRec) + continue + + #if jBrowseOut: + # xRec.sub_features = [] + + i = 0 + for cleaveBase in orgIDs[findCleave]: + tempQuals = xRec.qualifiers.copy() + i += 1 + tempQuals["ID"] = xRec.id + "_cleavage_" + str(i) + + xRec.sub_features.append( + gffSeqFeature( + FeatureLocation( + cdss[cdsOff].location.start + (cleaveBase * 3) - 1, + cdss[cdsOff].location.start + (cleaveBase * 3) + 1, + ), + type="cleavage_site", + strand=xRec.location.strand, + qualifiers=tempQuals, + ) + ) + keepSeq.append(xRec) + + gff.features = keepSeq + gffWrite([gff], sys.stdout) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="add parent gene features to CDSs") + parser.add_argument( + "lipoIn", type=argparse.FileType("r"), help="LipoP tool's .txt output" + ) + parser.add_argument( + "gff3In", type=argparse.FileType("r"), help="GFF3 to rebase LipoP results" + ) + parser.add_argument( + "--jBrowseOut", + type=bool, + default=False, + help="Prepare Output for jBrowse instance", + ) + parser.add_argument( + "--filterSP2", + action='store_true', + help="Filter for only SPII sites", + ) + args = parser.parse_args() + lipoP_gff(**vars(args))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_lipop_conv/lipoP_to_gff3.xml Fri May 13 05:18:31 2022 +0000 @@ -0,0 +1,54 @@ +<tool id="edu.tamu.cpt.gff3.lipoP_to_gff3" name= "LipoP to GFF3" version="1.0"> + <description>Adds LipoP results to GFF3</description> + <macros> + <import>macros.xml</import> + <import>cpt-macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ +python $__tool_directory__/lipoP_to_gff3.py + +"$lipoIn" +"$gff3In" +--jBrowseOut "$jBrowseOut" +$filterSP2 +> $stdout + +]]></command> + <inputs> + <param label="LipoP Output" name="lipoIn" type="data" format="txt"/> + <param label="GFF3 for Rebasing" name="gff3In" type="data" format="gff3"/> + <param label="Output to jBrowse" name="jBrowseOut" type="boolean" truevalue="True" falsevalue="" help="Strip non-cleavage features from GFF3 (for viewing in Apollo)"/> + <param name="filterSP2" truevalue="--filterSP2" falsevalue="" type="boolean" label="Filter for only SPII Cleavage sites" checked="true"/> + </inputs> + <outputs> + <data format="gff3" name="stdout"/> + </outputs> + <tests> + <test> + <param name="lipoIn" value="LipoToGFF_In.txt" /> + <param name="gff3In" value="LipoToGFF_In.gff3" /> + <param name="jBrowseOut" value="True" /> + <param name="filterSP2" value="True" /> + <output name="stdout" value="LipoToGFF_Out.gff3" /> + </test> + </tests> + <help><![CDATA[ +**What it does** + +Adds the cleavage sites from a LipoP run to a GFF3 file's feature list. Must use +the .txt output of LipoP (ensure .html is turned off). The most common way this +tool will be utilized is to take a GFF3, use the GFF3 Feature Sequence Export +tool (https://cpt.tamu.edu/galaxy/root?tool_id=edu.tamu.cpt.gff3.export_seq) to +get a multi-FASTA of the CDSs, run that multi-FASTA through LipoP, and then +recombine the LipoP results with the original GFF3 file with this tool. + +Currently, only CleavII results will be added with this tool. + +"Output to jBrowse" will remove all gene features that do not have a CleavII +result from the LipoP, and remove all sub features of the gene except for the +cleavage sites. This is useful for viewing in Apollo, but should most likely +not be used if you plan to run this output through more tools. + ]]></help> + <expand macro="citations-2020" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_lipop_conv/macros.xml Fri May 13 05:18:31 2022 +0000 @@ -0,0 +1,85 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.6">python</requirement> + <requirement type="package" version="1.77">biopython</requirement> + <requirement type="package" version="1.1.3">cpt_gffparser</requirement> + <yield/> + </requirements> + </xml> + <token name="@BLAST_TSV@"> + "$blast_tsv" + </token> + <xml name="blast_tsv"> + <param label="Blast Results" help="TSV/tabular (25 Column)" + name="blast_tsv" type="data" format="tabular" /> + </xml> + + <token name="@BLAST_XML@"> + "$blast_xml" + </token> + <xml name="blast_xml"> + <param label="Blast Results" help="XML format" + name="blast_xml" type="data" format="blastxml" /> + </xml> + <xml name="gff3_with_fasta"> + <param label="Genome Sequences" name="fasta" type="data" format="fasta" /> + <param label="Genome Annotations" name="gff3" type="data" format="gff3" /> + </xml> + <xml name="genome_selector"> + <conditional name="reference_genome"> + <param name="reference_genome_source" type="select" label="Reference Genome"> + <option value="history" selected="True">From History</option> + <option value="cached">Locally Cached</option> + </param> + <when value="cached"> + <param name="fasta_indexes" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"/> + </param> + </when> + <when value="history"> + <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> + </when> + </conditional> + </xml> + <xml name="gff3_input"> + <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> + </xml> + <xml name="input/gff3+fasta"> + <expand macro="gff3_input" /> + <expand macro="genome_selector" /> + </xml> + <token name="@INPUT_GFF@"> + "$gff3_data" + </token> + <token name="@INPUT_FASTA@"> +#if str($reference_genome.reference_genome_source) == 'cached': + "${reference_genome.fasta_indexes.fields.path}" +#else if str($reference_genome.reference_genome_source) == 'history': + genomeref.fa +#end if + </token> + <token name="@GENOME_SELECTOR_PRE@"> +#if $reference_genome.reference_genome_source == 'history': + ln -s $reference_genome.genome_fasta genomeref.fa; +#end if + </token> + <token name="@GENOME_SELECTOR@"> +#if str($reference_genome.reference_genome_source) == 'cached': + "${reference_genome.fasta_indexes.fields.path}" +#else if str($reference_genome.reference_genome_source) == 'history': + genomeref.fa +#end if + </token> + <xml name="input/fasta"> + <param label="Fasta file" name="sequences" type="data" format="fasta"/> + </xml> + + <token name="@SEQUENCE@"> + "$sequences" + </token> + <xml name="input/fasta/protein"> + <param label="Protein fasta file" name="sequences" type="data" format="fasta"/> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_lipop_conv/test-data/LipoToGFF_In.gff3 Fri May 13 05:18:31 2022 +0000 @@ -0,0 +1,302 @@ +##gff-version 3 +##sequence-region testseq_2018-03-08 1 9216 +testseq_2018-03-08 cpt.fixModel gene 52 147 . - . ID=ORF.0.472_0.8077298255 +testseq_2018-03-08 cpt.fixModel mRNA 52 147 . - . ID=ORF.0.472_0.8077298255.mRNA;Parent=ORF.0.472_0.8077298255 +testseq_2018-03-08 getOrfsOrCds CDS 52 147 . - 0 ID=ORF.0.472_0.8077298255.CDS;Parent=ORF.0.472_0.8077298255.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 160 162 . - . ID=ORF.0.472_0.8077298255.rbs-0;Parent=ORF.0.472_0.8077298255 +testseq_2018-03-08 cpt.fixModel gene 154 339 . - . ID=ORF.0.465_0.466377183402 +testseq_2018-03-08 cpt.fixModel mRNA 154 339 . - . ID=ORF.0.465_0.466377183402.mRNA;Parent=ORF.0.465_0.466377183402 +testseq_2018-03-08 getOrfsOrCds CDS 154 339 . - 0 ID=ORF.0.465_0.466377183402.CDS;Parent=ORF.0.465_0.466377183402.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 347 349 . - . ID=ORF.0.465_0.466377183402.rbs-0;Parent=ORF.0.465_0.466377183402 +testseq_2018-03-08 cpt.fixModel gene 154 324 . - . ID=ORF.0.466_0.685859290271 +testseq_2018-03-08 cpt.fixModel mRNA 154 324 . - . ID=ORF.0.466_0.685859290271.mRNA;Parent=ORF.0.466_0.685859290271 +testseq_2018-03-08 getOrfsOrCds CDS 154 324 . - 0 ID=ORF.0.466_0.685859290271.CDS;Parent=ORF.0.466_0.685859290271.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 335 337 . - . ID=ORF.0.466_0.685859290271.rbs-0;Parent=ORF.0.466_0.685859290271 +testseq_2018-03-08 cpt.fixModel gene 154 297 . - . ID=ORF.0.468_0.803001272192 +testseq_2018-03-08 cpt.fixModel mRNA 154 297 . - . ID=ORF.0.468_0.803001272192.mRNA;Parent=ORF.0.468_0.803001272192 +testseq_2018-03-08 getOrfsOrCds CDS 154 297 . - 0 ID=ORF.0.468_0.803001272192.CDS;Parent=ORF.0.468_0.803001272192.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 306 311 . - . ID=ORF.0.468_0.803001272192.rbs-0;Parent=ORF.0.468_0.803001272192 +testseq_2018-03-08 cpt.fixModel gene 314 490 . - . ID=ORF.0.708_0.889453606077 +testseq_2018-03-08 cpt.fixModel mRNA 314 490 . - . ID=ORF.0.708_0.889453606077.mRNA;Parent=ORF.0.708_0.889453606077 +testseq_2018-03-08 getOrfsOrCds CDS 314 490 . - 0 ID=ORF.0.708_0.889453606077.CDS;Parent=ORF.0.708_0.889453606077.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 500 502 . - . ID=ORF.0.708_0.889453606077.rbs-0;Parent=ORF.0.708_0.889453606077 +testseq_2018-03-08 cpt.fixModel gene 487 672 . - . ID=ORF.0.458_0.61399204562 +testseq_2018-03-08 cpt.fixModel mRNA 487 672 . - . ID=ORF.0.458_0.61399204562.mRNA;Parent=ORF.0.458_0.61399204562 +testseq_2018-03-08 getOrfsOrCds CDS 487 672 . - 0 ID=ORF.0.458_0.61399204562.CDS;Parent=ORF.0.458_0.61399204562.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 678 681 . - . ID=ORF.0.458_0.61399204562.rbs-0;Parent=ORF.0.458_0.61399204562 +testseq_2018-03-08 cpt.fixModel gene 487 666 . - . ID=ORF.0.459_0.323250347541 +testseq_2018-03-08 cpt.fixModel mRNA 487 666 . - . ID=ORF.0.459_0.323250347541.mRNA;Parent=ORF.0.459_0.323250347541 +testseq_2018-03-08 getOrfsOrCds CDS 487 666 . - 0 ID=ORF.0.459_0.323250347541.CDS;Parent=ORF.0.459_0.323250347541.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 678 681 . - . ID=ORF.0.459_0.323250347541.rbs-0;Parent=ORF.0.459_0.323250347541 +testseq_2018-03-08 cpt.fixModel gene 487 657 . - . ID=ORF.0.460_0.509039455004 +testseq_2018-03-08 cpt.fixModel mRNA 487 657 . - . ID=ORF.0.460_0.509039455004.mRNA;Parent=ORF.0.460_0.509039455004 +testseq_2018-03-08 getOrfsOrCds CDS 487 657 . - 0 ID=ORF.0.460_0.509039455004.CDS;Parent=ORF.0.460_0.509039455004.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 665 670 . - . ID=ORF.0.460_0.509039455004.rbs-0;Parent=ORF.0.460_0.509039455004 +testseq_2018-03-08 cpt.fixModel gene 487 654 . - . ID=ORF.0.461_0.392081904542 +testseq_2018-03-08 cpt.fixModel mRNA 487 654 . - . ID=ORF.0.461_0.392081904542.mRNA;Parent=ORF.0.461_0.392081904542 +testseq_2018-03-08 getOrfsOrCds CDS 487 654 . - 0 ID=ORF.0.461_0.392081904542.CDS;Parent=ORF.0.461_0.392081904542.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 665 669 . - . ID=ORF.0.461_0.392081904542.rbs-0;Parent=ORF.0.461_0.392081904542 +testseq_2018-03-08 cpt.fixModel gene 644 904 . - . ID=ORF.0.699_0.764949625216 +testseq_2018-03-08 cpt.fixModel mRNA 644 904 . - . ID=ORF.0.699_0.764949625216.mRNA;Parent=ORF.0.699_0.764949625216 +testseq_2018-03-08 getOrfsOrCds CDS 644 904 . - 0 ID=ORF.0.699_0.764949625216.CDS;Parent=ORF.0.699_0.764949625216.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 914 918 . - . ID=ORF.0.699_0.764949625216.rbs-0;Parent=ORF.0.699_0.764949625216 +testseq_2018-03-08 cpt.fixModel gene 644 802 . - . ID=ORF.0.703_0.981371874022 +testseq_2018-03-08 cpt.fixModel mRNA 644 802 . - . ID=ORF.0.703_0.981371874022.mRNA;Parent=ORF.0.703_0.981371874022 +testseq_2018-03-08 getOrfsOrCds CDS 644 802 . - 0 ID=ORF.0.703_0.981371874022.CDS;Parent=ORF.0.703_0.981371874022.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 811 814 . - . ID=ORF.0.703_0.981371874022.rbs-0;Parent=ORF.0.703_0.981371874022 +testseq_2018-03-08 cpt.fixModel gene 644 775 . - . ID=ORF.0.705_0.438813830323 +testseq_2018-03-08 cpt.fixModel mRNA 644 775 . - . ID=ORF.0.705_0.438813830323.mRNA;Parent=ORF.0.705_0.438813830323 +testseq_2018-03-08 getOrfsOrCds CDS 644 775 . - 0 ID=ORF.0.705_0.438813830323.CDS;Parent=ORF.0.705_0.438813830323.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 788 790 . - . ID=ORF.0.705_0.438813830323.rbs-0;Parent=ORF.0.705_0.438813830323 +testseq_2018-03-08 cpt.fixModel gene 932 2659 . - . ID=ORF.0.622_0.865794102081 +testseq_2018-03-08 cpt.fixModel mRNA 932 2659 . - . ID=ORF.0.622_0.865794102081.mRNA;Parent=ORF.0.622_0.865794102081 +testseq_2018-03-08 getOrfsOrCds CDS 932 2659 . - 0 ID=ORF.0.622_0.865794102081.CDS;Parent=ORF.0.622_0.865794102081.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 2672 2674 . - . ID=ORF.0.622_0.865794102081.rbs-0;Parent=ORF.0.622_0.865794102081 +testseq_2018-03-08 cpt.fixModel gene 932 2650 . - . ID=ORF.0.623_0.846988205141 +testseq_2018-03-08 cpt.fixModel mRNA 932 2650 . - . ID=ORF.0.623_0.846988205141.mRNA;Parent=ORF.0.623_0.846988205141 +testseq_2018-03-08 getOrfsOrCds CDS 932 2650 . - 0 ID=ORF.0.623_0.846988205141.CDS;Parent=ORF.0.623_0.846988205141.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 2659 2662 . - . ID=ORF.0.623_0.846988205141.rbs-0;Parent=ORF.0.623_0.846988205141 +testseq_2018-03-08 cpt.fixModel gene 932 2605 . - . ID=ORF.0.625_0.0578111846669 +testseq_2018-03-08 cpt.fixModel mRNA 932 2605 . - . ID=ORF.0.625_0.0578111846669.mRNA;Parent=ORF.0.625_0.0578111846669 +testseq_2018-03-08 getOrfsOrCds CDS 932 2605 . - 0 ID=ORF.0.625_0.0578111846669.CDS;Parent=ORF.0.625_0.0578111846669.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 2618 2620 . - . ID=ORF.0.625_0.0578111846669.rbs-0;Parent=ORF.0.625_0.0578111846669 +testseq_2018-03-08 cpt.fixModel gene 932 2572 . - . ID=ORF.0.626_0.303786861772 +testseq_2018-03-08 cpt.fixModel mRNA 932 2572 . - . ID=ORF.0.626_0.303786861772.mRNA;Parent=ORF.0.626_0.303786861772 +testseq_2018-03-08 getOrfsOrCds CDS 932 2572 . - 0 ID=ORF.0.626_0.303786861772.CDS;Parent=ORF.0.626_0.303786861772.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 2584 2586 . - . ID=ORF.0.626_0.303786861772.rbs-0;Parent=ORF.0.626_0.303786861772 +testseq_2018-03-08 cpt.fixModel gene 932 2518 . - . ID=ORF.0.630_0.467112600707 +testseq_2018-03-08 cpt.fixModel mRNA 932 2518 . - . ID=ORF.0.630_0.467112600707.mRNA;Parent=ORF.0.630_0.467112600707 +testseq_2018-03-08 getOrfsOrCds CDS 932 2518 . - 0 ID=ORF.0.630_0.467112600707.CDS;Parent=ORF.0.630_0.467112600707.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 2526 2528 . - . ID=ORF.0.630_0.467112600707.rbs-0;Parent=ORF.0.630_0.467112600707 +testseq_2018-03-08 cpt.fixModel gene 932 2509 . - . ID=ORF.0.631_0.2883116125 +testseq_2018-03-08 cpt.fixModel mRNA 932 2509 . - . ID=ORF.0.631_0.2883116125.mRNA;Parent=ORF.0.631_0.2883116125 +testseq_2018-03-08 getOrfsOrCds CDS 932 2509 . - 0 ID=ORF.0.631_0.2883116125.CDS;Parent=ORF.0.631_0.2883116125.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 2522 2524 . - . ID=ORF.0.631_0.2883116125.rbs-0;Parent=ORF.0.631_0.2883116125 +testseq_2018-03-08 cpt.fixModel gene 932 2404 . - . ID=ORF.0.636_0.876600016398 +testseq_2018-03-08 cpt.fixModel mRNA 932 2404 . - . ID=ORF.0.636_0.876600016398.mRNA;Parent=ORF.0.636_0.876600016398 +testseq_2018-03-08 getOrfsOrCds CDS 932 2404 . - 0 ID=ORF.0.636_0.876600016398.CDS;Parent=ORF.0.636_0.876600016398.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 2416 2418 . - . ID=ORF.0.636_0.876600016398.rbs-0;Parent=ORF.0.636_0.876600016398 +testseq_2018-03-08 cpt.fixModel gene 932 2356 . - . ID=ORF.0.640_0.0888066128056 +testseq_2018-03-08 cpt.fixModel mRNA 932 2356 . - . ID=ORF.0.640_0.0888066128056.mRNA;Parent=ORF.0.640_0.0888066128056 +testseq_2018-03-08 getOrfsOrCds CDS 932 2356 . - 0 ID=ORF.0.640_0.0888066128056.CDS;Parent=ORF.0.640_0.0888066128056.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 2366 2368 . - . ID=ORF.0.640_0.0888066128056.rbs-0;Parent=ORF.0.640_0.0888066128056 +testseq_2018-03-08 cpt.fixModel gene 932 2098 . - . ID=ORF.0.655_0.212962186525 +testseq_2018-03-08 cpt.fixModel mRNA 932 2098 . - . ID=ORF.0.655_0.212962186525.mRNA;Parent=ORF.0.655_0.212962186525 +testseq_2018-03-08 getOrfsOrCds CDS 932 2098 . - 0 ID=ORF.0.655_0.212962186525.CDS;Parent=ORF.0.655_0.212962186525.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 2108 2111 . - . ID=ORF.0.655_0.212962186525.rbs-0;Parent=ORF.0.655_0.212962186525 +testseq_2018-03-08 cpt.fixModel gene 932 2020 . - . ID=ORF.0.659_0.370352364369 +testseq_2018-03-08 cpt.fixModel mRNA 932 2020 . - . ID=ORF.0.659_0.370352364369.mRNA;Parent=ORF.0.659_0.370352364369 +testseq_2018-03-08 getOrfsOrCds CDS 932 2020 . - 0 ID=ORF.0.659_0.370352364369.CDS;Parent=ORF.0.659_0.370352364369.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 2031 2034 . - . ID=ORF.0.659_0.370352364369.rbs-0;Parent=ORF.0.659_0.370352364369 +testseq_2018-03-08 cpt.fixModel gene 932 1996 . - . ID=ORF.0.660_0.561664408596 +testseq_2018-03-08 cpt.fixModel mRNA 932 1996 . - . ID=ORF.0.660_0.561664408596.mRNA;Parent=ORF.0.660_0.561664408596 +testseq_2018-03-08 getOrfsOrCds CDS 932 1996 . - 0 ID=ORF.0.660_0.561664408596.CDS;Parent=ORF.0.660_0.561664408596.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 2009 2011 . - . ID=ORF.0.660_0.561664408596.rbs-0;Parent=ORF.0.660_0.561664408596 +testseq_2018-03-08 cpt.fixModel gene 932 1924 . - . ID=ORF.0.662_0.547739243117 +testseq_2018-03-08 cpt.fixModel mRNA 932 1924 . - . ID=ORF.0.662_0.547739243117.mRNA;Parent=ORF.0.662_0.547739243117 +testseq_2018-03-08 getOrfsOrCds CDS 932 1924 . - 0 ID=ORF.0.662_0.547739243117.CDS;Parent=ORF.0.662_0.547739243117.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 1930 1933 . - . ID=ORF.0.662_0.547739243117.rbs-0;Parent=ORF.0.662_0.547739243117 +testseq_2018-03-08 cpt.fixModel gene 932 1780 . - . ID=ORF.0.667_0.381504311163 +testseq_2018-03-08 cpt.fixModel mRNA 932 1780 . - . ID=ORF.0.667_0.381504311163.mRNA;Parent=ORF.0.667_0.381504311163 +testseq_2018-03-08 getOrfsOrCds CDS 932 1780 . - 0 ID=ORF.0.667_0.381504311163.CDS;Parent=ORF.0.667_0.381504311163.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 1787 1789 . - . ID=ORF.0.667_0.381504311163.rbs-0;Parent=ORF.0.667_0.381504311163 +testseq_2018-03-08 cpt.fixModel gene 1303 1413 . - . ID=ORF.0.457_0.112605087319 +testseq_2018-03-08 cpt.fixModel mRNA 1303 1413 . - . ID=ORF.0.457_0.112605087319.mRNA;Parent=ORF.0.457_0.112605087319 +testseq_2018-03-08 getOrfsOrCds CDS 1303 1413 . - 0 ID=ORF.0.457_0.112605087319.CDS;Parent=ORF.0.457_0.112605087319.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 1421 1424 . - . ID=ORF.0.457_0.112605087319.rbs-0;Parent=ORF.0.457_0.112605087319 +testseq_2018-03-08 cpt.fixModel gene 2673 3473 . - . ID=ORF.0.518_0.704496503167 +testseq_2018-03-08 cpt.fixModel mRNA 2673 3473 . - . ID=ORF.0.518_0.704496503167.mRNA;Parent=ORF.0.518_0.704496503167 +testseq_2018-03-08 getOrfsOrCds CDS 2673 3473 . - 0 ID=ORF.0.518_0.704496503167.CDS;Parent=ORF.0.518_0.704496503167.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 3484 3488 . - . ID=ORF.0.518_0.704496503167.rbs-0;Parent=ORF.0.518_0.704496503167 +testseq_2018-03-08 cpt.fixModel gene 2673 3140 . - . ID=ORF.0.531_0.284124356131 +testseq_2018-03-08 cpt.fixModel mRNA 2673 3140 . - . ID=ORF.0.531_0.284124356131.mRNA;Parent=ORF.0.531_0.284124356131 +testseq_2018-03-08 getOrfsOrCds CDS 2673 3140 . - 0 ID=ORF.0.531_0.284124356131.CDS;Parent=ORF.0.531_0.284124356131.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 3153 3155 . - . ID=ORF.0.531_0.284124356131.rbs-0;Parent=ORF.0.531_0.284124356131 +testseq_2018-03-08 cpt.fixModel gene 2673 3077 . - . ID=ORF.0.534_0.230486359187 +testseq_2018-03-08 cpt.fixModel mRNA 2673 3077 . - . ID=ORF.0.534_0.230486359187.mRNA;Parent=ORF.0.534_0.230486359187 +testseq_2018-03-08 getOrfsOrCds CDS 2673 3077 . - 0 ID=ORF.0.534_0.230486359187.CDS;Parent=ORF.0.534_0.230486359187.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 3083 3085 . - . ID=ORF.0.534_0.230486359187.rbs-0;Parent=ORF.0.534_0.230486359187 +testseq_2018-03-08 cpt.fixModel gene 2673 2765 . - . ID=ORF.0.549_0.435747482069 +testseq_2018-03-08 cpt.fixModel mRNA 2673 2765 . - . ID=ORF.0.549_0.435747482069.mRNA;Parent=ORF.0.549_0.435747482069 +testseq_2018-03-08 getOrfsOrCds CDS 2673 2765 . - 0 ID=ORF.0.549_0.435747482069.CDS;Parent=ORF.0.549_0.435747482069.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 2774 2777 . - . ID=ORF.0.549_0.435747482069.rbs-0;Parent=ORF.0.549_0.435747482069 +testseq_2018-03-08 cpt.fixModel gene 3362 3739 . - . ID=ORF.0.603_0.488926379773 +testseq_2018-03-08 cpt.fixModel mRNA 3362 3739 . - . ID=ORF.0.603_0.488926379773.mRNA;Parent=ORF.0.603_0.488926379773 +testseq_2018-03-08 getOrfsOrCds CDS 3362 3739 . - 0 ID=ORF.0.603_0.488926379773.CDS;Parent=ORF.0.603_0.488926379773.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 3749 3754 . - . ID=ORF.0.603_0.488926379773.rbs-0;Parent=ORF.0.603_0.488926379773 +testseq_2018-03-08 cpt.fixModel gene 3362 3706 . - . ID=ORF.0.605_0.950422684088 +testseq_2018-03-08 cpt.fixModel mRNA 3362 3706 . - . ID=ORF.0.605_0.950422684088.mRNA;Parent=ORF.0.605_0.950422684088 +testseq_2018-03-08 getOrfsOrCds CDS 3362 3706 . - 0 ID=ORF.0.605_0.950422684088.CDS;Parent=ORF.0.605_0.950422684088.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 3719 3721 . - . ID=ORF.0.605_0.950422684088.rbs-0;Parent=ORF.0.605_0.950422684088 +testseq_2018-03-08 cpt.fixModel gene 3362 3688 . - . ID=ORF.0.606_0.329949811104 +testseq_2018-03-08 cpt.fixModel mRNA 3362 3688 . - . ID=ORF.0.606_0.329949811104.mRNA;Parent=ORF.0.606_0.329949811104 +testseq_2018-03-08 getOrfsOrCds CDS 3362 3688 . - 0 ID=ORF.0.606_0.329949811104.CDS;Parent=ORF.0.606_0.329949811104.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 3699 3702 . - . ID=ORF.0.606_0.329949811104.rbs-0;Parent=ORF.0.606_0.329949811104 +testseq_2018-03-08 cpt.fixModel gene 3362 3550 . - . ID=ORF.0.611_0.815705221168 +testseq_2018-03-08 cpt.fixModel mRNA 3362 3550 . - . ID=ORF.0.611_0.815705221168.mRNA;Parent=ORF.0.611_0.815705221168 +testseq_2018-03-08 getOrfsOrCds CDS 3362 3550 . - 0 ID=ORF.0.611_0.815705221168.CDS;Parent=ORF.0.611_0.815705221168.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 3559 3561 . - . ID=ORF.0.611_0.815705221168.rbs-0;Parent=ORF.0.611_0.815705221168 +testseq_2018-03-08 cpt.fixModel gene 3362 3493 . - . ID=ORF.0.613_0.104890641676 +testseq_2018-03-08 cpt.fixModel mRNA 3362 3493 . - . ID=ORF.0.613_0.104890641676.mRNA;Parent=ORF.0.613_0.104890641676 +testseq_2018-03-08 getOrfsOrCds CDS 3362 3493 . - 0 ID=ORF.0.613_0.104890641676.CDS;Parent=ORF.0.613_0.104890641676.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 3506 3508 . - . ID=ORF.0.613_0.104890641676.rbs-0;Parent=ORF.0.613_0.104890641676 +testseq_2018-03-08 cpt.fixModel gene 3433 3537 . + . ID=ORF.0.17_0.711047642618 +testseq_2018-03-08 cpt.fixModel mRNA 3433 3537 . + . ID=ORF.0.17_0.711047642618.mRNA;Parent=ORF.0.17_0.711047642618 +testseq_2018-03-08 getOrfsOrCds CDS 3433 3537 . + 0 ID=ORF.0.17_0.711047642618.CDS;Parent=ORF.0.17_0.711047642618.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 3419 3421 . + . ID=ORF.0.17_0.711047642618.rbs-0;Parent=ORF.0.17_0.711047642618 +testseq_2018-03-08 cpt.fixModel gene 3986 4114 . + . ID=ORF.0.139_0.904626958426 +testseq_2018-03-08 cpt.fixModel mRNA 3986 4114 . + . ID=ORF.0.139_0.904626958426.mRNA;Parent=ORF.0.139_0.904626958426 +testseq_2018-03-08 getOrfsOrCds CDS 3986 4114 . + 0 ID=ORF.0.139_0.904626958426.CDS;Parent=ORF.0.139_0.904626958426.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 3971 3973 . + . ID=ORF.0.139_0.904626958426.rbs-0;Parent=ORF.0.139_0.904626958426 +testseq_2018-03-08 cpt.fixModel gene 4006 4101 . - . ID=ORF.0.445_0.286571403109 +testseq_2018-03-08 cpt.fixModel mRNA 4006 4101 . - . ID=ORF.0.445_0.286571403109.mRNA;Parent=ORF.0.445_0.286571403109 +testseq_2018-03-08 getOrfsOrCds CDS 4006 4101 . - 0 ID=ORF.0.445_0.286571403109.CDS;Parent=ORF.0.445_0.286571403109.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 4108 4110 . - . ID=ORF.0.445_0.286571403109.rbs-0;Parent=ORF.0.445_0.286571403109 +testseq_2018-03-08 cpt.fixModel gene 4071 4190 . + . ID=ORF.0.345_0.971616620883 +testseq_2018-03-08 cpt.fixModel mRNA 4071 4190 . + . ID=ORF.0.345_0.971616620883.mRNA;Parent=ORF.0.345_0.971616620883 +testseq_2018-03-08 getOrfsOrCds CDS 4071 4190 . + 0 ID=ORF.0.345_0.971616620883.CDS;Parent=ORF.0.345_0.971616620883.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 4057 4059 . + . ID=ORF.0.345_0.971616620883.rbs-0;Parent=ORF.0.345_0.971616620883 +testseq_2018-03-08 cpt.fixModel gene 4095 4190 . + . ID=ORF.0.347_0.0208968983552 +testseq_2018-03-08 cpt.fixModel mRNA 4095 4190 . + . ID=ORF.0.347_0.0208968983552.mRNA;Parent=ORF.0.347_0.0208968983552 +testseq_2018-03-08 getOrfsOrCds CDS 4095 4190 . + 0 ID=ORF.0.347_0.0208968983552.CDS;Parent=ORF.0.347_0.0208968983552.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 4087 4089 . + . ID=ORF.0.347_0.0208968983552.rbs-0;Parent=ORF.0.347_0.0208968983552 +testseq_2018-03-08 cpt.fixModel gene 4134 4229 . - . ID=ORF.0.517_0.929120702544 +testseq_2018-03-08 cpt.fixModel mRNA 4134 4229 . - . ID=ORF.0.517_0.929120702544.mRNA;Parent=ORF.0.517_0.929120702544 +testseq_2018-03-08 getOrfsOrCds CDS 4134 4229 . - 0 ID=ORF.0.517_0.929120702544.CDS;Parent=ORF.0.517_0.929120702544.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 4241 4243 . - . ID=ORF.0.517_0.929120702544.rbs-0;Parent=ORF.0.517_0.929120702544 +testseq_2018-03-08 cpt.fixModel gene 4574 5500 . + . ID=ORF.0.146_0.351389104617 +testseq_2018-03-08 cpt.fixModel mRNA 4574 5500 . + . ID=ORF.0.146_0.351389104617.mRNA;Parent=ORF.0.146_0.351389104617 +testseq_2018-03-08 getOrfsOrCds CDS 4574 5500 . + 0 ID=ORF.0.146_0.351389104617.CDS;Parent=ORF.0.146_0.351389104617.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 4560 4563 . + . ID=ORF.0.146_0.351389104617.rbs-0;Parent=ORF.0.146_0.351389104617 +testseq_2018-03-08 cpt.fixModel gene 5029 5181 . - . ID=ORF.0.439_0.445866101899 +testseq_2018-03-08 cpt.fixModel mRNA 5029 5181 . - . ID=ORF.0.439_0.445866101899.mRNA;Parent=ORF.0.439_0.445866101899 +testseq_2018-03-08 getOrfsOrCds CDS 5029 5181 . - 0 ID=ORF.0.439_0.445866101899.CDS;Parent=ORF.0.439_0.445866101899.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 5188 5192 . - . ID=ORF.0.439_0.445866101899.rbs-0;Parent=ORF.0.439_0.445866101899 +testseq_2018-03-08 cpt.fixModel gene 5029 5160 . - . ID=ORF.0.440_0.915263915342 +testseq_2018-03-08 cpt.fixModel mRNA 5029 5160 . - . ID=ORF.0.440_0.915263915342.mRNA;Parent=ORF.0.440_0.915263915342 +testseq_2018-03-08 getOrfsOrCds CDS 5029 5160 . - 0 ID=ORF.0.440_0.915263915342.CDS;Parent=ORF.0.440_0.915263915342.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 5170 5172 . - . ID=ORF.0.440_0.915263915342.rbs-0;Parent=ORF.0.440_0.915263915342 +testseq_2018-03-08 cpt.fixModel gene 5393 5500 . + . ID=ORF.0.183_0.0663532791257 +testseq_2018-03-08 cpt.fixModel mRNA 5393 5500 . + . ID=ORF.0.183_0.0663532791257.mRNA;Parent=ORF.0.183_0.0663532791257 +testseq_2018-03-08 getOrfsOrCds CDS 5393 5500 . + 0 ID=ORF.0.183_0.0663532791257.CDS;Parent=ORF.0.183_0.0663532791257.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 5381 5383 . + . ID=ORF.0.183_0.0663532791257.rbs-0;Parent=ORF.0.183_0.0663532791257 +testseq_2018-03-08 cpt.fixModel gene 5570 5689 . + . ID=ORF.0.185_0.343675913625 +testseq_2018-03-08 cpt.fixModel mRNA 5570 5689 . + . ID=ORF.0.185_0.343675913625.mRNA;Parent=ORF.0.185_0.343675913625 +testseq_2018-03-08 getOrfsOrCds CDS 5570 5689 . + 0 ID=ORF.0.185_0.343675913625.CDS;Parent=ORF.0.185_0.343675913625.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 5562 5564 . + . ID=ORF.0.185_0.343675913625.rbs-0;Parent=ORF.0.185_0.343675913625 +testseq_2018-03-08 cpt.fixModel gene 6095 6205 . - . ID=ORF.0.580_0.42130451371 +testseq_2018-03-08 cpt.fixModel mRNA 6095 6205 . - . ID=ORF.0.580_0.42130451371.mRNA;Parent=ORF.0.580_0.42130451371 +testseq_2018-03-08 getOrfsOrCds CDS 6095 6205 . - 0 ID=ORF.0.580_0.42130451371.CDS;Parent=ORF.0.580_0.42130451371.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 6218 6220 . - . ID=ORF.0.580_0.42130451371.rbs-0;Parent=ORF.0.580_0.42130451371 +testseq_2018-03-08 cpt.fixModel gene 6166 6282 . - . ID=ORF.0.429_0.211525337226 +testseq_2018-03-08 cpt.fixModel mRNA 6166 6282 . - . ID=ORF.0.429_0.211525337226.mRNA;Parent=ORF.0.429_0.211525337226 +testseq_2018-03-08 getOrfsOrCds CDS 6166 6282 . - 0 ID=ORF.0.429_0.211525337226.CDS;Parent=ORF.0.429_0.211525337226.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 6288 6290 . - . ID=ORF.0.429_0.211525337226.rbs-0;Parent=ORF.0.429_0.211525337226 +testseq_2018-03-08 cpt.fixModel gene 6206 6973 . + . ID=ORF.0.202_0.502577350308 +testseq_2018-03-08 cpt.fixModel mRNA 6206 6973 . + . ID=ORF.0.202_0.502577350308.mRNA;Parent=ORF.0.202_0.502577350308 +testseq_2018-03-08 getOrfsOrCds CDS 6206 6973 . + 0 ID=ORF.0.202_0.502577350308.CDS;Parent=ORF.0.202_0.502577350308.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 6196 6198 . + . ID=ORF.0.202_0.502577350308.rbs-0;Parent=ORF.0.202_0.502577350308 +testseq_2018-03-08 cpt.fixModel gene 6545 6973 . + . ID=ORF.0.217_0.854168148494 +testseq_2018-03-08 cpt.fixModel mRNA 6545 6973 . + . ID=ORF.0.217_0.854168148494.mRNA;Parent=ORF.0.217_0.854168148494 +testseq_2018-03-08 getOrfsOrCds CDS 6545 6973 . + 0 ID=ORF.0.217_0.854168148494.CDS;Parent=ORF.0.217_0.854168148494.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 6530 6532 . + . ID=ORF.0.217_0.854168148494.rbs-0;Parent=ORF.0.217_0.854168148494 +testseq_2018-03-08 cpt.fixModel gene 6704 6973 . + . ID=ORF.0.224_0.295192659405 +testseq_2018-03-08 cpt.fixModel mRNA 6704 6973 . + . ID=ORF.0.224_0.295192659405.mRNA;Parent=ORF.0.224_0.295192659405 +testseq_2018-03-08 getOrfsOrCds CDS 6704 6973 . + 0 ID=ORF.0.224_0.295192659405.CDS;Parent=ORF.0.224_0.295192659405.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 6692 6695 . + . ID=ORF.0.224_0.295192659405.rbs-0;Parent=ORF.0.224_0.295192659405 +testseq_2018-03-08 cpt.fixModel gene 6978 7094 . + . ID=ORF.0.355_0.773691408662 +testseq_2018-03-08 cpt.fixModel mRNA 6978 7094 . + . ID=ORF.0.355_0.773691408662.mRNA;Parent=ORF.0.355_0.773691408662 +testseq_2018-03-08 getOrfsOrCds CDS 6978 7094 . + 0 ID=ORF.0.355_0.773691408662.CDS;Parent=ORF.0.355_0.773691408662.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 6967 6971 . + . ID=ORF.0.355_0.773691408662.rbs-0;Parent=ORF.0.355_0.773691408662 +testseq_2018-03-08 cpt.fixModel gene 7016 7156 . - . ID=ORF.0.571_0.245647554641 +testseq_2018-03-08 cpt.fixModel mRNA 7016 7156 . - . ID=ORF.0.571_0.245647554641.mRNA;Parent=ORF.0.571_0.245647554641 +testseq_2018-03-08 getOrfsOrCds CDS 7016 7156 . - 0 ID=ORF.0.571_0.245647554641.CDS;Parent=ORF.0.571_0.245647554641.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 7163 7166 . - . ID=ORF.0.571_0.245647554641.rbs-0;Parent=ORF.0.571_0.245647554641 +testseq_2018-03-08 cpt.fixModel gene 7056 7244 . - . ID=ORF.0.492_0.914947831416 +testseq_2018-03-08 cpt.fixModel mRNA 7056 7244 . - . ID=ORF.0.492_0.914947831416.mRNA;Parent=ORF.0.492_0.914947831416 +testseq_2018-03-08 getOrfsOrCds CDS 7056 7244 . - 0 ID=ORF.0.492_0.914947831416.CDS;Parent=ORF.0.492_0.914947831416.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 7250 7253 . - . ID=ORF.0.492_0.914947831416.rbs-0;Parent=ORF.0.492_0.914947831416 +testseq_2018-03-08 cpt.fixModel gene 7056 7229 . - . ID=ORF.0.494_0.190486747638 +testseq_2018-03-08 cpt.fixModel mRNA 7056 7229 . - . ID=ORF.0.494_0.190486747638.mRNA;Parent=ORF.0.494_0.190486747638 +testseq_2018-03-08 getOrfsOrCds CDS 7056 7229 . - 0 ID=ORF.0.494_0.190486747638.CDS;Parent=ORF.0.494_0.190486747638.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 7235 7237 . - . ID=ORF.0.494_0.190486747638.rbs-0;Parent=ORF.0.494_0.190486747638 +testseq_2018-03-08 cpt.fixModel gene 7072 7395 . + . ID=ORF.0.33_0.821816667683 +testseq_2018-03-08 cpt.fixModel mRNA 7072 7395 . + . ID=ORF.0.33_0.821816667683.mRNA;Parent=ORF.0.33_0.821816667683 +testseq_2018-03-08 getOrfsOrCds CDS 7072 7395 . + 0 ID=ORF.0.33_0.821816667683.CDS;Parent=ORF.0.33_0.821816667683.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 7061 7065 . + . ID=ORF.0.33_0.821816667683.rbs-0;Parent=ORF.0.33_0.821816667683 +testseq_2018-03-08 cpt.fixModel gene 7078 7395 . + . ID=ORF.0.34_0.707053863467 +testseq_2018-03-08 cpt.fixModel mRNA 7078 7395 . + . ID=ORF.0.34_0.707053863467.mRNA;Parent=ORF.0.34_0.707053863467 +testseq_2018-03-08 getOrfsOrCds CDS 7078 7395 . + 0 ID=ORF.0.34_0.707053863467.CDS;Parent=ORF.0.34_0.707053863467.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 7063 7066 . + . ID=ORF.0.34_0.707053863467.rbs-0;Parent=ORF.0.34_0.707053863467 +testseq_2018-03-08 cpt.fixModel gene 7379 7855 . + . ID=ORF.0.231_0.000923123852602 +testseq_2018-03-08 cpt.fixModel mRNA 7379 7855 . + . ID=ORF.0.231_0.000923123852602.mRNA;Parent=ORF.0.231_0.000923123852602 +testseq_2018-03-08 getOrfsOrCds CDS 7379 7855 . + 0 ID=ORF.0.231_0.000923123852602.CDS;Parent=ORF.0.231_0.000923123852602.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 7369 7372 . + . ID=ORF.0.231_0.000923123852602.rbs-0;Parent=ORF.0.231_0.000923123852602 +testseq_2018-03-08 cpt.fixModel gene 7418 7855 . + . ID=ORF.0.233_0.405974692709 +testseq_2018-03-08 cpt.fixModel mRNA 7418 7855 . + . ID=ORF.0.233_0.405974692709.mRNA;Parent=ORF.0.233_0.405974692709 +testseq_2018-03-08 getOrfsOrCds CDS 7418 7855 . + 0 ID=ORF.0.233_0.405974692709.CDS;Parent=ORF.0.233_0.405974692709.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 7404 7406 . + . ID=ORF.0.233_0.405974692709.rbs-0;Parent=ORF.0.233_0.405974692709 +testseq_2018-03-08 cpt.fixModel gene 7658 7855 . + . ID=ORF.0.237_0.755472071473 +testseq_2018-03-08 cpt.fixModel mRNA 7658 7855 . + . ID=ORF.0.237_0.755472071473.mRNA;Parent=ORF.0.237_0.755472071473 +testseq_2018-03-08 getOrfsOrCds CDS 7658 7855 . + 0 ID=ORF.0.237_0.755472071473.CDS;Parent=ORF.0.237_0.755472071473.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 7650 7652 . + . ID=ORF.0.237_0.755472071473.rbs-0;Parent=ORF.0.237_0.755472071473 +testseq_2018-03-08 cpt.fixModel gene 7664 7855 . + . ID=ORF.0.238_0.914046339376 +testseq_2018-03-08 cpt.fixModel mRNA 7664 7855 . + . ID=ORF.0.238_0.914046339376.mRNA;Parent=ORF.0.238_0.914046339376 +testseq_2018-03-08 getOrfsOrCds CDS 7664 7855 . + 0 ID=ORF.0.238_0.914046339376.CDS;Parent=ORF.0.238_0.914046339376.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 7650 7653 . + . ID=ORF.0.238_0.914046339376.rbs-0;Parent=ORF.0.238_0.914046339376 +testseq_2018-03-08 cpt.fixModel gene 7806 7922 . + . ID=ORF.0.365_0.2945108684 +testseq_2018-03-08 cpt.fixModel mRNA 7806 7922 . + . ID=ORF.0.365_0.2945108684.mRNA;Parent=ORF.0.365_0.2945108684 +testseq_2018-03-08 getOrfsOrCds CDS 7806 7922 . + 0 ID=ORF.0.365_0.2945108684.CDS;Parent=ORF.0.365_0.2945108684.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 7791 7793 . + . ID=ORF.0.365_0.2945108684.rbs-0;Parent=ORF.0.365_0.2945108684 +testseq_2018-03-08 cpt.fixModel gene 7852 8313 . + . ID=ORF.0.50_0.415010657017 +testseq_2018-03-08 cpt.fixModel mRNA 7852 8313 . + . ID=ORF.0.50_0.415010657017.mRNA;Parent=ORF.0.50_0.415010657017 +testseq_2018-03-08 getOrfsOrCds CDS 7852 8313 . + 0 ID=ORF.0.50_0.415010657017.CDS;Parent=ORF.0.50_0.415010657017.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 7839 7841 . + . ID=ORF.0.50_0.415010657017.rbs-0;Parent=ORF.0.50_0.415010657017 +testseq_2018-03-08 cpt.fixModel gene 8072 8254 . + . ID=ORF.0.247_0.938715889806 +testseq_2018-03-08 cpt.fixModel mRNA 8072 8254 . + . ID=ORF.0.247_0.938715889806.mRNA;Parent=ORF.0.247_0.938715889806 +testseq_2018-03-08 getOrfsOrCds CDS 8072 8254 . + 0 ID=ORF.0.247_0.938715889806.CDS;Parent=ORF.0.247_0.938715889806.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 8060 8064 . + . ID=ORF.0.247_0.938715889806.rbs-0;Parent=ORF.0.247_0.938715889806 +testseq_2018-03-08 cpt.fixModel gene 8128 8313 . + . ID=ORF.0.65_0.403948729686 +testseq_2018-03-08 cpt.fixModel mRNA 8128 8313 . + . ID=ORF.0.65_0.403948729686.mRNA;Parent=ORF.0.65_0.403948729686 +testseq_2018-03-08 getOrfsOrCds CDS 8128 8313 . + 0 ID=ORF.0.65_0.403948729686.CDS;Parent=ORF.0.65_0.403948729686.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 8116 8118 . + . ID=ORF.0.65_0.403948729686.rbs-0;Parent=ORF.0.65_0.403948729686 +testseq_2018-03-08 cpt.fixModel gene 8152 8640 . - . ID=ORF.0.380_0.771335496557 +testseq_2018-03-08 cpt.fixModel mRNA 8152 8640 . - . ID=ORF.0.380_0.771335496557.mRNA;Parent=ORF.0.380_0.771335496557 +testseq_2018-03-08 getOrfsOrCds CDS 8152 8640 . - 0 ID=ORF.0.380_0.771335496557.CDS;Parent=ORF.0.380_0.771335496557.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 8652 8654 . - . ID=ORF.0.380_0.771335496557.rbs-0;Parent=ORF.0.380_0.771335496557 +testseq_2018-03-08 cpt.fixModel gene 8152 8436 . - . ID=ORF.0.391_0.169373954797 +testseq_2018-03-08 cpt.fixModel mRNA 8152 8436 . - . ID=ORF.0.391_0.169373954797.mRNA;Parent=ORF.0.391_0.169373954797 +testseq_2018-03-08 getOrfsOrCds CDS 8152 8436 . - 0 ID=ORF.0.391_0.169373954797.CDS;Parent=ORF.0.391_0.169373954797.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 8444 8446 . - . ID=ORF.0.391_0.169373954797.rbs-0;Parent=ORF.0.391_0.169373954797 +testseq_2018-03-08 cpt.fixModel gene 8152 8271 . - . ID=ORF.0.400_0.811321232506 +testseq_2018-03-08 cpt.fixModel mRNA 8152 8271 . - . ID=ORF.0.400_0.811321232506.mRNA;Parent=ORF.0.400_0.811321232506 +testseq_2018-03-08 getOrfsOrCds CDS 8152 8271 . - 0 ID=ORF.0.400_0.811321232506.CDS;Parent=ORF.0.400_0.811321232506.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 8281 8284 . - . ID=ORF.0.400_0.811321232506.rbs-0;Parent=ORF.0.400_0.811321232506 +testseq_2018-03-08 cpt.fixModel gene 8339 8782 . + . ID=ORF.0.260_0.577298671452 +testseq_2018-03-08 cpt.fixModel mRNA 8339 8782 . + . ID=ORF.0.260_0.577298671452.mRNA;Parent=ORF.0.260_0.577298671452 +testseq_2018-03-08 getOrfsOrCds CDS 8339 8782 . + 0 ID=ORF.0.260_0.577298671452.CDS;Parent=ORF.0.260_0.577298671452.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 8330 8332 . + . ID=ORF.0.260_0.577298671452.rbs-0;Parent=ORF.0.260_0.577298671452 +testseq_2018-03-08 cpt.fixModel gene 8360 8782 . + . ID=ORF.0.261_0.357298653378 +testseq_2018-03-08 cpt.fixModel mRNA 8360 8782 . + . ID=ORF.0.261_0.357298653378.mRNA;Parent=ORF.0.261_0.357298653378 +testseq_2018-03-08 getOrfsOrCds CDS 8360 8782 . + 0 ID=ORF.0.261_0.357298653378.CDS;Parent=ORF.0.261_0.357298653378.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 8348 8351 . + . ID=ORF.0.261_0.357298653378.rbs-0;Parent=ORF.0.261_0.357298653378 +testseq_2018-03-08 cpt.fixModel gene 8453 8782 . + . ID=ORF.0.268_0.501011908227 +testseq_2018-03-08 cpt.fixModel mRNA 8453 8782 . + . ID=ORF.0.268_0.501011908227.mRNA;Parent=ORF.0.268_0.501011908227 +testseq_2018-03-08 getOrfsOrCds CDS 8453 8782 . + 0 ID=ORF.0.268_0.501011908227.CDS;Parent=ORF.0.268_0.501011908227.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 8438 8440 . + . ID=ORF.0.268_0.501011908227.rbs-0;Parent=ORF.0.268_0.501011908227 +testseq_2018-03-08 cpt.fixModel gene 8504 8782 . + . ID=ORF.0.269_0.219984821414 +testseq_2018-03-08 cpt.fixModel mRNA 8504 8782 . + . ID=ORF.0.269_0.219984821414.mRNA;Parent=ORF.0.269_0.219984821414 +testseq_2018-03-08 getOrfsOrCds CDS 8504 8782 . + 0 ID=ORF.0.269_0.219984821414.CDS;Parent=ORF.0.269_0.219984821414.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 8493 8495 . + . ID=ORF.0.269_0.219984821414.rbs-0;Parent=ORF.0.269_0.219984821414 +testseq_2018-03-08 cpt.fixModel gene 8621 8782 . + . ID=ORF.0.278_0.44001518346 +testseq_2018-03-08 cpt.fixModel mRNA 8621 8782 . + . ID=ORF.0.278_0.44001518346.mRNA;Parent=ORF.0.278_0.44001518346 +testseq_2018-03-08 getOrfsOrCds CDS 8621 8782 . + 0 ID=ORF.0.278_0.44001518346.CDS;Parent=ORF.0.278_0.44001518346.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 8612 8614 . + . ID=ORF.0.278_0.44001518346.rbs-0;Parent=ORF.0.278_0.44001518346 +testseq_2018-03-08 cpt.fixModel gene 8944 9198 . + . ID=ORF.0.81_0.839099082128 +testseq_2018-03-08 cpt.fixModel mRNA 8944 9198 . + . ID=ORF.0.81_0.839099082128.mRNA;Parent=ORF.0.81_0.839099082128 +testseq_2018-03-08 getOrfsOrCds CDS 8944 9198 . + 0 ID=ORF.0.81_0.839099082128.CDS;Parent=ORF.0.81_0.839099082128.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 8929 8931 . + . ID=ORF.0.81_0.839099082128.rbs-0;Parent=ORF.0.81_0.839099082128 +testseq_2018-03-08 cpt.fixModel gene 9037 9198 . + . ID=ORF.0.87_0.518549362319 +testseq_2018-03-08 cpt.fixModel mRNA 9037 9198 . + . ID=ORF.0.87_0.518549362319.mRNA;Parent=ORF.0.87_0.518549362319 +testseq_2018-03-08 getOrfsOrCds CDS 9037 9198 . + 0 ID=ORF.0.87_0.518549362319.CDS;Parent=ORF.0.87_0.518549362319.mRNA +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 9022 9024 . + . ID=ORF.0.87_0.518549362319.rbs-0;Parent=ORF.0.87_0.518549362319
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_lipop_conv/test-data/LipoToGFF_In.txt Fri May 13 05:18:31 2022 +0000 @@ -0,0 +1,336 @@ +# ORF.0.472_0.8077298255.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.472_0.8077298255.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.465_0.466377183402.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.465_0.466377183402.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.466_0.685859290271.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.466_0.685859290271.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.468_0.803001272192.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.468_0.803001272192.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.708_0.889453606077.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.708_0.889453606077.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.458_0.61399204562.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.458_0.61399204562.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.459_0.323250347541.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.459_0.323250347541.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.460_0.509039455004.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.460_0.509039455004.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.461_0.392081904542.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.461_0.392081904542.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.699_0.764949625216.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.699_0.764949625216.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.703_0.981371874022.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.703_0.981371874022.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.705_0.438813830323.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.705_0.438813830323.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.622_0.865794102081.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.622_0.865794102081.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.623_0.846988205141.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.623_0.846988205141.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.625_0.0578111846669.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.625_0.0578111846669.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.626_0.303786861772.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.626_0.303786861772.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.630_0.467112600707.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.630_0.467112600707.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.631_0.2883116125.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.631_0.2883116125.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.636_0.876600016398.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.636_0.876600016398.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.640_0.0888066128056.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.640_0.0888066128056.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.655_0.212962186525.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.655_0.212962186525.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.659_0.370352364369.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.659_0.370352364369.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.660_0.561664408596.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.660_0.561664408596.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.662_0.547739243117.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.662_0.547739243117.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.667_0.381504311163.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.667_0.381504311163.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.457_0.112605087319.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.457_0.112605087319.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.518_0.704496503167.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.518_0.704496503167.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.531_0.284124356131.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.531_0.284124356131.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.534_0.230486359187.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.534_0.230486359187.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.549_0.435747482069.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.549_0.435747482069.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.603_0.488926379773.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.603_0.488926379773.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.605_0.950422684088.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.605_0.950422684088.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.606_0.329949811104.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.606_0.329949811104.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.611_0.815705221168.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.611_0.815705221168.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.613_0.104890641676.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.613_0.104890641676.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.17_0.711047642618.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.17_0.711047642618.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.139_0.904626958426.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.139_0.904626958426.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.445_0.286571403109.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.445_0.286571403109.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.345_0.971616620883.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.345_0.971616620883.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.347_0.0208968983552.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.347_0.0208968983552.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.517_0.929120702544.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.517_0.929120702544.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.146_0.351389104617.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.146_0.351389104617.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.439_0.445866101899.CDS TMH score=6.51858 margin=6.713639 +# Cut-off=-3 +ORF.0.439_0.445866101899.CDS LipoP1.0:Best TMH 1 1 6.51858 +ORF.0.439_0.445866101899.CDS LipoP1.0:Margin TMH 1 1 6.713639 +ORF.0.439_0.445866101899.CDS LipoP1.0:Class SpI 1 1 -0.195059 +ORF.0.439_0.445866101899.CDS LipoP1.0:Class CYT 1 1 -0.200913 +ORF.0.439_0.445866101899.CDS LipoP1.0:Signal CleavI 20 21 -0.295218 # SPGVP|CIMLL +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.440_0.915263915342.CDS TMH score=0.241158 margin=0.442071 +# Cut-off=-3 +ORF.0.440_0.915263915342.CDS LipoP1.0:Best TMH 1 1 0.241158 +ORF.0.440_0.915263915342.CDS LipoP1.0:Margin TMH 1 1 0.442071 +ORF.0.440_0.915263915342.CDS LipoP1.0:Class CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.183_0.0663532791257.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.183_0.0663532791257.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.185_0.343675913625.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.185_0.343675913625.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.580_0.42130451371.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.580_0.42130451371.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.429_0.211525337226.CDS CYT score=-0.200913 margin=0.370359 +# Cut-off=-3 +ORF.0.429_0.211525337226.CDS LipoP1.0:Best CYT 1 1 -0.200913 +ORF.0.429_0.211525337226.CDS LipoP1.0:Margin CYT 1 1 0.370359 +ORF.0.429_0.211525337226.CDS LipoP1.0:Class TMH 1 1 -0.571272 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.202_0.502577350308.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.202_0.502577350308.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.217_0.854168148494.CDS CYT score=-0.200913 margin=1.810677 +# Cut-off=-3 +ORF.0.217_0.854168148494.CDS LipoP1.0:Best CYT 1 1 -0.200913 +ORF.0.217_0.854168148494.CDS LipoP1.0:Margin CYT 1 1 1.810677 +ORF.0.217_0.854168148494.CDS LipoP1.0:Class SpI 1 1 -2.01159 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.224_0.295192659405.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.224_0.295192659405.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.355_0.773691408662.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.355_0.773691408662.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.571_0.245647554641.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.571_0.245647554641.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.492_0.914947831416.CDS CYT score=-0.200913 margin=0.188252 +# Cut-off=-3 +ORF.0.492_0.914947831416.CDS LipoP1.0:Best CYT 1 1 -0.200913 +ORF.0.492_0.914947831416.CDS LipoP1.0:Margin CYT 1 1 0.188252 +ORF.0.492_0.914947831416.CDS LipoP1.0:Class TMH 1 1 -0.389165 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.494_0.190486747638.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.494_0.190486747638.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.33_0.821816667683.CDS CYT score=-0.200913 margin=1.151907 +# Cut-off=-3 +ORF.0.33_0.821816667683.CDS LipoP1.0:Best CYT 1 1 -0.200913 +ORF.0.33_0.821816667683.CDS LipoP1.0:Margin CYT 1 1 1.151907 +ORF.0.33_0.821816667683.CDS LipoP1.0:Class TMH 1 1 -1.35282 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.34_0.707053863467.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.34_0.707053863467.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.231_0.000923123852602.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.231_0.000923123852602.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.233_0.405974692709.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.233_0.405974692709.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.237_0.755472071473.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.237_0.755472071473.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.238_0.914046339376.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.238_0.914046339376.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.365_0.2945108684.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.365_0.2945108684.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.50_0.415010657017.CDS SpII score=5.92551 margin=3.72509 cleavage=17-18 Pos+2=L +# Cut-off=-3 +ORF.0.50_0.415010657017.CDS LipoP1.0:Best SpII 1 1 5.92551 +ORF.0.50_0.415010657017.CDS LipoP1.0:Margin SpII 1 1 3.72509 +ORF.0.50_0.415010657017.CDS LipoP1.0:Class SpI 1 1 2.20042 +ORF.0.50_0.415010657017.CDS LipoP1.0:Class CYT 1 1 -0.200913 +ORF.0.50_0.415010657017.CDS LipoP1.0:Signal CleavII 17 18 5.9255 # ICIIV|CLSWA Pos+2=L +ORF.0.50_0.415010657017.CDS LipoP1.0:Signal CleavI 22 23 2.16267 # CLSWA|VNHYR +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.247_0.938715889806.CDS SpII score=19.8902 margin=11.77152 cleavage=19-20 Pos+2=T +# Cut-off=-3 +ORF.0.247_0.938715889806.CDS LipoP1.0:Best SpII 1 1 19.8902 +ORF.0.247_0.938715889806.CDS LipoP1.0:Margin SpII 1 1 11.77152 +ORF.0.247_0.938715889806.CDS LipoP1.0:Class SpI 1 1 8.11868 +ORF.0.247_0.938715889806.CDS LipoP1.0:Class CYT 1 1 -0.200913 +ORF.0.247_0.938715889806.CDS LipoP1.0:Class TMH 1 1 -1.32568 +ORF.0.247_0.938715889806.CDS LipoP1.0:Signal CleavII 19 20 19.8902 # LVVVG|CTSKQ Pos+2=T +ORF.0.247_0.938715889806.CDS LipoP1.0:Signal CleavI 25 26 6.80431 # TSKQS|VSQCV +ORF.0.247_0.938715889806.CDS LipoP1.0:Signal CleavI 19 20 6.49651 # LVVVG|CTSKQ +ORF.0.247_0.938715889806.CDS LipoP1.0:Signal CleavI 22 23 5.34572 # VGCTS|KQSVS +ORF.0.247_0.938715889806.CDS LipoP1.0:Signal CleavI 23 24 3.96804 # GCTSK|QSVSQ +ORF.0.247_0.938715889806.CDS LipoP1.0:Signal CleavI 26 27 2.72646 # SKQSV|SQCVK +ORF.0.247_0.938715889806.CDS LipoP1.0:Signal CleavI 27 28 2.57107 # KQSVS|QCVKP +ORF.0.247_0.938715889806.CDS LipoP1.0:Signal CleavI 24 25 1.65562 # CTSKQ|SVSQC +ORF.0.247_0.938715889806.CDS LipoP1.0:Signal CleavI 17 18 1.37856 # LPLVV|VGCTS +ORF.0.247_0.938715889806.CDS LipoP1.0:Signal CleavI 21 22 -0.782641 # VVGCT|SKQSV +ORF.0.247_0.938715889806.CDS LipoP1.0:Signal CleavI 28 29 -1.09651 # QSVSQ|CVKPP +ORF.0.247_0.938715889806.CDS LipoP1.0:Signal CleavI 20 21 -2.99138 # VVVGC|TSKQS +# ORF.0.65_0.403948729686.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.65_0.403948729686.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.380_0.771335496557.CDS CYT score=-0.200913 margin=1.869487 +# Cut-off=-3 +ORF.0.380_0.771335496557.CDS LipoP1.0:Best CYT 1 1 -0.200913 +ORF.0.380_0.771335496557.CDS LipoP1.0:Margin CYT 1 1 1.869487 +ORF.0.380_0.771335496557.CDS LipoP1.0:Class TMH 1 1 -2.0704 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.391_0.169373954797.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.391_0.169373954797.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.400_0.811321232506.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.400_0.811321232506.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.260_0.577298671452.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.260_0.577298671452.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.261_0.357298653378.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.261_0.357298653378.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.268_0.501011908227.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.268_0.501011908227.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.269_0.219984821414.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.269_0.219984821414.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.278_0.44001518346.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.278_0.44001518346.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.81_0.839099082128.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.81_0.839099082128.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted +# ORF.0.87_0.518549362319.CDS CYT score=-0.200913 +# Cut-off=-3 +ORF.0.87_0.518549362319.CDS LipoP1.0:Best CYT 1 1 -0.200913 +# NO PLOT made - less than 4 putative cleavage sites predicted
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_lipop_conv/test-data/LipoToGFF_Out.gff3 Fri May 13 05:18:31 2022 +0000 @@ -0,0 +1,12 @@ +##gff-version 3 +##sequence-region testseq_2018-03-08 1 9216 +testseq_2018-03-08 cpt.fixModel gene 7852 8313 . + . ID=ORF.0.50_0.415010657017; +testseq_2018-03-08 cpt.fixModel mRNA 7852 8313 . + . ID=ORF.0.50_0.415010657017.mRNA;Parent=ORF.0.50_0.415010657017; +testseq_2018-03-08 getOrfsOrCds CDS 7852 8313 . + 0 ID=ORF.0.50_0.415010657017.CDS;Parent=ORF.0.50_0.415010657017.mRNA; +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 7839 7841 . + . ID=ORF.0.50_0.415010657017.rbs-0;Parent=ORF.0.50_0.415010657017; +testseq_2018-03-08 feature cleavage_site 7902 7903 . + . ID=ORF.0.50_0.415010657017_cleavage_1;Parent=ORF.0.50_0.415010657017; +testseq_2018-03-08 cpt.fixModel gene 8072 8254 . + . ID=ORF.0.247_0.938715889806; +testseq_2018-03-08 cpt.fixModel mRNA 8072 8254 . + . ID=ORF.0.247_0.938715889806.mRNA;Parent=ORF.0.247_0.938715889806; +testseq_2018-03-08 getOrfsOrCds CDS 8072 8254 . + 0 ID=ORF.0.247_0.938715889806.CDS;Parent=ORF.0.247_0.938715889806.mRNA; +testseq_2018-03-08 CPT_ShineFind Shine_Dalgarno_sequence 8060 8064 . + . ID=ORF.0.247_0.938715889806.rbs-0;Parent=ORF.0.247_0.938715889806; +testseq_2018-03-08 feature cleavage_site 8128 8129 . + . ID=ORF.0.247_0.938715889806_cleavage_1;Parent=ORF.0.247_0.938715889806;