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Commit message:
planemo upload commit edc74553919d09dcbe27fcadf144612c1ad3a2a2 |
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added:
cpt-macros.xml gff3.py macros.xml phage_annotation_table.py phage_annotation_table.xml phageqc_report_annotation_table.html phageqc_report_annotation_table.tsv test-data/NC_001416_Table_In.fasta test-data/NC_001416_Table_In.gff3 test-data/PhageTable_Out.html test-data/PhageTable_Out.tabular |
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removed:
cpt_annotation_table/cpt-macros.xml cpt_annotation_table/gff3.py cpt_annotation_table/macros.xml cpt_annotation_table/phage_annotation_table.py cpt_annotation_table/phage_annotation_table.xml cpt_annotation_table/phageqc_report_annotation_table.html cpt_annotation_table/phageqc_report_annotation_table.tsv cpt_annotation_table/test-data/NC_001416_Table_In.fasta cpt_annotation_table/test-data/NC_001416_Table_In.gff3 cpt_annotation_table/test-data/PhageTable_Out.html cpt_annotation_table/test-data/PhageTable_Out.tabular |
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| diff -r 6a4d1bd8ac1d -r 32e011fa615c cpt-macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt-macros.xml Wed Apr 26 03:42:32 2023 +0000 |
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| @@ -0,0 +1,115 @@ +<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> + <requirement type="package" version="1.2.2">cpt_gffparser</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@unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } +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 + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } +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> |
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| diff -r 6a4d1bd8ac1d -r 32e011fa615c cpt_annotation_table/cpt-macros.xml --- a/cpt_annotation_table/cpt-macros.xml Fri Jun 17 12:19:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,115 +0,0 @@ -<?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> |
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| diff -r 6a4d1bd8ac1d -r 32e011fa615c cpt_annotation_table/gff3.py --- a/cpt_annotation_table/gff3.py Fri Jun 17 12:19:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,346 +0,0 @@\n-import copy\n-import logging\n-\n-log = logging.getLogger()\n-log.setLevel(logging.WARN)\n-\n-\n-def feature_lambda(\n- feature_list,\n- test,\n- test_kwargs,\n- subfeatures=True,\n- parent=None,\n- invert=False,\n- recurse=True,\n-):\n- """Recursively search through features, testing each with a test function, yielding matches.\n-\n- GFF3 is a hierachical data structure, so we need to be able to recursively\n- search through features. E.g. if you\'re looking for a feature with\n- ID=\'bob.42\', you can\'t just do a simple list comprehension with a test\n- case. You don\'t know how deeply burried bob.42 will be in the feature tree. This is where feature_lambda steps in.\n-\n- :type feature_list: list\n- :param feature_list: an iterable of features\n-\n- :type test: function reference\n- :param test: a closure with the method signature (feature, **kwargs) where\n- the kwargs are those passed in the next argument. This\n- function should return True or False, True if the feature is\n- to be yielded as part of the main feature_lambda function, or\n- False if it is to be ignored. This function CAN mutate the\n- features passed to it (think "apply").\n-\n- :type test_kwargs: dictionary\n- :param test_kwargs: kwargs to pass to your closure when it is called.\n-\n- :type subfeatures: boolean\n- :param subfeatures: when a feature is matched, should just that feature be\n- yielded to the caller, or should the entire sub_feature\n- tree for that feature be included? subfeatures=True is\n- useful in cases such as searching for a gene feature,\n- and wanting to know what RBS/Shine_Dalgarno_sequences\n- are in the sub_feature tree (which can be accomplished\n- with two feature_lambda calls). subfeatures=False is\n- useful in cases when you want to process (and possibly\n- return) the entire feature tree, such as applying a\n- qualifier to every single feature.\n-\n- :type invert: boolean\n- :param invert: Negate/invert the result of the filter.\n-\n- :rtype: yielded list\n- :return: Yields a list of matching features.\n- """\n- # Either the top level set of [features] or the subfeature attribute\n- for feature in feature_list:\n- feature._parent = parent\n- if not parent:\n- # Set to self so we cannot go above root.\n- feature._parent = feature\n- test_result = test(feature, **test_kwargs)\n- # if (not invert and test_result) or (invert and not test_result):\n- if invert ^ test_result:\n- if not subfeatures:\n- feature_copy = copy.deepcopy(feature)\n- feature_copy.sub_features = list()\n- yield feature_copy\n- else:\n- yield feature\n-\n- if recurse and hasattr(feature, "sub_features"):\n- for x in feature_lambda(\n- feature.sub_features,\n- test,\n- test_kwargs,\n- subfeatures=subfeatures,\n- parent=feature,\n- invert=invert,\n- recurse=recurse,\n- ):\n- yield x\n-\n-\n-def fetchParent(feature):\n- if not hasattr(feature, "_parent") or feature._parent is None:\n- return feature\n- else:\n- return fetchParent(feature._parent)\n-\n-\n-def feature_test_true(feature, **kwargs):\n- return True\n-\n-\n-def feature_test_type(feature, **kwargs):\n- if "type" in kwargs:\n- return str(feature.type).upper() == str(kwargs["type"]).upper()\n- elif "types" in kwargs:\n- for x in kwargs["types"]:\n- if str(feature.type).upper() == str(x).upper():\n- return True\n- return False\n- raise Exception("Incorrect feature_test_type call, ne'..b'feature.location.start,\n- # feature.location.end,\n- # feature.location.strand\n- # )\n- return result\n-\n-\n-def get_gff3_id(gene):\n- return gene.qualifiers.get("Name", [gene.id])[0]\n-\n-\n-def ensure_location_in_bounds(start=0, end=0, parent_length=0):\n- # This prevents frameshift errors\n- while start < 0:\n- start += 3\n- while end < 0:\n- end += 3\n- while start > parent_length:\n- start -= 3\n- while end > parent_length:\n- end -= 3\n- return (start, end)\n-\n-\n-def coding_genes(feature_list):\n- for x in genes(feature_list):\n- if (\n- len(\n- list(\n- feature_lambda(\n- x.sub_features,\n- feature_test_type,\n- {"type": "CDS"},\n- subfeatures=False,\n- )\n- )\n- )\n- > 0\n- ):\n- yield x\n-\n-\n-def genes(feature_list, feature_type="gene", sort=False):\n- """\n- Simple filter to extract gene features from the feature set.\n- """\n-\n- if not sort:\n- for x in feature_lambda(\n- feature_list, feature_test_type, {"type": feature_type}, subfeatures=True\n- ):\n- yield x\n- else:\n- data = list(genes(feature_list, feature_type=feature_type, sort=False))\n- data = sorted(data, key=lambda feature: feature.location.start)\n- for x in data:\n- yield x\n-\n-\n-def wa_unified_product_name(feature):\n- """\n- Try and figure out a name. We gave conflicting instructions, so\n- this isn\'t as trivial as it should be. Sometimes it will be in\n- \'product\' or \'Product\', othertimes in \'Name\'\n- """\n- # Manually applied tags.\n- protein_product = feature.qualifiers.get(\n- "product", feature.qualifiers.get("Product", [None])\n- )[0]\n-\n- # If neither of those are available ...\n- if protein_product is None:\n- # And there\'s a name...\n- if "Name" in feature.qualifiers:\n- if not is_uuid(feature.qualifiers["Name"][0]):\n- protein_product = feature.qualifiers["Name"][0]\n-\n- return protein_product\n-\n-\n-def is_uuid(name):\n- return name.count("-") == 4 and len(name) == 36\n-\n-\n-def get_rbs_from(gene):\n- # Normal RBS annotation types\n- rbs_rbs = list(\n- feature_lambda(\n- gene.sub_features, feature_test_type, {"type": "RBS"}, subfeatures=False\n- )\n- )\n- rbs_sds = list(\n- feature_lambda(\n- gene.sub_features,\n- feature_test_type,\n- {"type": "Shine_Dalgarno_sequence"},\n- subfeatures=False,\n- )\n- )\n- # Fraking apollo\n- apollo_exons = list(\n- feature_lambda(\n- gene.sub_features, feature_test_type, {"type": "exon"}, subfeatures=False\n- )\n- )\n- apollo_exons = [x for x in apollo_exons if len(x) < 10]\n- # These are more NCBI\'s style\n- regulatory_elements = list(\n- feature_lambda(\n- gene.sub_features,\n- feature_test_type,\n- {"type": "regulatory"},\n- subfeatures=False,\n- )\n- )\n- rbs_regulatory = list(\n- feature_lambda(\n- regulatory_elements,\n- feature_test_quals,\n- {"regulatory_class": ["ribosome_binding_site"]},\n- subfeatures=False,\n- )\n- )\n- # Here\'s hoping you find just one ;)\n- return rbs_rbs + rbs_sds + rbs_regulatory + apollo_exons\n-\n-\n-def nice_name(record):\n- """\n- get the real name rather than NCBI IDs and so on. If fails, will return record.id\n- """\n- name = record.id\n- likely_parental_contig = list(genes(record.features, feature_type="contig"))\n- if len(likely_parental_contig) == 1:\n- name = likely_parental_contig[0].qualifiers.get("organism", [name])[0]\n- return name\n-\n-\n-def fsort(it):\n- for i in sorted(it, key=lambda x: int(x.location.start)):\n- yield i\n' |
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| diff -r 6a4d1bd8ac1d -r 32e011fa615c cpt_annotation_table/macros.xml --- a/cpt_annotation_table/macros.xml Fri Jun 17 12:19:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,23 +0,0 @@ -<?xml version="1.0"?> -<macros> - <xml name="requirements"> - <requirements> - <requirement type="package" version="3.8.13">python</requirement> - <requirement type="package" version="1.79">biopython</requirement> - <requirement type="package" version="1.2.2">cpt_gffparser</requirement> - <yield/> - </requirements> - </xml> - <xml name="genome_selector"> - <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> - </xml> - <xml name="gff3_input"> - <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> - </xml> - <token name="@GENOME_SELECTOR_PRE@"> - ln -s $genome_fasta genomeref.fa; - </token> - <token name="@GENOME_SELECTOR@"> - genomeref.fa - </token> -</macros> |
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| diff -r 6a4d1bd8ac1d -r 32e011fa615c cpt_annotation_table/phage_annotation_table.py --- a/cpt_annotation_table/phage_annotation_table.py Fri Jun 17 12:19:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,608 +0,0 @@\n-#!/usr/bin/env python\n-# vim: set fileencoding=utf-8\n-import os\n-import argparse\n-from gff3 import genes, get_gff3_id, get_rbs_from, feature_test_true, feature_lambda, feature_test_type\n-from CPT_GFFParser import gffParse, gffWrite\n-from Bio import SeqIO\n-from jinja2 import Environment, FileSystemLoader\n-import logging\n-from math import floor\n-\n-logging.basicConfig(level=logging.DEBUG)\n-log = logging.getLogger(name="pat")\n-\n-# Path to script, required because of Galaxy.\n-SCRIPT_PATH = os.path.dirname(os.path.realpath(__file__))\n-# Path to the HTML template for the report\n-\n-def genes_all(feature_list, feature_type=["gene"], sort=False):\n- """\n- Simple filter to extract gene features from the feature set.\n- """\n-\n- if not sort:\n- for x in feature_lambda(\n- feature_list, feature_test_type, {"types": feature_type}, subfeatures=True\n- ):\n- yield x\n- else:\n- data = list(genes_all(feature_list, feature_type, sort=False))\n- data = sorted(data, key=lambda feature: feature.location.start)\n- for x in data:\n- yield x\n-\n-def checkSubs(feature, qualName):\n- subFeats = []\n- res = ""\n- subFeats = feature.sub_features\n- while (len(subFeats) > 0):\n- for feat in subFeats:\n- for i in feat.qualifiers.keys():\n- for j in qualName:\n- if i == j:\n- if res == "":\n- res = feat.qualifiers[i][0]\n- else:\n- res += "; " + feat.qualifiers[i][0]\n- if res != "":\n- return res \n- tempFeats = []\n- for feat in subFeats: # Should be breadth-first results\n- for x in feat.sub_features:\n- tempFeats.append(x)\n- subFeats = tempFeats\n- return res \n-\n-def annotation_table_report(record, types, wanted_cols, gaf_data, searchSubs):\n- getTypes = []\n- for x in [y.strip() for y in types.split(",")]:\n- getTypes.append(x)\n- getTypes.append("gene")\n- sorted_features = list(genes_all(record.features, getTypes, sort=True))\n- if wanted_cols is None or len(wanted_cols.strip()) == 0:\n- return [], []\n- useSubs = searchSubs\n-\n- def rid(record, feature):\n- """Organism ID\n- """\n- return record.id\n-\n- def id(record, feature):\n- """ID\n- """\n- return feature.id\n-\n- def featureType(record, feature):\n- """Type\n- """\n- return feature.type\n-\n- def name(record, feature):\n- """Name\n- """\n- for x in ["Name", "name"]:\n- for y in feature.qualifiers.keys():\n- if x == y:\n- return feature.qualifiers[x][0]\n- if useSubs:\n- res = checkSubs(feature, ["Name", "name"])\n- if res != "":\n- return res \n- return "None"\n- def start(record, feature):\n- """Boundary\n- """\n- return str(feature.location.start + 1)\n-\n- def end(record, feature):\n- """Boundary\n- """\n- return str(feature.location.end)\n-\n- def location(record, feature):\n- """Location\n- """\n- return str(feature.location.start + 1) + "..{0.end}".format(feature.location)\n-\n- def length(record, feature):\n- """CDS Length (AA)\n- """\n- \n- if feature.type == "CDS":\n- cdss = [feature]\n- else:\n- cdss = list(genes(feature.sub_features, feature_type="CDS", sort=True))\n- \n- if cdss == []:\n- return "None"\n- res = (sum([len(cds) for cds in cdss]) / 3) - 1\n- if floor(res) == res:\n- res = int(res)\n- return str(res)\n-\n- def notes(record, feature):\n- """User entered Notes"""\n- for x in ["Note", "note", "Notes", "notes"]:\n- for y in feature.qualifiers.keys():\n- if x == y:\n- return feature.qualifiers[x][0]\n- if useSubs:\n- res = checkSubs(feature, ["Note", "note", "Notes", "notes"])\n- '..b'- # \'10d04a01-5ed8-49c8-b724-d6aa4df5a98d\': {\n- # \'annotation_extension\': \'\',\n- # \'aspect\': \'\',\n- # \'assigned_by\': \'CPT\',\n- # \'date\': \'2017-05-04T16:25:22.161916Z\',\n- # \'db\': \'UniProtKB\',\n- # \'db_reference\': \'GO_REF:0000100\',\n- # \'evidence_code\': \'ISA\',\n- # \'gene\': \'0d307196-833d-46e8-90e9-d80f7a041d88\',\n- # \'go_id\': \'GO:0039660\',\n- # \'go_term\': \'structural constituent of virion\',\n- # \'id\': \'10d04a01-5ed8-49c8-b724-d6aa4df5a98d\',\n- # \'notes\': \'hit was putative minor structural protein\',\n- # \'owner\': \'amarc1@tamu.edu\',\n- # \'with_or_from\': \'UNIREF90:B2ZYZ7\'\n- # },\n- for row in file:\n- if row.startswith("#"):\n- # Header\n- cols = (\n- row.strip().replace("# ", "").replace("GO Term", "go_term").split("\\t")\n- )\n- else:\n- line = row.strip().split("\\t")\n- tmp = dict(zip(cols, line))\n- if "gene" not in tmp.keys():\n- continue\n- if tmp["gene"] not in data:\n- data[tmp["gene"]] = []\n-\n- data[tmp["gene"]].append(tmp)\n- return data\n-\n-\n-def evaluate_and_report(\n- annotations,\n- genome,\n- types="gene",\n- reportTemplateName="phage_annotation_validator.html",\n- annotationTableCols="",\n- gafData=None,\n- searchSubs = False,\n-):\n- """\n- Generate our HTML evaluation of the genome\n- """\n- # Get features from GFF file\n- seq_dict = SeqIO.to_dict(SeqIO.parse(genome, "fasta"))\n- # Get the first GFF3 record\n- # TODO: support multiple GFF3 files.\n- at_table_data = []\n- gaf = {}\n- if gafData:\n- gaf = parseGafData(gafData)\n-\n- for record in gffParse(annotations, base_dict=seq_dict):\n- if reportTemplateName.endswith(".html"):\n- record.id = record.id.replace(".", "-")\n- log.info("Producing an annotation table for %s" % record.id)\n- annotation_table_data, annotation_table_col_names = annotation_table_report(\n- record, types, annotationTableCols, gaf, searchSubs\n- )\n- at_table_data.append((record, annotation_table_data))\n- # break\n-\n- # This is data that will go into our HTML template\n- kwargs = {\n- "annotation_table_data": at_table_data,\n- "annotation_table_col_names": annotation_table_col_names,\n- }\n-\n- env = Environment(\n- loader=FileSystemLoader(SCRIPT_PATH), trim_blocks=True, lstrip_blocks=True\n- )\n- if reportTemplateName.endswith(".html"):\n- env.filters["nice_id"] = str(get_gff3_id).replace(".", "-")\n- else:\n- env.filters["nice_id"] = get_gff3_id\n-\n- def join(listy):\n- return "\\n".join(listy)\n-\n- env.filters.update({"join": join})\n- tpl = env.get_template(reportTemplateName)\n- return tpl.render(**kwargs).encode("utf-8")\n-\n-\n-if __name__ == "__main__":\n- parser = argparse.ArgumentParser(\n- description="rebase gff3 features against parent locations", epilog=""\n- )\n- parser.add_argument(\n- "annotations", type=argparse.FileType("r"), help="Parent GFF3 annotations"\n- )\n- parser.add_argument("genome", type=argparse.FileType("r"), help="Genome Sequence")\n-\n- parser.add_argument(\n- "--types",\n- help="Select extra types to display in output (Will always include gene)",\n- )\n-\n- parser.add_argument(\n- "--reportTemplateName",\n- help="Report template file name",\n- default="phageqc_report_full.html",\n- )\n- parser.add_argument(\n- "--annotationTableCols",\n- help="Select columns to report in the annotation table output format",\n- )\n- parser.add_argument(\n- "--gafData", help="CPT GAF-like table", type=argparse.FileType("r")\n- )\n- parser.add_argument(\n- "--searchSubs", help="Attempt to populate fields from sub-features if qualifier is empty", action="store_true"\n- )\n-\n- args = parser.parse_args()\n-\n- print(evaluate_and_report(**vars(args)).decode("utf-8"))\n' |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c cpt_annotation_table/phage_annotation_table.xml --- a/cpt_annotation_table/phage_annotation_table.xml Fri Jun 17 12:19:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,112 +0,0 @@ -<?xml version="1.0"?> -<tool id="edu.tamu.cpt2.phage.annotation_table" name="Annotation Table" version="20.0.0.1"> - <description>from gff3 formatted datasets</description> - <macros> - <import>macros.xml</import> - <import>cpt-macros.xml</import> - </macros> - <expand macro="requirements"> - <requirement type="package" version="2.10.1">jinja2</requirement> - </expand> - <command detect_errors="aggressive"><![CDATA[ -@GENOME_SELECTOR_PRE@ - -python $__tool_directory__/phage_annotation_table.py -$gff3_data -@GENOME_SELECTOR@ ---types "$extraTypes" ---reportTemplateName "$report_format" ---annotationTableCols "$cols,$gaf_cols" -#if $gaf_data: ---gafData "$gaf_data" -#end if -$checkSubfeats -> $output]]></command> - <inputs> - <expand macro="gff3_input" /> - <expand macro="genome_selector" /> - <param label="Extra sub-feature types to include (Comma-separated, Will always include gene)" optional="True" name="extraTypes" type="text" value =""/> - <param label="Columns" type="select" name="cols" multiple="True"> - <option value="rid" selected="true">Record ID</option> - <option value="id" selected="true">ID</option> - <option value="type" selected="true">Type</option> - <option value="name" selected="true">Name</option> - - <option value="location" selected="true">Location</option> - <option value="start" selected="true">Feature Start</option> - <option value="end" selected="true">Feature End</option> - <option value="strand" selected="true">Strand</option> - <option value="length" selected="true">Length</option> - - <option value="sd_seq" selected="true">SD sequence</option> - <option value="sd_spacing" selected="true">SD spacing</option> - <option value="start_codon" selected="true">Start codon</option> - <option value="stop_codon" selected="true">Stop codon</option> - - <option value="ig_dist" selected="true">Distance to next upstream feature</option> - <option value="upstream_feature__name" selected="true">Name of upstream feature</option> - - <option value="owner" selected="true">Owner</option> - <option value="date_created" selected="true">Date created</option> - <option value="date_last_modified" selected="true">Date last modified</option> - - <option value="notes" selected="true">Notes</option> - <option value="description" selected="true">Description</option> - <option value="product" selected="true">Product</option> - <option value="dbxrefs" selected="true">DBxrefs</option> - <option value="qualifiers" selected="true">Qualifiers</option> - </param> - - <param label="GAF Data" name="gaf_data" type="data" format="tabular" optional="True" - help="Optional GAF Data Table. This usually comes from the CPT CACAO GAF Data Export tool. The [GAF] Columns below are ONLY available when this data is populated."/> - <param label="GAF Columns" type="select" name="gaf_cols" multiple="True"> - <!-- GAF Specific Fields --> - <option value="gaf_annotation_extension" selected="false">GAF Annotation Extension</option> - <option value="gaf_aspect" selected="false">GAF Aspect</option> - <option value="gaf_assigned_by" selected="false">GAF Assigned By</option> - <option value="gaf_date" selected="false">GAF Date</option> - <option value="gaf_db" selected="false">GAF DB</option> - <option value="gaf_db_reference" selected="false">GAF DB Reference</option> - <option value="gaf_evidence_code" selected="false">GAF Evidence Code</option> - <option value="gaf_gene" selected="false">GAF Gene</option> - <option value="gaf_go_id" selected="false">GAF GO ID</option> - <option value="gaf_go_term" selected="false">GAF GO Term</option> - <option value="gaf_id" selected="false">GAF ID</option> - <option value="gaf_notes" selected="false">GAF Notes</option> - <option value="gaf_owner" selected="false">GAF Owner</option> - <option value="gaf_with_or_from" selected="false">GAF with_or_from</option> - </param> - <param name="checkSubfeats" label="Search sub-features for fields if gene does not define them" type="boolean" truevalue="--searchSubs" falsevalue=""/> - <param label="Report Format" type="select" name="report_format"> - <option value="phageqc_report_annotation_table.html" selected="true">HTML Table</option> - <option value="phageqc_report_annotation_table.tsv">Tabular (Excel Compatible) Table</option> - </param> - </inputs> - <outputs> - <data format="html" name="output"> - <change_format> - <when format="tabular" input="report_format" value="phageqc_report_annotation_table.tsv"/> - </change_format> - </data> - </outputs> - <tests> - <test> - <param name="reference_genome_source" value="history" /> - <param name="genome_fasta" value="NC_001416_Table_In.fasta" /> - <param name="gff3_data" value="NC_001416_Table_In.gff3" /> - <param name="report_format" value="phageqc_report_annotation_table.html" /> - <output name="output" file="PhageTable_Out.html" /> - </test> - <test> - <param name="reference_genome_source" value="history" /> - <param name="genome_fasta" value="NC_001416_Table_In.fasta" /> - <param name="gff3_data" value="NC_001416_Table_In.gff3" /> - <param name="report_format" value="phageqc_report_annotation_table.tsv" /> - <output name="output" file="PhageTable_Out.tabular" /> - </test> - </tests> - <help><![CDATA[ -Generate an "annotation table" of a genome, with user-configurable data columns -]]></help> - <expand macro="citations" /> -</tool> |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c cpt_annotation_table/phageqc_report_annotation_table.html --- a/cpt_annotation_table/phageqc_report_annotation_table.html Fri Jun 17 12:19:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,244 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> - <meta http-equiv="X-UA-Compatible" content="IE=edge"> - <meta name="viewport" content="width=device-width, initial-scale=1"> - <!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags --> - <meta name="description" content=""> - <meta name="author" content=""> - <title>Annotation Table</title> - <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.2/jquery.min.js"></script> - <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" crossorigin="anonymous"> - <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap-theme.min.css" crossorigin="anonymous"> - <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/js/bootstrap.min.js" crossorigin="anonymous"></script> - - <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.11/css/jquery.dataTables.css"> - <script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/1.10.11/js/jquery.dataTables.js"></script> - <style type="text/css"> -/* - * Base structure - */ - -/* Move down content because we have a fixed navbar that is 50px tall */ -body { - padding-top: 50px; -} - -h3:before { - display: block; - content: " "; - margin-top: -50px; - height: 50px; - visibility: hidden; -} - -/* - * Global add-ons - */ - -.sub-header { - padding-bottom: 10px; - border-bottom: 1px solid #eee; -} - -/* - * Top navigation - * Hide default border to remove 1px line. - */ -.navbar-fixed-top { - border: 0; -} - -/* - * Sidebar - */ - -/* Hide for mobile, show later */ -.sidebar { - display: none; -} -@media (min-width: 768px) { - .sidebar { - position: fixed; - top: 51px; - bottom: 0; - left: 0; - z-index: 1000; - display: block; - padding: 20px; - overflow-x: hidden; - overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */ - background-color: #f5f5f5; - border-right: 1px solid #eee; - } -} - -/* Sidebar navigation */ -.nav-sidebar { - margin-right: -21px; /* 20px padding + 1px border */ - margin-bottom: 20px; - margin-left: -20px; -} -.nav-sidebar > li > a { - padding-right: 20px; - padding-left: 20px; -} -.nav-sidebar > .active > a, -.nav-sidebar > .active > a:hover, -.nav-sidebar > .active > a:focus { - color: #fff; - background-color: #428bca; -} - - -/* - * Main content - */ - -.main { - padding: 20px; -} -@media (min-width: 768px) { - .main { - padding-right: 40px; - padding-left: 40px; - } -} -.main .page-header { - margin-top: 0; -} - - -/* - * Placeholder dashboard ideas - */ - -.placeholders { - margin-bottom: 30px; - text-align: center; -} -.placeholders h4 { - margin-bottom: 0; -} -.placeholder { - margin-bottom: 20px; -} -.placeholder img { - display: inline-block; - border-radius: 50%; -} - -td.moron { - font-size: 150%; - padding: 0px; - color: gray; -} -.strand_emph { - text-decoration: underline; - color: black; -} - - </style> - <!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries --> - <!--[if lt IE 9]> - <script src="//oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script> - <script src="//oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> - <![endif]--> - </head> - <body> - - <nav class="navbar navbar-inverse navbar-fixed-top"> - <div class="container-fluid"> - <div class="navbar-header"> - <a class="navbar-brand" href="#">Annotation Table</a> - </div> - </div> - </nav> - - <div class="container-fluid"> - <div class="row"> - <div class="col-md-12 main" id="main"> - <ul class="nav nav-tabs" role="tablist" id="myTabs"> - <li role="presentation" class="active"><a href="#overview" role="tab" data-toggle="tab">Overview</a></li> - {% for (record, data) in annotation_table_data %} - <li role="presentation"><a href="#{{ record.id }}" role="tab" data-toggle="tab">{{ record.id }}</a></li> - {% endfor %} - </ul> - - <!-- Tab panes --> - <div class="tab-content"> - <div role="tabpanel" class="tab-pane active" id="overview"> - Data on each organism will be accessible from the tabs above. - </div> - {% for (record, data) in annotation_table_data %} - <div role="tabpanel" class="tab-pane" id="{{ record.id }}"> - <table class="table table-striped" id="data"> - <thead> - <tr> - {% for col in annotation_table_col_names %} - <th>{{ col[0] }}</th> - {% endfor %} - </tr> - </thead> - <tbody> - {% for row in data %} - <tr> - {% for col in row %} - <td>{% if col is not string %}<ul>{% for val in col %}<li>{{ val }}</li>{% endfor %}</ul>{% else %}{{ col }}{% endif %}</td> - {% endfor %} - </tr> - {% endfor %} - </tbody> - </table> - </div> - {% endfor %} - </div> - </div> - </div> - </div> - - <script type="text/javascript"> - $(document).ready( function () { - - - -$('#myTabs a').click(function (e) { - e.preventDefault() - $(this).tab('show') -}) - - - -jQuery.fn.dataTable.ext.type.detect.unshift( function ( data ) { - if ( typeof data !== 'string' ) { - return null; - } - - var matches = data.match(/^(\d+)\.\.(\d+)/); - return matches ? 'genomic' : null; -} ); - - - -jQuery.extend( jQuery.fn.dataTableExt.oSort, { - "genomic-pre": function ( a ) { - var matches = a.match(/^(\d+)\.\.(\d+)/); - console.log(a + " " + matches[1]); - return parseInt(matches[1]); - }, - - "genomic-asc": function ( a, b ) { - return ((a < b) ? -1 : ((a > b) ? 1 : 0)); - }, - - "genomic-desc": function ( a, b ) { - return ((a < b) ? 1 : ((a > b) ? -1 : 0)); - } -} ); - - $('table').DataTable(); - }); - </script> - </body> -</html> |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c cpt_annotation_table/phageqc_report_annotation_table.tsv --- a/cpt_annotation_table/phageqc_report_annotation_table.tsv Fri Jun 17 12:19:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,8 +0,0 @@ -{% for (record, dataset) in annotation_table_data %} -# {% for col in annotation_table_col_names %}{{ col[0] }} {% endfor %} -{% for row in dataset %} - -{% for col in row %} -{% if col is not string %}"{{ col | join }}"{% else %}{{ col }}{% endif %} {% endfor %} -{% endfor %} -{% endfor %} |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c cpt_annotation_table/test-data/NC_001416_Table_In.fasta --- a/cpt_annotation_table/test-data/NC_001416_Table_In.fasta Fri Jun 17 12:19:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,810 +0,0 @@\n->NC_001416.1_phage_lambda\n-GGGCGGCGACCTCGCGGGTTTTCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCG\n-TTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACG\n-ACAGGTGCTGAAAGCGAGGCTTTTTGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGTCCGT\n-GGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGACATTTTCGGTGCGAGTATCCG\n-TACCATTCAGAACTGGCAGGAACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTAA\n-TGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAAT\n-TGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCGGCAGGCCAGCGAGGCAGATCT\n-CCAGCCAGGAACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGACGCACA\n-GGAACTGAAGAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGT\n-GCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGCTCCCCCTGTCGGTGCA\n-GCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAA\n-AGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATAT\n-CGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCA\n-GGCCGGAGCCACAGACCGCCGTTGAATGGGCGGATGCTAATTACTATCTCCCGAAAGAAT\n-CCGCATACCAGGAAGGGCGCTGGGAAACACTGCCCTTTCAGCGGGCCATCATGAATGCGA\n-TGGGCAGCGACTACATCCGTGAGGTGAATGTGGTGAAGTCTGCCCGTGTCGGTTATTCCA\n-AAATGCTGCTGGGTGTTTATGCCTACTTTATAGAGCATAAGCAGCGCAACACCCTTATCT\n-GGTTGCCGACGGATGGTGATGCCGAGAACTTTATGAAAACCCACGTTGAGCCGACTATTC\n-GTGATATTCCGTCGCTGCTGGCGCTGGCCCCGTGGTATGGCAAAAAGCACCGGGATAACA\n-CGCTCACCATGAAGCGTTTCACTAATGGGCGTGGCTTCTGGTGCCTGGGCGGTAAAGCGG\n-CAAAAAACTACCGTGAAAAGTCGGTGGATGTGGCGGGTTATGATGAACTTGCTGCTTTTG\n-ATGATGATATTGAACAGGAAGGCTCTCCGACGTTCCTGGGTGACAAGCGTATTGAAGGCT\n-CGGTCTGGCCAAAGTCCATCCGTGGCTCCACGCCAAAAGTGAGAGGCACCTGTCAGATTG\n-AGCGTGCAGCCAGTGAATCCCCGCATTTTATGCGTTTTCATGTTGCCTGCCCGCATTGCG\n-GGGAGGAGCAGTATCTTAAATTTGGCGACAAAGAGACGCCGTTTGGCCTCAAATGGACGC\n-CGGATGACCCCTCCAGCGTGTTTTATCTCTGCGAGCATAATGCCTGCGTCATCCGCCAGC\n-AGGAGCTGGACTTTACTGATGCCCGTTATATCTGCGAAAAGACCGGGATCTGGACCCGTG\n-ATGGCATTCTCTGGTTTTCGTCATCCGGTGAAGAGATTGAGCCACCTGACAGTGTGACCT\n-TTCACATCTGGACAGCGTACAGCCCGTTCACCACCTGGGTGCAGATTGTCAAAGACTGGA\n-TGAAAACGAAAGGGGATACGGGAAAACGTAAAACCTTCGTAAACACCACGCTCGGTGAGA\n-CGTGGGAGGCGAAAATTGGCGAACGTCCGGATGCTGAAGTGATGGCAGAGCGGAAAGAGC\n-ATTATTCAGCGCCCGTTCCTGACCGTGTGGCTTACCTGACCGCCGGTATCGACTCCCAGC\n-TGGACCGCTACGAAATGCGCGTATGGGGATGGGGGCCGGGTGAGGAAAGCTGGCTGATTG\n-ACCGGCAGATTATTATGGGCCGCCACGACGATGAACAGACGCTGCTGCGTGTGGATGAGG\n-CCATCAATAAAACCTATACCCGCCGGAATGGTGCAGAAATGTCGATATCCCGTATCTGCT\n-GGGATACTGGCGGGATTGACCCGACCATTGTGTATGAACGCTCGAAAAAACATGGGCTGT\n-TCCGGGTGATCCCCATTAAAGGGGCATCCGTCTACGGAAAGCCGGTGGCCAGCATGCCAC\n-GTAAGCGAAACAAAAACGGGGTTTACCTTACCGAAATCGGTACGGATACCGCGAAAGAGC\n-AGATTTATAACCGCTTCACACTGACGCCGGAAGGGGATGAACCGCTTCCCGGTGCCGTTC\n-ACTTCCCGAATAACCCGGATATTTTTGATCTGACCGAAGCGCAGCAGCTGACTGCTGAAG\n-AGCAGGTCGAAAAATGGGTGGATGGCAGGAAAAAAATACTGTGGGACAGCAAAAAGCGAC\n-GCAATGAGGCACTCGACTGCTTCGTTTATGCGCTGGCGGCGCTGCGCATCAGTATTTCCC\n-GCTGGCAGCTGGATCTCAGTGCGCTGCTGGCGAGCCTGCAGGAAGAGGATGGTGCAGCAA\n-CCAACAAGAAAACACTGGCAGATTACGCCCGTGCCTTATCCGGAGAGGATGAATGACGCG\n-ACAGGAAGAACTTGCCGCTGCCCGTGCGGCACTGCATGACCTGATGACAGGTAAACGGGT\n-GGCAACAGTACAGAAAGACGGACGAAGGGTGGAGTTTACGGCCACTTCCGTGTCTGACCT\n-GAAAAAATATATTGCAGAGCTGGAAGTGCAGACCGGCATGACACAGCGACGCAGGGGACC\n-TGCAGGATTTTATGTATGAAAACGCCCACCATTCCCACCCTTCTGGGGCCGGACGGCATG\n-ACATCGCTGCGCGAATATGCCGGTTATCACGGCGGTGGCAGCGGATTTGGAGGGCAGTTG\n-CGGTCGTGGAACCCACCGAGTGAAAGTGTGGATGCAGCCCTGTTGCCCAACTTTACCCGT\n-GGCAATGCCCGCGCAGACGATCTGGTACGCAATAACGGCTATGCCGCCAACGCCATCCAG\n-CTGCATCAGGATCATATCGTCGGGTCTTTTTTCCGGCTCAGTCATCGCCCAAGCTGGCGC\n-TATCTGGGCATCGGGGAGGAAGAAGCCCGTGCCTTTTCCCGCGAGGTTGAAGCGGCATGG\n-AAAGAGTTTGCCGAGGATGACTGCTGCTGCATTGACGTTGAGCGAAAACGCACGTTTACC\n-ATGATGATTCGGGAAGGTGTGGCCATGCACGCCTTTAACGGTGAACTGTTCGTTCAGGCC\n-ACCTGGGATACCAGTTCGTCGCGGCTTTTCCGGACACAGTTCCGGATGGTCAGCCCGAAG\n-CGCATCAGCAACCCGAACAATACCGGCGACAGCCGGAACTGCCGTGCCGGTGTGCAGATT\n-AATGACAGCGGTGCGGCGCTGGGATATTACGTCAGCGAGGACGGGTATCCTGGCTGGATG\n-CCGCAGAAATGGACATGGATACCCCGTGAGTTACCCGGCGGGCGCGCCTCGTTCATTCAC\n-GTTTTTGAACCCGTGGAGGACGGGCAGACTCGCGGTGCAAATGTGTTTTACAGCGTGATG\n-GAGCAGATGAAGATGCTCGACACGCTGCAGAACACGCAGCTGCAGAGCGCCATTGTGAAG\n-GCGATGTATGCCGCCACCATTGAGAGTGAGCTGGATACGCAGTCAGCGATGGATTTTATT\n-CTGGGCGCGAACAGTCAGGAGCAGCGGGAAAGGCTGACCGGCTGGATTGGTGAAATTGCC\n-GCGTATTACGCCGCAGCGCCGGTCCGGCTGGGAGGCGCAAAAGTACC'..b'CGCTTA\n-CTACCGATTCCGCCTAGTTGGTCACTTCGACGTATCGTCTGGAACTCCAACCATCGCAGG\n-CAGAGAGGTCTGCAAAATGCAATCCCGAAACAGTTCGCAGGTAATAGTTAGAGCCTGCAT\n-AACGGTTTCGGGATTTTTTATATCTGCACAACAGGTAAGAGCATTGAGTCGATAATCGTG\n-AAGAGTCGGCGAGCCTGGTTAGCCAGTGCTCTTTCCGTTGTGCTGAATTAAGCGAATACC\n-GGAAGCAGAACCGGATCACCAAATGCGTACAGGCGTCATCGCCGCCCAGCAACAGCACAA\n-CCCAAACTGAGCCGTAGCCACTGTCTGTCCTGAATTCATTAGTAATAGTTACGCTGCGGC\n-CTTTTACACATGACCTTCGTGAAAGCGGGTGGCAGGAGGTCGCGCTAACAACCTCCTGCC\n-GTTTTGCCCGTGCATATCGGTCACGAACAAATCTGATTACTAAACACAGTAGCCTGGATT\n-TGTTCTATCAGTAATCGACCTTATTCCTAATTAAATAGAGCAAATCCCCTTATTGGGGGT\n-AAGACATGAAGATGCCAGAAAAACATGACCTGTTGGCCGCCATTCTCGCGGCAAAGGAAC\n-AAGGCATCGGGGCAATCCTTGCGTTTGCAATGGCGTACCTTCGCGGCAGATATAATGGCG\n-GTGCGTTTACAAAAACAGTAATCGACGCAACGATGTGCGCCATTATCGCCTGGTTCATTC\n-GTGACCTTCTCGACTTCGCCGGACTAAGTAGCAATCTCGCTTATATAACGAGCGTGTTTA\n-TCGGCTACATCGGTACTGACTCGATTGGTTCGCTTATCAAACGCTTCGCTGCTAAAAAAG\n-CCGGAGTAGAAGATGGTAGAAATCAATAATCAACGTAAGGCGTTCCTCGATATGCTGGCG\n-TGGTCGGAGGGAACTGATAACGGACGTCAGAAAACCAGAAATCATGGTTATGACGTCATT\n-GTAGGCGGAGAGCTATTTACTGATTACTCCGATCACCCTCGCAAACTTGTCACGCTAAAC\n-CCAAAACTCAAATCAACAGGCGCCGGACGCTACCAGCTTCTTTCCCGTTGGTGGGATGCC\n-TACCGCAAGCAGCTTGGCCTGAAAGACTTCTCTCCGAAAAGTCAGGACGCTGTGGCATTG\n-CAGCAGATTAAGGAGCGTGGCGCTTTACCTATGATTGATCGTGGTGATATCCGTCAGGCA\n-ATCGACCGTTGCAGCAATATCTGGGCTTCACTGCCGGGCGCTGGTTATGGTCAGTTCGAG\n-CATAAGGCTGACAGCCTGATTGCAAAATTCAAAGAAGCGGGCGGAACGGTCAGAGAGATT\n-GATGTATGAGCAGAGTCACCGCGATTATCTCCGCTCTGGTTATCTGCATCATCGTCTGCC\n-TGTCATGGGCTGTTAATCATTACCGTGATAACGCCATTACCTACAAAGCCCAGCGCGACA\n-AAAATGCCAGAGAACTGAAGCTGGCGAACGCGGCAATTACTGACATGCAGATGCGTCAGC\n-GTGATGTTGCTGCGCTCGATGCAAAATACACGAAGGAGTTAGCTGATGCTAAAGCTGAAA\n-ATGATGCTCTGCGTGATGATGTTGCCGCTGGTCGTCGTCGGTTGCACATCAAAGCAGTCT\n-GTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGAC\n-TGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAA\n-AACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGTTGCCCATATC\n-GATGGGCAACTCATGCAATTATTGTGAGCAATACACACGCGCTTCCAGCGGAGTATAAAT\n-GCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAAC\n-AACATTTTCTGCGCCGCCACAAATTTTGGCTGCATCGACAGTTTTCTTCTGCCCAATTCC\n-AGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTG\n-AACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAG\n-CATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGA\n-AAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTA\n-TGTCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGG\n-GGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAACGATGCACACAGGGTTTAGCGCG\n-TACACGTATTGCATTATGCCAACGCCCCGGTGCTGACACGGAAGAAACCGGACGTTATGA\n-TTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTAT\n-CAAAGGTATAGTAATATCTTTTATGTTCATGGATATTTGTAACCCATCGGAAAACTCCTG\n-CTTTAGCAAGATTTTCCCTGTATTGCTGAAATGTGATTTCTCTTGATTTCAACCTATCAT\n-AGGACGTTTCTATAAGATGCGTGTTTCTTGAGAATTTAACATTTACAACCTTTTTAAGTC\n-CTTTTATTAACACGGTGTTATCGTTTTCTAACACGATGTGAATATTATCTGTGGCTAGAT\n-AGTAAATATAATGTGAGACGTTGTGACGTTTTAGTTCAGAATAAAACAATTCACAGTCTA\n-AATCTTTTCGCACTTGATCGAATATTTCTTTAAAAATGGCAACCTGAGCCATTGGTAAAA\n-CCTTCCATGTGATACGAGGGCGCGTAGTTTGCATTATCGTTTTTATCGTTTCAATCTGGT\n-CTGACCTCCTTGTGTTTTGTTGATGATTTATGTCAAATATTAGGAATGTTTTCACTTAAT\n-AGTATTGGTTGCGTAACAAAGTGCGGTCCTGCTGGCATTCTGGAGGGAAATACAACCGAC\n-AGATGTATGTAAGGCCAACGTGCTCAAATCTTCATACAGAAAGATTTGAAGTAATATTTT\n-AACCGCTAGATGAAGAGCAAGCGCATGGAGCGACAAAATGAATAAAGAACAATCTGCTGA\n-TGATCCCTCCGTGGATCTGATTCGTGTAAAAAATATGCTTAATAGCACCATTTCTATGAG\n-TTACCCTGATGTTGTAATTGCATGTATAGAACATAAGGTGTCTCTGGAAGCATTCAGAGC\n-AATTGAGGCAGCGTTGGTGAAGCACGATAATAATATGAAGGATTATTCCCTGGTGGTTGA\n-CTGATCACCATAACTGCTAATCATTCAAACTATTTAGTCTGTGACAGAGCCAACACGCAG\n-TCTGTCACTGTCAGGAAAGTGGTAAAACTGCAACTCAATTACTGCAATGCCCTCGTAATT\n-AAGTGAATTTACAATATCGTCCTGTTCGGAGGGAAGAACGCGGGATGTTCATTCTTCATC\n-ACTTTTAATTGATGTATATGCTCTCTTTTCTGACGTTAGTCTCCGACGGCAGGCTTCAAT\n-GACCCAGGCTGAGAAATTCCCGGACCCTTTTTGCTCAAGAGCGATGTTAATTTGTTCAAT\n-CATTTGGTTAGGAAAGCGGATGTTGCGGGTTGTTGTTCTGCGGGTTCTGTTCTTCGTTGA\n-CATGAGGTTGCCCCGTATTCAGTGTCGCTGATTTGTATTGTCTGAAGTTGTTTTTACGTT\n-AAGTTGATGCAGATCAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTT\n-GATGGCCTCCACGCACGTTGTGATATGTAGATGATAATCATTATCACTTTACGGGTCCTT\n-TCCGGTGATCCGACAGGTTACG\n' |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c cpt_annotation_table/test-data/NC_001416_Table_In.gff3 --- a/cpt_annotation_table/test-data/NC_001416_Table_In.gff3 Fri Jun 17 12:19:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,476 +0,0 @@\n-##gff-version 3\n-##sequence-region NC_001416.1_phage_lambda 1 48502\n-NC_001416.1_phage_lambda\t.\tgene\t14261\t14875\t.\t+\t.\towner=jolenerr@tamu.edu;ID=cdb58372-2440-4e07-bcc4-739e0aba461f;date_last_modified=2020-05-27;Name=tail tip assembly protein K;date_creation=2020-05-13\n-NC_001416.1_phage_lambda\t.\tmRNA\t14261\t14875\t.\t+\t.\towner=jolenerr@tamu.edu;Parent=cdb58372-2440-4e07-bcc4-739e0aba461f;ID=c53587ff-12d9-4a3a-a7ac-e87e54c5232b;date_last_modified=2020-05-27;Name=tail tip assembly protein K;date_creation=2020-05-13\n-NC_001416.1_phage_lambda\t.\tCDS\t14276\t14875\t.\t+\t0\tParent=c53587ff-12d9-4a3a-a7ac-e87e54c5232b;ID=2d4171c3-93b5-4c30-afba-9a0969dd4a6f;Name=2d4171c3-93b5-4c30-afba-9a0969dd4a6f\n-NC_001416.1_phage_lambda\t.\texon\t14276\t14875\t.\t+\t.\tParent=c53587ff-12d9-4a3a-a7ac-e87e54c5232b;ID=782a319b-3988-4cb2-aedf-47242382005c;Name=782a319b-3988-4cb2-aedf-47242382005c\n-NC_001416.1_phage_lambda\t.\texon\t14261\t14265\t.\t+\t.\tParent=c53587ff-12d9-4a3a-a7ac-e87e54c5232b;ID=709a9728-db34-4010-bfc3-41b0687edb80;Name=709a9728-db34-4010-bfc3-41b0687edb80\n-###\n-NC_001416.1_phage_lambda\t.\tgene\t47727\t47944\t.\t+\t.\towner=jolenerr@tamu.edu;ID=e3d29177-18a8-4bc0-8d91-15e5760f3bd3;date_last_modified=2020-05-13;Name=NC_001416.1_phage_lambda.gene_60;date_creation=2020-05-13\n-NC_001416.1_phage_lambda\t.\tmRNA\t47727\t47944\t.\t+\t.\towner=jolenerr@tamu.edu;Parent=e3d29177-18a8-4bc0-8d91-15e5760f3bd3;ID=90e550aa-f463-46d2-bec4-87aa38e63ee2;date_last_modified=2020-05-13;Name=NC_001416.1_phage_lambda.gene_60-00001;date_creation=2020-05-13\n-NC_001416.1_phage_lambda\t.\tCDS\t47738\t47944\t.\t+\t0\tParent=90e550aa-f463-46d2-bec4-87aa38e63ee2;ID=586909d5-f3a6-44bb-8e9e-5a5230b2127a;Name=586909d5-f3a6-44bb-8e9e-5a5230b2127a\n-NC_001416.1_phage_lambda\t.\texon\t47727\t47730\t.\t+\t.\tParent=90e550aa-f463-46d2-bec4-87aa38e63ee2;ID=bf5e1837-0469-4372-9652-7677fee29843;Name=bf5e1837-0469-4372-9652-7677fee29843\n-NC_001416.1_phage_lambda\t.\texon\t47738\t47944\t.\t+\t.\tParent=90e550aa-f463-46d2-bec4-87aa38e63ee2;ID=14232a86-ebfe-4f10-aa28-2910207542f7;Name=14232a86-ebfe-4f10-aa28-2910207542f7\n-###\n-NC_001416.1_phage_lambda\t.\tgene\t13416\t14127\t.\t+\t.\towner=jolenerr@tamu.edu;ID=11a10b01-003c-4900-aae9-46139ae23652;date_last_modified=2020-05-27;Name=tail tip protein L;date_creation=2020-05-13\n-NC_001416.1_phage_lambda\t.\tmRNA\t13416\t14127\t.\t+\t.\towner=jolenerr@tamu.edu;Parent=11a10b01-003c-4900-aae9-46139ae23652;ID=07cc76d7-d0f4-447f-a851-3aeaee1b71ac;date_last_modified=2020-05-27;Name=tail tip protein L;date_creation=2020-05-13\n-NC_001416.1_phage_lambda\t.\tCDS\t13429\t14127\t.\t+\t0\tParent=07cc76d7-d0f4-447f-a851-3aeaee1b71ac;ID=37a2e1ad-d49c-43d3-b33b-727c848e2a38;Name=37a2e1ad-d49c-43d3-b33b-727c848e2a38\n-NC_001416.1_phage_lambda\t.\texon\t13429\t14127\t.\t+\t.\tParent=07cc76d7-d0f4-447f-a851-3aeaee1b71ac;ID=008fa66b-e5b3-489b-8d99-208103afde8f;Name=008fa66b-e5b3-489b-8d99-208103afde8f\n-NC_001416.1_phage_lambda\t.\texon\t13416\t13419\t.\t+\t.\tParent=07cc76d7-d0f4-447f-a851-3aeaee1b71ac;ID=0a4ad3d9-21dc-4fab-badb-a94e4493c397;Name=0a4ad3d9-21dc-4fab-badb-a94e4493c397\n-###\n-NC_001416.1_phage_lambda\t.\tgene\t19641\t20855\t.\t+\t.\towner=jolenerr@tamu.edu;ID=e7267f7d-4717-4e28-a1a0-564b10661248;date_last_modified=2020-05-27;Name=tail fiber protein stf;date_creation=2020-05-13\n-NC_001416.1_phage_lambda\t.\tmRNA\t19641\t20855\t.\t+\t.\towner=jolenerr@tamu.edu;Parent=e7267f7d-4717-4e28-a1a0-564b10661248;ID=b7a5dc48-88c5-4edc-9081-091ef39ff3ea;date_last_modified=2020-05-27;Name=tail fiber protein stf;date_creation=2020-05-13\n-NC_001416.1_phage_lambda\t.\texon\t19641\t19644\t.\t+\t.\tParent=b7a5dc48-88c5-4edc-9081-091ef39ff3ea;ID=e794f054-733e-4b10-99df-128b37cd80e8;Name=e794f054-733e-4b10-99df-128b37cd80e8\n-NC_001416.1_phage_lambda\t.\tCDS\t19650\t20855\t.\t+\t0\tParent=b7a5dc48-88c5-4edc-9081-091ef39ff3ea;ID=f1584714-9cc6-4209-8730-0d7c199cff35;Name=f1584714-9cc6-4209-8730-0d7c199cff35\n-NC_001416.1_phage_lambda\t.\texon\t19650\t20855\t.\t+\t.\tParent=b7a5dc48-88c5-4edc-9081-091ef39ff3ea;ID=b44a883e-e4e2-4432-b665-355a803943dc;Name=b44a883e-e4e2-4432-b665-35'..b'.\tgene\t38031\t38241\t.\t+\t.\towner=jason.gill@tamu.edu;Note=added by JJG;ID=d731b2bf-e9f9-484f-8851-814510c6a5ec;date_last_modified=2020-05-27;Name=regulatory protein cro;date_creation=2019-02-07\n-NC_001416.1_phage_lambda\t.\tmRNA\t38031\t38241\t.\t+\t.\towner=jason.gill@tamu.edu;Parent=d731b2bf-e9f9-484f-8851-814510c6a5ec;ID=5cfd706b-b814-43f9-b604-fc8c179f853a;date_last_modified=2020-05-27;Name=regulatory protein cro;date_creation=2019-02-07\n-NC_001416.1_phage_lambda\t.\texon\t38031\t38035\t.\t+\t.\tParent=5cfd706b-b814-43f9-b604-fc8c179f853a;ID=041be549-96a8-42a3-b5eb-258ebb4ffd5f;Name=041be549-96a8-42a3-b5eb-258ebb4ffd5f\n-NC_001416.1_phage_lambda\t.\tCDS\t38041\t38241\t.\t+\t0\tParent=5cfd706b-b814-43f9-b604-fc8c179f853a;ID=97688d3e-13d8-48fd-9e05-2d919293f914;Name=97688d3e-13d8-48fd-9e05-2d919293f914\n-NC_001416.1_phage_lambda\t.\texon\t38041\t38241\t.\t+\t.\tParent=5cfd706b-b814-43f9-b604-fc8c179f853a;ID=e6686b84-108a-4c8f-a5b9-64b92b6dc5b5;Name=e6686b84-108a-4c8f-a5b9-64b92b6dc5b5\n-###\n-NC_001416.1_phage_lambda\t.\tgene\t38345\t38653\t.\t+\t.\towner=jason.gill@tamu.edu;Note=added by JJG;ID=1b331cf3-0897-4489-aa55-b14669ea5998;date_last_modified=2020-05-27;Name=regulatory protein cII;date_creation=2019-02-07\n-NC_001416.1_phage_lambda\t.\tmRNA\t38345\t38653\t.\t+\t.\towner=jason.gill@tamu.edu;Parent=1b331cf3-0897-4489-aa55-b14669ea5998;ID=b970dd3f-9787-459c-84ed-5b839b85b9e7;date_last_modified=2020-05-27;Name=regulatory protein cII;date_creation=2019-02-07\n-NC_001416.1_phage_lambda\t.\tCDS\t38360\t38653\t.\t+\t0\tParent=b970dd3f-9787-459c-84ed-5b839b85b9e7;ID=c4ae3e6a-4e56-412d-8ece-0036053910ef;Name=c4ae3e6a-4e56-412d-8ece-0036053910ef\n-NC_001416.1_phage_lambda\t.\texon\t38360\t38653\t.\t+\t.\tParent=b970dd3f-9787-459c-84ed-5b839b85b9e7;ID=c29fe89e-348d-4da7-b313-85c362f92307;Name=c29fe89e-348d-4da7-b313-85c362f92307\n-NC_001416.1_phage_lambda\t.\texon\t38345\t38348\t.\t+\t.\tParent=b970dd3f-9787-459c-84ed-5b839b85b9e7;ID=b2199555-1cbb-443c-92d3-fa5a0a17670e;Name=b2199555-1cbb-443c-92d3-fa5a0a17670e\n-###\n-NC_001416.1_phage_lambda\t.\tgene\t30392\t30626\t.\t-\t.\towner=jolenerr@tamu.edu;Note=Contains InterPro domain IPR000962;ID=4fba3f9c-cbc0-4454-b278-efe088695fef;date_last_modified=2020-05-27;Name=DksA/TraR C4-type zinc finger domain-containing protein;date_creation=2020-05-13\n-NC_001416.1_phage_lambda\t.\tmRNA\t30392\t30626\t.\t-\t.\towner=jolenerr@tamu.edu;Parent=4fba3f9c-cbc0-4454-b278-efe088695fef;ID=7dfc2c2d-a50d-4e77-b673-2dcd16c2ef3b;date_last_modified=2020-05-27;Name=DksA/TraR C4-type zinc finger domain-containing protein;date_creation=2020-05-13\n-NC_001416.1_phage_lambda\t.\texon\t30624\t30626\t.\t-\t.\tParent=7dfc2c2d-a50d-4e77-b673-2dcd16c2ef3b;ID=cbf0bbe9-fdae-426f-a6ce-40926606c1ca;Name=cbf0bbe9-fdae-426f-a6ce-40926606c1ca\n-NC_001416.1_phage_lambda\t.\tCDS\t30392\t30613\t.\t-\t0\tParent=7dfc2c2d-a50d-4e77-b673-2dcd16c2ef3b;ID=1fa7e4a7-9200-45d9-b9fd-21e36b254897;Name=1fa7e4a7-9200-45d9-b9fd-21e36b254897\n-NC_001416.1_phage_lambda\t.\texon\t30392\t30613\t.\t-\t.\tParent=7dfc2c2d-a50d-4e77-b673-2dcd16c2ef3b;ID=529064a4-a072-48ec-bd67-0eb3011ae53c;Name=529064a4-a072-48ec-bd67-0eb3011ae53c\n-###\n-NC_001416.1_phage_lambda\t.\tgene\t46174\t46368\t.\t+\t.\towner=jolenerr@tamu.edu;ID=18e578e1-38cb-4846-96e8-0190a5a26369;date_last_modified=2020-05-13;Name=o-spanin Rz1;date_creation=2020-05-13\n-NC_001416.1_phage_lambda\t.\tmRNA\t46174\t46368\t.\t+\t.\towner=jolenerr@tamu.edu;Parent=18e578e1-38cb-4846-96e8-0190a5a26369;ID=b4c199b2-1838-43c0-a09d-77718a49dbe2;date_last_modified=2020-05-13;Name=o-spanin Rz1;date_creation=2020-05-13\n-NC_001416.1_phage_lambda\t.\tCDS\t46186\t46368\t.\t+\t0\tParent=b4c199b2-1838-43c0-a09d-77718a49dbe2;ID=7ac7bb1c-0d6d-4476-8a02-8ad963da6156;Name=7ac7bb1c-0d6d-4476-8a02-8ad963da6156\n-NC_001416.1_phage_lambda\t.\texon\t46174\t46178\t.\t+\t.\tParent=b4c199b2-1838-43c0-a09d-77718a49dbe2;ID=668e24d1-fcea-459e-bbf3-6132bbb9854e;Name=668e24d1-fcea-459e-bbf3-6132bbb9854e\n-NC_001416.1_phage_lambda\t.\texon\t46186\t46368\t.\t+\t.\tParent=b4c199b2-1838-43c0-a09d-77718a49dbe2;ID=f8d07a76-6f8d-4100-9ba6-cec0e3a033f9;Name=f8d07a76-6f8d-4100-9ba6-cec0e3a033f9\n' |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c cpt_annotation_table/test-data/PhageTable_Out.html --- a/cpt_annotation_table/test-data/PhageTable_Out.html Fri Jun 17 12:19:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,2124 +0,0 @@\n-<!DOCTYPE html>\n-<html lang="en">\n- <head>\n- <meta charset="utf-8">\n- <meta http-equiv="X-UA-Compatible" content="IE=edge">\n- <meta name="viewport" content="width=device-width, initial-scale=1">\n- <!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->\n- <meta name="description" content="">\n- <meta name="author" content="">\n- <title>Annotation Table</title>\n- <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.2/jquery.min.js"></script>\n-\t<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" crossorigin="anonymous">\n-\t<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap-theme.min.css" crossorigin="anonymous">\n-\t<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/js/bootstrap.min.js" crossorigin="anonymous"></script>\n-\n- <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.11/css/jquery.dataTables.css">\n- <script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/1.10.11/js/jquery.dataTables.js"></script>\n- <style type="text/css">\n-/*\n- * Base structure\n- */\n-\n-/* Move down content because we have a fixed navbar that is 50px tall */\n-body {\n- padding-top: 50px;\n-}\n-\n-h3:before {\n- display: block;\n- content: " ";\n- margin-top: -50px;\n- height: 50px;\n- visibility: hidden;\n-}\n-\n-/*\n- * Global add-ons\n- */\n-\n-.sub-header {\n- padding-bottom: 10px;\n- border-bottom: 1px solid #eee;\n-}\n-\n-/*\n- * Top navigation\n- * Hide default border to remove 1px line.\n- */\n-.navbar-fixed-top {\n- border: 0;\n-}\n-\n-/*\n- * Sidebar\n- */\n-\n-/* Hide for mobile, show later */\n-.sidebar {\n- display: none;\n-}\n-@media (min-width: 768px) {\n- .sidebar {\n- position: fixed;\n- top: 51px;\n- bottom: 0;\n- left: 0;\n- z-index: 1000;\n- display: block;\n- padding: 20px;\n- overflow-x: hidden;\n- overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */\n- background-color: #f5f5f5;\n- border-right: 1px solid #eee;\n- }\n-}\n-\n-/* Sidebar navigation */\n-.nav-sidebar {\n- margin-right: -21px; /* 20px padding + 1px border */\n- margin-bottom: 20px;\n- margin-left: -20px;\n-}\n-.nav-sidebar > li > a {\n- padding-right: 20px;\n- padding-left: 20px;\n-}\n-.nav-sidebar > .active > a,\n-.nav-sidebar > .active > a:hover,\n-.nav-sidebar > .active > a:focus {\n- color: #fff;\n- background-color: #428bca;\n-}\n-\n-\n-/*\n- * Main content\n- */\n-\n-.main {\n- padding: 20px;\n-}\n-@media (min-width: 768px) {\n- .main {\n- padding-right: 40px;\n- padding-left: 40px;\n- }\n-}\n-.main .page-header {\n- margin-top: 0;\n-}\n-\n-\n-/*\n- * Placeholder dashboard ideas\n- */\n-\n-.placeholders {\n- margin-bottom: 30px;\n- text-align: center;\n-}\n-.placeholders h4 {\n- margin-bottom: 0;\n-}\n-.placeholder {\n- margin-bottom: 20px;\n-}\n-.placeholder img {\n- display: inline-block;\n- border-radius: 50%;\n-}\n-\n-td.moron {\n- font-size: 150%;\n- padding: 0px;\n- color: gray;\n-}\n-.strand_emph {\n- text-decoration: underline;\n- color: black;\n-}\n-\n- </style>\n- <!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries -->\n- <!--[if lt IE 9]>\n- <script src="//oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>\n- <script src="//oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>\n- <![endif]-->\n- </head>\n- <body>\n-\n- <nav class="navbar navbar-inverse navbar-fixed-top">\n- <div class="container-fluid">\n- <div class="navbar-header">\n- <a class="navbar-brand" href="#">Annotation Table</a>\n- </div>\n- </div>\n- </nav>\n-\n- <div class="container-fluid">\n- <div class="row">\n- <div class="col-md-12 main" id="main">\n- <ul class="nav nav-tabs" role="tablist" id="myTabs">\n- <li role="presentation" class="active"><a href="#overview" role="tab" data-toggle="tab">Overview</a></li>\n- '..b' <td>None</td>\n- <td>None</td>\n- <td>None</td>\n- <td>None</td>\n- </tr>\n- <tr>\n- <td>NC_001416-1_phage_lambda</td>\n- <td>e3d29177-18a8-4bc0-8d91-15e5760f3bd3</td>\n- <td>gene</td>\n- <td>NC_001416.1_phage_lambda.gene_60</td>\n- <td>47727..47944</td>\n- <td>47727</td>\n- <td>47944</td>\n- <td>+</td>\n- <td>68</td>\n- <td>GGAG</td>\n- <td>7</td>\n- <td>ATG</td>\n- <td>TGA</td>\n- <td>74</td>\n- <td>752f31a0-018a-4223-a7f9-72685604b7a3</td>\n- <td>jolenerr@tamu.edu</td>\n- <td>2020-05-13</td>\n- <td>2020-05-13</td>\n- <td>None</td>\n- <td>None</td>\n- <td>None</td>\n- <td>None</td>\n- </tr>\n- <tr>\n- <td>NC_001416-1_phage_lambda</td>\n- <td>e0b009e4-729e-4d97-b818-ec0cbebcb1f4</td>\n- <td>gene</td>\n- <td>NC_001416.1_phage_lambda.orf00102</td>\n- <td>48109..48314</td>\n- <td>48109</td>\n- <td>48314</td>\n- <td>-</td>\n- <td>64</td>\n- <td>GGGG</td>\n- <td>7</td>\n- <td>ATG</td>\n- <td>TGA</td>\n- <td>None</td>\n- <td>None</td>\n- <td>jolenerr@tamu.edu</td>\n- <td>2020-05-13</td>\n- <td>2020-05-13</td>\n- <td>None</td>\n- <td>None</td>\n- <td>None</td>\n- <td>None</td>\n- </tr>\n- </tbody>\n- </table>\n- </div>\n- </div>\n- </div>\n- </div>\n- </div>\n-\n- <script type="text/javascript">\n- $(document).ready( function () {\n-\n-\n-\n-$(\'#myTabs a\').click(function (e) {\n-\te.preventDefault()\n-\t$(this).tab(\'show\')\n-})\n-\n-\n-\n-jQuery.fn.dataTable.ext.type.detect.unshift( function ( data ) {\n- if ( typeof data !== \'string\' ) {\n- return null;\n- }\n-\n- var matches = data.match(/^(\\d+)\\.\\.(\\d+)/);\n- return matches ? \'genomic\' : null;\n-} );\n-\n-\n-\n-jQuery.extend( jQuery.fn.dataTableExt.oSort, {\n- "genomic-pre": function ( a ) {\n- var matches = a.match(/^(\\d+)\\.\\.(\\d+)/);\n- console.log(a + " " + matches[1]);\n- return parseInt(matches[1]);\n- },\n-\n- "genomic-asc": function ( a, b ) {\n- return ((a < b) ? -1 : ((a > b) ? 1 : 0));\n- },\n-\n- "genomic-desc": function ( a, b ) {\n- return ((a < b) ? 1 : ((a > b) ? -1 : 0));\n- }\n-} );\n-\n- $(\'table\').DataTable();\n- });\n- </script>\n- </body>\n-</html>\n' |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c cpt_annotation_table/test-data/PhageTable_Out.tabular --- a/cpt_annotation_table/test-data/PhageTable_Out.tabular Fri Jun 17 12:19:58 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,79 +0,0 @@\n-# Organism ID\tID\tType\tName\tLocation\tBoundary\tBoundary\tStrand\tCDS Length (AA)\tShine-Dalgarno sequence\tShine-Dalgarno spacing\tStart Codon\tStop Codon\tDistance to next upstream gene on same strand\tNext gene upstream\tOwner\tCreated\tLast Modified\tUser entered Notes\tDescription\tProduct\tDBxrefs\t\n-NC_001416.1_phage_lambda\t1185c0aa-14c4-45c3-ab0d-889bbfdbf137\tgene\tterminase small subunit\t181..736\t181\t736\t+\t181\tGGA\t7\tATG\tTAA\tNone\tNone\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t6d452f5a-9508-40c1-9d43-d98831ca8919\tgene\tterminase large subunit\t701..2636\t701\t2636\t+\t641\tGGGT\t6\tGTG\tTGA\t-36\t1185c0aa-14c4-45c3-ab0d-889bbfdbf137\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t38175e36-b9e9-48ea-9d1c-7f115fae7194\tgene\thead completion protein\t2622..2839\t2622\t2839\t+\t68\tGGAG\t7\tATG\tTGA\t-15\t6d452f5a-9508-40c1-9d43-d98831ca8919\tjolenerr@tamu.edu\t2020-05-13\t2020-05-28\tInterPro domain IPR004174\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t0695da41-cce8-4f07-a27a-eb42ac82ae56\tgene\tportal protein B\t2824..4437\t2824\t4437\t+\t533\tAGGA\t8\tATG\tTAA\t-16\t38175e36-b9e9-48ea-9d1c-7f115fae7194\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t422aab41-ac49-4818-b87e-9331023dcacf\tgene\tcapsid assembly protein\t4406..5737\t4406\t5737\t+\t673\t"GGAG, AGGAGG"\t"-609, 6"\t"GTG (4417..5737:1), GTG (5035..5737:1)"\tTAA\t-32\t0695da41-cce8-4f07-a27a-eb42ac82ae56\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t274304d3-079e-4e08-aa11-219235e1aacb\tgene\tcapsid decoration protein\t5739..6079\t5739\t6079\t+\t110\tGGA\t5\tATG\tTAA\t1\t422aab41-ac49-4818-b87e-9331023dcacf\tjolenerr@tamu.edu\t2020-05-13\t2020-05-28\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t4f815f9e-5092-4db3-b722-0d912c116293\tgene\tmajor capsid protein\t6099..7160\t6099\t7160\t+\t350\tAGG\t6\tGTG\tTAA\t19\t274304d3-079e-4e08-aa11-219235e1aacb\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t4da662d1-028a-43e2-9b50-f48ad03bdd64\tgene\tDNA packaging protein FI\t7173..7600\t7173\t7600\t+\t136\tGGGG\t13\tGTG\tTAA\t12\t4f815f9e-5092-4db3-b722-0d912c116293\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t638d1ac5-aea4-4988-b46d-01cf79793dfb\tgene\thead-tail connector protein FII\t7603..7965\t7603\t7965\t+\t117\tGGAG\t5\tGTG\tTGA\t2\t4da662d1-028a-43e2-9b50-f48ad03bdd64\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\tb541056e-bf91-4113-bce7-86bab4d27f76\tgene\ttail completion protein Z\t7968..8555\t7968\t8555\t+\t192\tGGGG\t5\tATG\tTGA\t2\t638d1ac5-aea4-4988-b46d-01cf79793dfb\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\tfca8745c-c433-4845-9430-c8a9dd4dc37b\tgene\ttail tube terminator protein U\t8535..8947\t8535\t8947\t+\t131\tAGGA\t13\tATG\tTGA\t-21\tb541056e-bf91-4113-bce7-86bab4d27f76\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\td9ee7b0e-b4a7-48cf-8c4b-aa95ca8863e0\tgene\ttail tube protein V\t8946..9695\t8946\t9695\t+\t246\tGAGG\t5\tATG\tTAA\t-2\tfca8745c-c433-4845-9430-c8a9dd4dc37b\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t0b5a859a-39f6-4c49-91b7-0b2def466374\tgene\ttape measure chaperone GT\t9699..10133\t9699\t10133\t+\t275\t"GGAG, GGAG"\t"8, 8"\t"ATG (9710..10133:1), ATG (9710..10115:1)"\tTGA\t3\td9ee7b0e-b4a7-48cf-8c4b-aa95ca8863e0\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\tc6a11d3b-7b9d-446f-ba16-3a642f3f6fbd\tgene\ttape measure chaperone GT\t10115..10549\t10115\t10549\t+\t144\tNone\tNone\tGTG\tTGA\t-19\t0b5a859a-39f6-4c49-91b7-0b2def466374\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t7ef9ffad-d420-4a1c-9a8d-2312dc04b558\tgene\ttape measure protein H\t10528..13103\t10528\t13103\t+\t853\tAGGAGG\t8\tATG\tTGA\t-22\tc6a11d3b-7b9d-446f-ba16-3a642f3f6fbd\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t55fe46da-9e0e-4454-aff9-f'..b'002363577\t42080..42272\t42080\t42272\t+\t60\tAGGAG\t5\tGTG\tTGA\t-44\tc402b694-7971-451b-aa24-4e70550eef2d\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t49135134-fa86-4df5-a0d7-b629ff152305\tgene\tCDS.0.1596_0.0419290277112\t42230..42439\t42230\t42439\t+\t66\tGGA\t6\tGTG\tTAA\t-43\t61a0d8bd-5b58-4077-bc04-2bcf4dee8939\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\ta8c3d9d2-cc66-4394-a821-ec0db2e411de\tgene\tNC_001416.1_phage_lambda.gene_51\t42419..43043\t42419\t43043\t+\t204\tGAGG\t6\tATG\tTGA\t-21\t49135134-fa86-4df5-a0d7-b629ff152305\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t0cea2875-2757-4c9b-97f5-7b0ec545394a\tgene\tNC_001416.1_phage_lambda.gene_52\t43032..43246\t43032\t43246\t+\t68\tGAG\t5\tATG\tTGA\t-12\ta8c3d9d2-cc66-4394-a821-ec0db2e411de\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t8ce6427a-594a-4320-955b-be6dd71ab223\tgene\tNC_001416.1_phage_lambda.gene_53\t43135..43889\t43135\t43889\t+\t221\tGGAG\t8\tATG\tTGA\t-112\t0cea2875-2757-4c9b-97f5-7b0ec545394a\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t1653554c-4be1-453b-a377-86e20759321a\tgene\tlate gene regulator\t43875..44509\t43875\t44509\t+\t207\tGGAG\t7\tATG\tTAG\t-15\t8ce6427a-594a-4320-955b-be6dd71ab223\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t6c3ab9c5-a407-47b8-89df-fa997262a409\tgene\tCDS.0.1630_0.132755174165\t44612..44815\t44612\t44815\t+\t64\tGGT\t6\tATG\tTAA\t102\t1653554c-4be1-453b-a377-86e20759321a\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t94064736-88a6-4e82-8c89-8226f57526e8\tgene\tantiholin S107\t45175..45509\t45175\t45509\t+\t213\t"GGGGG, GGGGG"\t"6, 6"\t"ATG (45185..45509:1), ATG (45191..45509:1)"\tTAA\t359\t6c3ab9c5-a407-47b8-89df-fa997262a409\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\tf8ba23df-ca21-4307-8f5a-ef8243f01acc\tgene\tendolysin R\t45483..45969\t45483\t45969\t+\t158\tGGAG\t6\tATG\tTGA\t-27\t94064736-88a6-4e82-8c89-8226f57526e8\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t4795342c-7959-44d9-925a-781f17371e7a\tgene\ti-spanin Rz\t45953..46427\t45953\t46427\t+\t153\tGAG\t10\tATG\tTAG\t-17\tf8ba23df-ca21-4307-8f5a-ef8243f01acc\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t18e578e1-38cb-4846-96e8-0190a5a26369\tgene\to-spanin Rz1\t46174..46368\t46174\t46368\t+\t60\tAGGAG\t7\tATG\tTGA\t-254\t4795342c-7959-44d9-925a-781f17371e7a\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t6eedd5c5-3c44-404a-af31-acee26522035\tgene\tbor\t46459..46763\t46459\t46763\t-\t97\tGGA\t8\tATG\tTAA\t132\t2da1b434-7877-4aa2-b88b-24922f70988b\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t2da1b434-7877-4aa2-b88b-24922f70988b\tgene\tCDS.0.3497_0.36888415839\t46896..47029\t46896\t47029\t-\t32\tGGGG\t10\tATG\tTAA\t12\t5d4e2403-4389-497c-a220-9740cd9935cc\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t5d4e2403-4389-497c-a220-9740cd9935cc\tgene\tCDS.0.2625_0.768191840841\t47042..47463\t47042\t47463\t-\t136\tAGGT\t7\tATG\tTAA\t645\te0b009e4-729e-4d97-b818-ec0cbebcb1f4\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\t752f31a0-018a-4223-a7f9-72685604b7a3\tgene\tCDS.0.864_0.667986446525\t47518..47652\t47518\t47652\t+\t40\tGGT\t9\tTTG\tTAA\t1149\t18e578e1-38cb-4846-96e8-0190a5a26369\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\te3d29177-18a8-4bc0-8d91-15e5760f3bd3\tgene\tNC_001416.1_phage_lambda.gene_60\t47727..47944\t47727\t47944\t+\t68\tGGAG\t7\tATG\tTGA\t74\t752f31a0-018a-4223-a7f9-72685604b7a3\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n-NC_001416.1_phage_lambda\te0b009e4-729e-4d97-b818-ec0cbebcb1f4\tgene\tNC_001416.1_phage_lambda.orf00102\t48109..48314\t48109\t48314\t-\t64\tGGGG\t7\tATG\tTGA\tNone\tNone\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n' |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c gff3.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gff3.py Wed Apr 26 03:42:32 2023 +0000 |
| [ |
| b'@@ -0,0 +1,346 @@\n+import copy\n+import logging\n+\n+log = logging.getLogger()\n+log.setLevel(logging.WARN)\n+\n+\n+def feature_lambda(\n+ feature_list,\n+ test,\n+ test_kwargs,\n+ subfeatures=True,\n+ parent=None,\n+ invert=False,\n+ recurse=True,\n+):\n+ """Recursively search through features, testing each with a test function, yielding matches.\n+\n+ GFF3 is a hierachical data structure, so we need to be able to recursively\n+ search through features. E.g. if you\'re looking for a feature with\n+ ID=\'bob.42\', you can\'t just do a simple list comprehension with a test\n+ case. You don\'t know how deeply burried bob.42 will be in the feature tree. This is where feature_lambda steps in.\n+\n+ :type feature_list: list\n+ :param feature_list: an iterable of features\n+\n+ :type test: function reference\n+ :param test: a closure with the method signature (feature, **kwargs) where\n+ the kwargs are those passed in the next argument. This\n+ function should return True or False, True if the feature is\n+ to be yielded as part of the main feature_lambda function, or\n+ False if it is to be ignored. This function CAN mutate the\n+ features passed to it (think "apply").\n+\n+ :type test_kwargs: dictionary\n+ :param test_kwargs: kwargs to pass to your closure when it is called.\n+\n+ :type subfeatures: boolean\n+ :param subfeatures: when a feature is matched, should just that feature be\n+ yielded to the caller, or should the entire sub_feature\n+ tree for that feature be included? subfeatures=True is\n+ useful in cases such as searching for a gene feature,\n+ and wanting to know what RBS/Shine_Dalgarno_sequences\n+ are in the sub_feature tree (which can be accomplished\n+ with two feature_lambda calls). subfeatures=False is\n+ useful in cases when you want to process (and possibly\n+ return) the entire feature tree, such as applying a\n+ qualifier to every single feature.\n+\n+ :type invert: boolean\n+ :param invert: Negate/invert the result of the filter.\n+\n+ :rtype: yielded list\n+ :return: Yields a list of matching features.\n+ """\n+ # Either the top level set of [features] or the subfeature attribute\n+ for feature in feature_list:\n+ feature._parent = parent\n+ if not parent:\n+ # Set to self so we cannot go above root.\n+ feature._parent = feature\n+ test_result = test(feature, **test_kwargs)\n+ # if (not invert and test_result) or (invert and not test_result):\n+ if invert ^ test_result:\n+ if not subfeatures:\n+ feature_copy = copy.deepcopy(feature)\n+ feature_copy.sub_features = list()\n+ yield feature_copy\n+ else:\n+ yield feature\n+\n+ if recurse and hasattr(feature, "sub_features"):\n+ for x in feature_lambda(\n+ feature.sub_features,\n+ test,\n+ test_kwargs,\n+ subfeatures=subfeatures,\n+ parent=feature,\n+ invert=invert,\n+ recurse=recurse,\n+ ):\n+ yield x\n+\n+\n+def fetchParent(feature):\n+ if not hasattr(feature, "_parent") or feature._parent is None:\n+ return feature\n+ else:\n+ return fetchParent(feature._parent)\n+\n+\n+def feature_test_true(feature, **kwargs):\n+ return True\n+\n+\n+def feature_test_type(feature, **kwargs):\n+ if "type" in kwargs:\n+ return str(feature.type).upper() == str(kwargs["type"]).upper()\n+ elif "types" in kwargs:\n+ for x in kwargs["types"]:\n+ if str(feature.type).upper() == str(x).upper():\n+ return True\n+ return False\n+ raise Exception("Incorrect feature_test'..b'feature.location.start,\n+ # feature.location.end,\n+ # feature.location.strand\n+ # )\n+ return result\n+\n+\n+def get_gff3_id(gene):\n+ return gene.qualifiers.get("Name", [gene.id])[0]\n+\n+\n+def ensure_location_in_bounds(start=0, end=0, parent_length=0):\n+ # This prevents frameshift errors\n+ while start < 0:\n+ start += 3\n+ while end < 0:\n+ end += 3\n+ while start > parent_length:\n+ start -= 3\n+ while end > parent_length:\n+ end -= 3\n+ return (start, end)\n+\n+\n+def coding_genes(feature_list):\n+ for x in genes(feature_list):\n+ if (\n+ len(\n+ list(\n+ feature_lambda(\n+ x.sub_features,\n+ feature_test_type,\n+ {"type": "CDS"},\n+ subfeatures=False,\n+ )\n+ )\n+ )\n+ > 0\n+ ):\n+ yield x\n+\n+\n+def genes(feature_list, feature_type="gene", sort=False):\n+ """\n+ Simple filter to extract gene features from the feature set.\n+ """\n+\n+ if not sort:\n+ for x in feature_lambda(\n+ feature_list, feature_test_type, {"type": feature_type}, subfeatures=True\n+ ):\n+ yield x\n+ else:\n+ data = list(genes(feature_list, feature_type=feature_type, sort=False))\n+ data = sorted(data, key=lambda feature: feature.location.start)\n+ for x in data:\n+ yield x\n+\n+\n+def wa_unified_product_name(feature):\n+ """\n+ Try and figure out a name. We gave conflicting instructions, so\n+ this isn\'t as trivial as it should be. Sometimes it will be in\n+ \'product\' or \'Product\', othertimes in \'Name\'\n+ """\n+ # Manually applied tags.\n+ protein_product = feature.qualifiers.get(\n+ "product", feature.qualifiers.get("Product", [None])\n+ )[0]\n+\n+ # If neither of those are available ...\n+ if protein_product is None:\n+ # And there\'s a name...\n+ if "Name" in feature.qualifiers:\n+ if not is_uuid(feature.qualifiers["Name"][0]):\n+ protein_product = feature.qualifiers["Name"][0]\n+\n+ return protein_product\n+\n+\n+def is_uuid(name):\n+ return name.count("-") == 4 and len(name) == 36\n+\n+\n+def get_rbs_from(gene):\n+ # Normal RBS annotation types\n+ rbs_rbs = list(\n+ feature_lambda(\n+ gene.sub_features, feature_test_type, {"type": "RBS"}, subfeatures=False\n+ )\n+ )\n+ rbs_sds = list(\n+ feature_lambda(\n+ gene.sub_features,\n+ feature_test_type,\n+ {"type": "Shine_Dalgarno_sequence"},\n+ subfeatures=False,\n+ )\n+ )\n+ # Fraking apollo\n+ apollo_exons = list(\n+ feature_lambda(\n+ gene.sub_features, feature_test_type, {"type": "exon"}, subfeatures=False\n+ )\n+ )\n+ apollo_exons = [x for x in apollo_exons if len(x) < 10]\n+ # These are more NCBI\'s style\n+ regulatory_elements = list(\n+ feature_lambda(\n+ gene.sub_features,\n+ feature_test_type,\n+ {"type": "regulatory"},\n+ subfeatures=False,\n+ )\n+ )\n+ rbs_regulatory = list(\n+ feature_lambda(\n+ regulatory_elements,\n+ feature_test_quals,\n+ {"regulatory_class": ["ribosome_binding_site"]},\n+ subfeatures=False,\n+ )\n+ )\n+ # Here\'s hoping you find just one ;)\n+ return rbs_rbs + rbs_sds + rbs_regulatory + apollo_exons\n+\n+\n+def nice_name(record):\n+ """\n+ get the real name rather than NCBI IDs and so on. If fails, will return record.id\n+ """\n+ name = record.id\n+ likely_parental_contig = list(genes(record.features, feature_type="contig"))\n+ if len(likely_parental_contig) == 1:\n+ name = likely_parental_contig[0].qualifiers.get("organism", [name])[0]\n+ return name\n+\n+\n+def fsort(it):\n+ for i in sorted(it, key=lambda x: int(x.location.start)):\n+ yield i\n' |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Apr 26 03:42:32 2023 +0000 |
| b |
| @@ -0,0 +1,74 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package">progressivemauve</requirement> + <!--<requirement type="package" version="2.7">python</requirement>--> + <requirement type="package" version="0.6.4">bcbiogff</requirement> + <yield/> + </requirements> + </xml> + <token name="@WRAPPER_VERSION@">2.4.0</token> + <xml name="citation/progressive_mauve"> + <citation type="doi">10.1371/journal.pone.0011147</citation> + </xml> + <xml name="citation/gepard"> + <citation type="doi">10.1093/bioinformatics/btm039</citation> + </xml> + <token name="@XMFA_INPUT@"> + '$xmfa' + </token> + <xml name="xmfa_input" token_formats="xmfa"> + <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/> + </xml> + <token name="@XMFA_FA_INPUT@"> + '$sequences' + </token> + <xml name="xmfa_fa_input"> + <param type="data" format="fasta" name="sequences" label="Sequences in alignment" help="These sequences should be the SAME DATASET that was used in the progressiveMauve run. Failing that, they should be provided in the same order as in original progressiveMauve run"/> + </xml> + <xml name="genome_selector"> + <conditional name="reference_genome"> + <param name="reference_genome_source" type="select" label="Reference Genome"> + <option value="history" selected="True">From History</option> + <option value="cached">Locally Cached</option> + </param> + <when value="cached"> + <param name="fasta_indexes" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"/> + </param> + </when> + <when value="history"> + <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> + </when> + </conditional> + </xml> + <xml name="gff3_input"> + <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> + </xml> + <xml name="input/gff3+fasta"> + <expand macro="gff3_input"/> + <expand macro="genome_selector"/> + </xml> + <token name="@INPUT_GFF@"> + '$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> +</macros> |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c phage_annotation_table.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phage_annotation_table.py Wed Apr 26 03:42:32 2023 +0000 |
| [ |
| b'@@ -0,0 +1,608 @@\n+#!/usr/bin/env python\n+# vim: set fileencoding=utf-8\n+import os\n+import argparse\n+from gff3 import (\n+ genes,\n+ get_gff3_id,\n+ get_rbs_from,\n+ feature_test_true,\n+ feature_lambda,\n+ feature_test_type,\n+)\n+from CPT_GFFParser import gffParse, gffWrite\n+from Bio import SeqIO\n+from jinja2 import Environment, FileSystemLoader\n+import logging\n+from math import floor\n+\n+logging.basicConfig(level=logging.DEBUG)\n+log = logging.getLogger(name="pat")\n+\n+# Path to script, required because of Galaxy.\n+SCRIPT_PATH = os.path.dirname(os.path.realpath(__file__))\n+# Path to the HTML template for the report\n+\n+\n+def genes_all(feature_list, feature_type=["gene"], sort=False):\n+ """\n+ Simple filter to extract gene features from the feature set.\n+ """\n+\n+ if not sort:\n+ for x in feature_lambda(\n+ feature_list, feature_test_type, {"types": feature_type}, subfeatures=True\n+ ):\n+ yield x\n+ else:\n+ data = list(genes_all(feature_list, feature_type, sort=False))\n+ data = sorted(data, key=lambda feature: feature.location.start)\n+ for x in data:\n+ yield x\n+\n+\n+def checkSubs(feature, qualName):\n+ subFeats = []\n+ res = ""\n+ subFeats = feature.sub_features\n+ while len(subFeats) > 0:\n+ for feat in subFeats:\n+ for i in feat.qualifiers.keys():\n+ for j in qualName:\n+ if i == j:\n+ if res == "":\n+ res = feat.qualifiers[i][0]\n+ else:\n+ res += "; " + feat.qualifiers[i][0]\n+ if res != "":\n+ return res\n+ tempFeats = []\n+ for feat in subFeats: # Should be breadth-first results\n+ for x in feat.sub_features:\n+ tempFeats.append(x)\n+ subFeats = tempFeats\n+ return res\n+\n+\n+def annotation_table_report(record, types, wanted_cols, gaf_data, searchSubs):\n+ getTypes = []\n+ for x in [y.strip() for y in types.split(",")]:\n+ getTypes.append(x)\n+ getTypes.append("gene")\n+ sorted_features = list(genes_all(record.features, getTypes, sort=True))\n+ if wanted_cols is None or len(wanted_cols.strip()) == 0:\n+ return [], []\n+ useSubs = searchSubs\n+\n+ def rid(record, feature):\n+ """Organism ID"""\n+ return record.id\n+\n+ def id(record, feature):\n+ """ID"""\n+ return feature.id\n+\n+ def featureType(record, feature):\n+ """Type"""\n+ return feature.type\n+\n+ def name(record, feature):\n+ """Name"""\n+ for x in ["Name", "name"]:\n+ for y in feature.qualifiers.keys():\n+ if x == y:\n+ return feature.qualifiers[x][0]\n+ if useSubs:\n+ res = checkSubs(feature, ["Name", "name"])\n+ if res != "":\n+ return res\n+ return "None"\n+\n+ def start(record, feature):\n+ """Boundary"""\n+ return str(feature.location.start + 1)\n+\n+ def end(record, feature):\n+ """Boundary"""\n+ return str(feature.location.end)\n+\n+ def location(record, feature):\n+ """Location"""\n+ return str(feature.location.start + 1) + "..{0.end}".format(feature.location)\n+\n+ def length(record, feature):\n+ """CDS Length (AA)"""\n+\n+ if feature.type == "CDS":\n+ cdss = [feature]\n+ else:\n+ cdss = list(genes(feature.sub_features, feature_type="CDS", sort=True))\n+\n+ if cdss == []:\n+ return "None"\n+ res = (sum([len(cds) for cds in cdss]) / 3) - 1\n+ if floor(res) == res:\n+ res = int(res)\n+ return str(res)\n+\n+ def notes(record, feature):\n+ """User entered Notes"""\n+ for x in ["Note", "note", "Notes", "notes"]:\n+ for y in feature.qualifiers.keys():\n+ if x == y:\n+ return feature.qualifiers[x][0]\n+ if useSubs:\n+ r'..b'd8-49c8-b724-d6aa4df5a98d\': {\n+ # \'annotation_extension\': \'\',\n+ # \'aspect\': \'\',\n+ # \'assigned_by\': \'CPT\',\n+ # \'date\': \'2017-05-04T16:25:22.161916Z\',\n+ # \'db\': \'UniProtKB\',\n+ # \'db_reference\': \'GO_REF:0000100\',\n+ # \'evidence_code\': \'ISA\',\n+ # \'gene\': \'0d307196-833d-46e8-90e9-d80f7a041d88\',\n+ # \'go_id\': \'GO:0039660\',\n+ # \'go_term\': \'structural constituent of virion\',\n+ # \'id\': \'10d04a01-5ed8-49c8-b724-d6aa4df5a98d\',\n+ # \'notes\': \'hit was putative minor structural protein\',\n+ # \'owner\': \'amarc1@tamu.edu\',\n+ # \'with_or_from\': \'UNIREF90:B2ZYZ7\'\n+ # },\n+ for row in file:\n+ if row.startswith("#"):\n+ # Header\n+ cols = (\n+ row.strip().replace("# ", "").replace("GO Term", "go_term").split("\\t")\n+ )\n+ else:\n+ line = row.strip().split("\\t")\n+ tmp = dict(zip(cols, line))\n+ if "gene" not in tmp.keys():\n+ continue\n+ if tmp["gene"] not in data:\n+ data[tmp["gene"]] = []\n+\n+ data[tmp["gene"]].append(tmp)\n+ return data\n+\n+\n+def evaluate_and_report(\n+ annotations,\n+ genome,\n+ types="gene",\n+ reportTemplateName="phage_annotation_validator.html",\n+ annotationTableCols="",\n+ gafData=None,\n+ searchSubs=False,\n+):\n+ """\n+ Generate our HTML evaluation of the genome\n+ """\n+ # Get features from GFF file\n+ seq_dict = SeqIO.to_dict(SeqIO.parse(genome, "fasta"))\n+ # Get the first GFF3 record\n+ # TODO: support multiple GFF3 files.\n+ at_table_data = []\n+ gaf = {}\n+ if gafData:\n+ gaf = parseGafData(gafData)\n+\n+ for record in gffParse(annotations, base_dict=seq_dict):\n+ if reportTemplateName.endswith(".html"):\n+ record.id = record.id.replace(".", "-")\n+ log.info("Producing an annotation table for %s" % record.id)\n+ annotation_table_data, annotation_table_col_names = annotation_table_report(\n+ record, types, annotationTableCols, gaf, searchSubs\n+ )\n+ at_table_data.append((record, annotation_table_data))\n+ # break\n+\n+ # This is data that will go into our HTML template\n+ kwargs = {\n+ "annotation_table_data": at_table_data,\n+ "annotation_table_col_names": annotation_table_col_names,\n+ }\n+\n+ env = Environment(\n+ loader=FileSystemLoader(SCRIPT_PATH), trim_blocks=True, lstrip_blocks=True\n+ )\n+ if reportTemplateName.endswith(".html"):\n+ env.filters["nice_id"] = str(get_gff3_id).replace(".", "-")\n+ else:\n+ env.filters["nice_id"] = get_gff3_id\n+\n+ def join(listy):\n+ return "\\n".join(listy)\n+\n+ env.filters.update({"join": join})\n+ tpl = env.get_template(reportTemplateName)\n+ return tpl.render(**kwargs).encode("utf-8")\n+\n+\n+if __name__ == "__main__":\n+ parser = argparse.ArgumentParser(\n+ description="rebase gff3 features against parent locations", epilog=""\n+ )\n+ parser.add_argument(\n+ "annotations", type=argparse.FileType("r"), help="Parent GFF3 annotations"\n+ )\n+ parser.add_argument("genome", type=argparse.FileType("r"), help="Genome Sequence")\n+\n+ parser.add_argument(\n+ "--types",\n+ help="Select extra types to display in output (Will always include gene)",\n+ )\n+\n+ parser.add_argument(\n+ "--reportTemplateName",\n+ help="Report template file name",\n+ default="phageqc_report_full.html",\n+ )\n+ parser.add_argument(\n+ "--annotationTableCols",\n+ help="Select columns to report in the annotation table output format",\n+ )\n+ parser.add_argument(\n+ "--gafData", help="CPT GAF-like table", type=argparse.FileType("r")\n+ )\n+ parser.add_argument(\n+ "--searchSubs",\n+ help="Attempt to populate fields from sub-features if qualifier is empty",\n+ action="store_true",\n+ )\n+\n+ args = parser.parse_args()\n+\n+ print(evaluate_and_report(**vars(args)).decode("utf-8"))\n' |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c phage_annotation_table.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phage_annotation_table.xml Wed Apr 26 03:42:32 2023 +0000 |
| [ |
| @@ -0,0 +1,104 @@ +<tool id="edu.tamu.cpt2.phage.annotation_table" name="Annotation Table" version="20.0.0.1"> + <description>from gff3 formatted datasets</description> + <macros> + <import>macros.xml</import> + <import>cpt-macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="2.10.1">jinja2</requirement> + </expand> + <command detect_errors="aggressive"><![CDATA[ +@GENOME_SELECTOR_PRE@ + +python '$__tool_directory__/phage_annotation_table.py' +'$gff3_data' +@GENOME_SELECTOR@ +--types "$extraTypes" +--reportTemplateName "$report_format" +--annotationTableCols "$cols,$gaf_cols" +#if $gaf_data: +--gafData "$gaf_data" +#end if +'$checkSubfeats' +> '$output']]></command> + <inputs> + <expand macro="gff3_input"/> + <expand macro="genome_selector"/> + <param label="Extra sub-feature types to include (Comma-separated, Will always include gene)" optional="True" name="extraTypes" type="text" value=""/> + <param label="Columns" type="select" name="cols" multiple="True"> + <option value="rid" selected="true">Record ID</option> + <option value="id" selected="true">ID</option> + <option value="type" selected="true">Type</option> + <option value="name" selected="true">Name</option> + <option value="location" selected="true">Location</option> + <option value="start" selected="true">Feature Start</option> + <option value="end" selected="true">Feature End</option> + <option value="strand" selected="true">Strand</option> + <option value="length" selected="true">Length</option> + <option value="sd_seq" selected="true">SD sequence</option> + <option value="sd_spacing" selected="true">SD spacing</option> + <option value="start_codon" selected="true">Start codon</option> + <option value="stop_codon" selected="true">Stop codon</option> + <option value="ig_dist" selected="true">Distance to next upstream feature</option> + <option value="upstream_feature__name" selected="true">Name of upstream feature</option> + <option value="owner" selected="true">Owner</option> + <option value="date_created" selected="true">Date created</option> + <option value="date_last_modified" selected="true">Date last modified</option> + <option value="notes" selected="true">Notes</option> + <option value="description" selected="true">Description</option> + <option value="product" selected="true">Product</option> + <option value="dbxrefs" selected="true">DBxrefs</option> + <option value="qualifiers" selected="true">Qualifiers</option> + </param> + <param label="GAF Data" name="gaf_data" type="data" format="tabular" optional="True" help="Optional GAF Data Table. This usually comes from the CPT CACAO GAF Data Export tool. The [GAF] Columns below are ONLY available when this data is populated."/> + <param label="GAF Columns" type="select" name="gaf_cols" multiple="True"> + <!-- GAF Specific Fields --> + <option value="gaf_annotation_extension" selected="false">GAF Annotation Extension</option> + <option value="gaf_aspect" selected="false">GAF Aspect</option> + <option value="gaf_assigned_by" selected="false">GAF Assigned By</option> + <option value="gaf_date" selected="false">GAF Date</option> + <option value="gaf_db" selected="false">GAF DB</option> + <option value="gaf_db_reference" selected="false">GAF DB Reference</option> + <option value="gaf_evidence_code" selected="false">GAF Evidence Code</option> + <option value="gaf_gene" selected="false">GAF Gene</option> + <option value="gaf_go_id" selected="false">GAF GO ID</option> + <option value="gaf_go_term" selected="false">GAF GO Term</option> + <option value="gaf_id" selected="false">GAF ID</option> + <option value="gaf_notes" selected="false">GAF Notes</option> + <option value="gaf_owner" selected="false">GAF Owner</option> + <option value="gaf_with_or_from" selected="false">GAF with_or_from</option> + </param> + <param name="checkSubfeats" label="Search sub-features for fields if gene does not define them" type="boolean" truevalue="--searchSubs" falsevalue=""/> + <param label="Report Format" type="select" name="report_format"> + <option value="phageqc_report_annotation_table.html" selected="true">HTML Table</option> + <option value="phageqc_report_annotation_table.tsv">Tabular (Excel Compatible) Table</option> + </param> + </inputs> + <outputs> + <data format="html" name="output"> + <change_format> + <when format="tabular" input="report_format" value="phageqc_report_annotation_table.tsv"/> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="reference_genome_source" value="history"/> + <param name="genome_fasta" value="NC_001416_Table_In.fasta"/> + <param name="gff3_data" value="NC_001416_Table_In.gff3"/> + <param name="report_format" value="phageqc_report_annotation_table.html"/> + <output name="output" file="PhageTable_Out.html"/> + </test> + <test> + <param name="reference_genome_source" value="history"/> + <param name="genome_fasta" value="NC_001416_Table_In.fasta"/> + <param name="gff3_data" value="NC_001416_Table_In.gff3"/> + <param name="report_format" value="phageqc_report_annotation_table.tsv"/> + <output name="output" file="PhageTable_Out.tabular"/> + </test> + </tests> + <help><![CDATA[ +Generate an "annotation table" of a genome, with user-configurable data columns +]]></help> + <expand macro="citations"/> +</tool> |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c phageqc_report_annotation_table.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phageqc_report_annotation_table.html Wed Apr 26 03:42:32 2023 +0000 |
| [ |
| @@ -0,0 +1,244 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> + <meta http-equiv="X-UA-Compatible" content="IE=edge"> + <meta name="viewport" content="width=device-width, initial-scale=1"> + <!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags --> + <meta name="description" content=""> + <meta name="author" content=""> + <title>Annotation Table</title> + <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.2/jquery.min.js"></script> + <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" crossorigin="anonymous"> + <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap-theme.min.css" crossorigin="anonymous"> + <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/js/bootstrap.min.js" crossorigin="anonymous"></script> + + <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.11/css/jquery.dataTables.css"> + <script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/1.10.11/js/jquery.dataTables.js"></script> + <style type="text/css"> +/* + * Base structure + */ + +/* Move down content because we have a fixed navbar that is 50px tall */ +body { + padding-top: 50px; +} + +h3:before { + display: block; + content: " "; + margin-top: -50px; + height: 50px; + visibility: hidden; +} + +/* + * Global add-ons + */ + +.sub-header { + padding-bottom: 10px; + border-bottom: 1px solid #eee; +} + +/* + * Top navigation + * Hide default border to remove 1px line. + */ +.navbar-fixed-top { + border: 0; +} + +/* + * Sidebar + */ + +/* Hide for mobile, show later */ +.sidebar { + display: none; +} +@media (min-width: 768px) { + .sidebar { + position: fixed; + top: 51px; + bottom: 0; + left: 0; + z-index: 1000; + display: block; + padding: 20px; + overflow-x: hidden; + overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */ + background-color: #f5f5f5; + border-right: 1px solid #eee; + } +} + +/* Sidebar navigation */ +.nav-sidebar { + margin-right: -21px; /* 20px padding + 1px border */ + margin-bottom: 20px; + margin-left: -20px; +} +.nav-sidebar > li > a { + padding-right: 20px; + padding-left: 20px; +} +.nav-sidebar > .active > a, +.nav-sidebar > .active > a:hover, +.nav-sidebar > .active > a:focus { + color: #fff; + background-color: #428bca; +} + + +/* + * Main content + */ + +.main { + padding: 20px; +} +@media (min-width: 768px) { + .main { + padding-right: 40px; + padding-left: 40px; + } +} +.main .page-header { + margin-top: 0; +} + + +/* + * Placeholder dashboard ideas + */ + +.placeholders { + margin-bottom: 30px; + text-align: center; +} +.placeholders h4 { + margin-bottom: 0; +} +.placeholder { + margin-bottom: 20px; +} +.placeholder img { + display: inline-block; + border-radius: 50%; +} + +td.moron { + font-size: 150%; + padding: 0px; + color: gray; +} +.strand_emph { + text-decoration: underline; + color: black; +} + + </style> + <!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries --> + <!--[if lt IE 9]> + <script src="//oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script> + <script src="//oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> + <![endif]--> + </head> + <body> + + <nav class="navbar navbar-inverse navbar-fixed-top"> + <div class="container-fluid"> + <div class="navbar-header"> + <a class="navbar-brand" href="#">Annotation Table</a> + </div> + </div> + </nav> + + <div class="container-fluid"> + <div class="row"> + <div class="col-md-12 main" id="main"> + <ul class="nav nav-tabs" role="tablist" id="myTabs"> + <li role="presentation" class="active"><a href="#overview" role="tab" data-toggle="tab">Overview</a></li> + {% for (record, data) in annotation_table_data %} + <li role="presentation"><a href="#{{ record.id }}" role="tab" data-toggle="tab">{{ record.id }}</a></li> + {% endfor %} + </ul> + + <!-- Tab panes --> + <div class="tab-content"> + <div role="tabpanel" class="tab-pane active" id="overview"> + Data on each organism will be accessible from the tabs above. + </div> + {% for (record, data) in annotation_table_data %} + <div role="tabpanel" class="tab-pane" id="{{ record.id }}"> + <table class="table table-striped" id="data"> + <thead> + <tr> + {% for col in annotation_table_col_names %} + <th>{{ col[0] }}</th> + {% endfor %} + </tr> + </thead> + <tbody> + {% for row in data %} + <tr> + {% for col in row %} + <td>{% if col is not string %}<ul>{% for val in col %}<li>{{ val }}</li>{% endfor %}</ul>{% else %}{{ col }}{% endif %}</td> + {% endfor %} + </tr> + {% endfor %} + </tbody> + </table> + </div> + {% endfor %} + </div> + </div> + </div> + </div> + + <script type="text/javascript"> + $(document).ready( function () { + + + +$('#myTabs a').click(function (e) { + e.preventDefault() + $(this).tab('show') +}) + + + +jQuery.fn.dataTable.ext.type.detect.unshift( function ( data ) { + if ( typeof data !== 'string' ) { + return null; + } + + var matches = data.match(/^(\d+)\.\.(\d+)/); + return matches ? 'genomic' : null; +} ); + + + +jQuery.extend( jQuery.fn.dataTableExt.oSort, { + "genomic-pre": function ( a ) { + var matches = a.match(/^(\d+)\.\.(\d+)/); + console.log(a + " " + matches[1]); + return parseInt(matches[1]); + }, + + "genomic-asc": function ( a, b ) { + return ((a < b) ? -1 : ((a > b) ? 1 : 0)); + }, + + "genomic-desc": function ( a, b ) { + return ((a < b) ? 1 : ((a > b) ? -1 : 0)); + } +} ); + + $('table').DataTable(); + }); + </script> + </body> +</html> |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c phageqc_report_annotation_table.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phageqc_report_annotation_table.tsv Wed Apr 26 03:42:32 2023 +0000 |
| [ |
| @@ -0,0 +1,8 @@ +{% for (record, dataset) in annotation_table_data %} +# {% for col in annotation_table_col_names %}{{ col[0] }} {% endfor %} +{% for row in dataset %} + +{% for col in row %} +{% if col is not string %}"{{ col | join }}"{% else %}{{ col }}{% endif %} {% endfor %} +{% endfor %} +{% endfor %} |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c test-data/NC_001416_Table_In.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_001416_Table_In.fasta Wed Apr 26 03:42:32 2023 +0000 |
| b |
| b'@@ -0,0 +1,810 @@\n+>NC_001416.1_phage_lambda\n+GGGCGGCGACCTCGCGGGTTTTCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCG\n+TTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACG\n+ACAGGTGCTGAAAGCGAGGCTTTTTGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGTCCGT\n+GGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGACATTTTCGGTGCGAGTATCCG\n+TACCATTCAGAACTGGCAGGAACAGGGAATGCCCGTTCTGCGAGGCGGTGGCAAGGGTAA\n+TGAGGTGCTTTATGACTCTGCCGCCGTCATAAAATGGTATGCCGAAAGGGATGCTGAAAT\n+TGAGAACGAAAAGCTGCGCCGGGAGGTTGAAGAACTGCGGCAGGCCAGCGAGGCAGATCT\n+CCAGCCAGGAACTATTGAGTACGAACGCCATCGACTTACGCGTGCGCAGGCCGACGCACA\n+GGAACTGAAGAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGT\n+GCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGCTCCCCCTGTCGGTGCA\n+GCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAA\n+AGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATAT\n+CGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCCGCGCCGGGCTTCGCTCACTGTTCA\n+GGCCGGAGCCACAGACCGCCGTTGAATGGGCGGATGCTAATTACTATCTCCCGAAAGAAT\n+CCGCATACCAGGAAGGGCGCTGGGAAACACTGCCCTTTCAGCGGGCCATCATGAATGCGA\n+TGGGCAGCGACTACATCCGTGAGGTGAATGTGGTGAAGTCTGCCCGTGTCGGTTATTCCA\n+AAATGCTGCTGGGTGTTTATGCCTACTTTATAGAGCATAAGCAGCGCAACACCCTTATCT\n+GGTTGCCGACGGATGGTGATGCCGAGAACTTTATGAAAACCCACGTTGAGCCGACTATTC\n+GTGATATTCCGTCGCTGCTGGCGCTGGCCCCGTGGTATGGCAAAAAGCACCGGGATAACA\n+CGCTCACCATGAAGCGTTTCACTAATGGGCGTGGCTTCTGGTGCCTGGGCGGTAAAGCGG\n+CAAAAAACTACCGTGAAAAGTCGGTGGATGTGGCGGGTTATGATGAACTTGCTGCTTTTG\n+ATGATGATATTGAACAGGAAGGCTCTCCGACGTTCCTGGGTGACAAGCGTATTGAAGGCT\n+CGGTCTGGCCAAAGTCCATCCGTGGCTCCACGCCAAAAGTGAGAGGCACCTGTCAGATTG\n+AGCGTGCAGCCAGTGAATCCCCGCATTTTATGCGTTTTCATGTTGCCTGCCCGCATTGCG\n+GGGAGGAGCAGTATCTTAAATTTGGCGACAAAGAGACGCCGTTTGGCCTCAAATGGACGC\n+CGGATGACCCCTCCAGCGTGTTTTATCTCTGCGAGCATAATGCCTGCGTCATCCGCCAGC\n+AGGAGCTGGACTTTACTGATGCCCGTTATATCTGCGAAAAGACCGGGATCTGGACCCGTG\n+ATGGCATTCTCTGGTTTTCGTCATCCGGTGAAGAGATTGAGCCACCTGACAGTGTGACCT\n+TTCACATCTGGACAGCGTACAGCCCGTTCACCACCTGGGTGCAGATTGTCAAAGACTGGA\n+TGAAAACGAAAGGGGATACGGGAAAACGTAAAACCTTCGTAAACACCACGCTCGGTGAGA\n+CGTGGGAGGCGAAAATTGGCGAACGTCCGGATGCTGAAGTGATGGCAGAGCGGAAAGAGC\n+ATTATTCAGCGCCCGTTCCTGACCGTGTGGCTTACCTGACCGCCGGTATCGACTCCCAGC\n+TGGACCGCTACGAAATGCGCGTATGGGGATGGGGGCCGGGTGAGGAAAGCTGGCTGATTG\n+ACCGGCAGATTATTATGGGCCGCCACGACGATGAACAGACGCTGCTGCGTGTGGATGAGG\n+CCATCAATAAAACCTATACCCGCCGGAATGGTGCAGAAATGTCGATATCCCGTATCTGCT\n+GGGATACTGGCGGGATTGACCCGACCATTGTGTATGAACGCTCGAAAAAACATGGGCTGT\n+TCCGGGTGATCCCCATTAAAGGGGCATCCGTCTACGGAAAGCCGGTGGCCAGCATGCCAC\n+GTAAGCGAAACAAAAACGGGGTTTACCTTACCGAAATCGGTACGGATACCGCGAAAGAGC\n+AGATTTATAACCGCTTCACACTGACGCCGGAAGGGGATGAACCGCTTCCCGGTGCCGTTC\n+ACTTCCCGAATAACCCGGATATTTTTGATCTGACCGAAGCGCAGCAGCTGACTGCTGAAG\n+AGCAGGTCGAAAAATGGGTGGATGGCAGGAAAAAAATACTGTGGGACAGCAAAAAGCGAC\n+GCAATGAGGCACTCGACTGCTTCGTTTATGCGCTGGCGGCGCTGCGCATCAGTATTTCCC\n+GCTGGCAGCTGGATCTCAGTGCGCTGCTGGCGAGCCTGCAGGAAGAGGATGGTGCAGCAA\n+CCAACAAGAAAACACTGGCAGATTACGCCCGTGCCTTATCCGGAGAGGATGAATGACGCG\n+ACAGGAAGAACTTGCCGCTGCCCGTGCGGCACTGCATGACCTGATGACAGGTAAACGGGT\n+GGCAACAGTACAGAAAGACGGACGAAGGGTGGAGTTTACGGCCACTTCCGTGTCTGACCT\n+GAAAAAATATATTGCAGAGCTGGAAGTGCAGACCGGCATGACACAGCGACGCAGGGGACC\n+TGCAGGATTTTATGTATGAAAACGCCCACCATTCCCACCCTTCTGGGGCCGGACGGCATG\n+ACATCGCTGCGCGAATATGCCGGTTATCACGGCGGTGGCAGCGGATTTGGAGGGCAGTTG\n+CGGTCGTGGAACCCACCGAGTGAAAGTGTGGATGCAGCCCTGTTGCCCAACTTTACCCGT\n+GGCAATGCCCGCGCAGACGATCTGGTACGCAATAACGGCTATGCCGCCAACGCCATCCAG\n+CTGCATCAGGATCATATCGTCGGGTCTTTTTTCCGGCTCAGTCATCGCCCAAGCTGGCGC\n+TATCTGGGCATCGGGGAGGAAGAAGCCCGTGCCTTTTCCCGCGAGGTTGAAGCGGCATGG\n+AAAGAGTTTGCCGAGGATGACTGCTGCTGCATTGACGTTGAGCGAAAACGCACGTTTACC\n+ATGATGATTCGGGAAGGTGTGGCCATGCACGCCTTTAACGGTGAACTGTTCGTTCAGGCC\n+ACCTGGGATACCAGTTCGTCGCGGCTTTTCCGGACACAGTTCCGGATGGTCAGCCCGAAG\n+CGCATCAGCAACCCGAACAATACCGGCGACAGCCGGAACTGCCGTGCCGGTGTGCAGATT\n+AATGACAGCGGTGCGGCGCTGGGATATTACGTCAGCGAGGACGGGTATCCTGGCTGGATG\n+CCGCAGAAATGGACATGGATACCCCGTGAGTTACCCGGCGGGCGCGCCTCGTTCATTCAC\n+GTTTTTGAACCCGTGGAGGACGGGCAGACTCGCGGTGCAAATGTGTTTTACAGCGTGATG\n+GAGCAGATGAAGATGCTCGACACGCTGCAGAACACGCAGCTGCAGAGCGCCATTGTGAAG\n+GCGATGTATGCCGCCACCATTGAGAGTGAGCTGGATACGCAGTCAGCGATGGATTTTATT\n+CTGGGCGCGAACAGTCAGGAGCAGCGGGAAAGGCTGACCGGCTGGATTGGTGAAATTGCC\n+GCGTATTACGCCGCAGCGCCGGTCCGGCTGGGAGGCGCAAAAGTACC'..b'CGCTTA\n+CTACCGATTCCGCCTAGTTGGTCACTTCGACGTATCGTCTGGAACTCCAACCATCGCAGG\n+CAGAGAGGTCTGCAAAATGCAATCCCGAAACAGTTCGCAGGTAATAGTTAGAGCCTGCAT\n+AACGGTTTCGGGATTTTTTATATCTGCACAACAGGTAAGAGCATTGAGTCGATAATCGTG\n+AAGAGTCGGCGAGCCTGGTTAGCCAGTGCTCTTTCCGTTGTGCTGAATTAAGCGAATACC\n+GGAAGCAGAACCGGATCACCAAATGCGTACAGGCGTCATCGCCGCCCAGCAACAGCACAA\n+CCCAAACTGAGCCGTAGCCACTGTCTGTCCTGAATTCATTAGTAATAGTTACGCTGCGGC\n+CTTTTACACATGACCTTCGTGAAAGCGGGTGGCAGGAGGTCGCGCTAACAACCTCCTGCC\n+GTTTTGCCCGTGCATATCGGTCACGAACAAATCTGATTACTAAACACAGTAGCCTGGATT\n+TGTTCTATCAGTAATCGACCTTATTCCTAATTAAATAGAGCAAATCCCCTTATTGGGGGT\n+AAGACATGAAGATGCCAGAAAAACATGACCTGTTGGCCGCCATTCTCGCGGCAAAGGAAC\n+AAGGCATCGGGGCAATCCTTGCGTTTGCAATGGCGTACCTTCGCGGCAGATATAATGGCG\n+GTGCGTTTACAAAAACAGTAATCGACGCAACGATGTGCGCCATTATCGCCTGGTTCATTC\n+GTGACCTTCTCGACTTCGCCGGACTAAGTAGCAATCTCGCTTATATAACGAGCGTGTTTA\n+TCGGCTACATCGGTACTGACTCGATTGGTTCGCTTATCAAACGCTTCGCTGCTAAAAAAG\n+CCGGAGTAGAAGATGGTAGAAATCAATAATCAACGTAAGGCGTTCCTCGATATGCTGGCG\n+TGGTCGGAGGGAACTGATAACGGACGTCAGAAAACCAGAAATCATGGTTATGACGTCATT\n+GTAGGCGGAGAGCTATTTACTGATTACTCCGATCACCCTCGCAAACTTGTCACGCTAAAC\n+CCAAAACTCAAATCAACAGGCGCCGGACGCTACCAGCTTCTTTCCCGTTGGTGGGATGCC\n+TACCGCAAGCAGCTTGGCCTGAAAGACTTCTCTCCGAAAAGTCAGGACGCTGTGGCATTG\n+CAGCAGATTAAGGAGCGTGGCGCTTTACCTATGATTGATCGTGGTGATATCCGTCAGGCA\n+ATCGACCGTTGCAGCAATATCTGGGCTTCACTGCCGGGCGCTGGTTATGGTCAGTTCGAG\n+CATAAGGCTGACAGCCTGATTGCAAAATTCAAAGAAGCGGGCGGAACGGTCAGAGAGATT\n+GATGTATGAGCAGAGTCACCGCGATTATCTCCGCTCTGGTTATCTGCATCATCGTCTGCC\n+TGTCATGGGCTGTTAATCATTACCGTGATAACGCCATTACCTACAAAGCCCAGCGCGACA\n+AAAATGCCAGAGAACTGAAGCTGGCGAACGCGGCAATTACTGACATGCAGATGCGTCAGC\n+GTGATGTTGCTGCGCTCGATGCAAAATACACGAAGGAGTTAGCTGATGCTAAAGCTGAAA\n+ATGATGCTCTGCGTGATGATGTTGCCGCTGGTCGTCGTCGGTTGCACATCAAAGCAGTCT\n+GTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGAC\n+TGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAA\n+AACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGTTGCCCATATC\n+GATGGGCAACTCATGCAATTATTGTGAGCAATACACACGCGCTTCCAGCGGAGTATAAAT\n+GCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTTAAC\n+AACATTTTCTGCGCCGCCACAAATTTTGGCTGCATCGACAGTTTTCTTCTGCCCAATTCC\n+AGAAACGAAGAAATGATGGGTGATGGTTTCCTTTGGTGCTACTGCTGCCGGTTTGTTTTG\n+AACAGTAAACGTCTGTTGAGCACATCCTGTAATAAGCAGGGCCAGCGCAGTAGCGAGTAG\n+CATTTTTTTCATGGTGTTATTCCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGA\n+AAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTA\n+TGTCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGG\n+GGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAACGATGCACACAGGGTTTAGCGCG\n+TACACGTATTGCATTATGCCAACGCCCCGGTGCTGACACGGAAGAAACCGGACGTTATGA\n+TTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTAT\n+CAAAGGTATAGTAATATCTTTTATGTTCATGGATATTTGTAACCCATCGGAAAACTCCTG\n+CTTTAGCAAGATTTTCCCTGTATTGCTGAAATGTGATTTCTCTTGATTTCAACCTATCAT\n+AGGACGTTTCTATAAGATGCGTGTTTCTTGAGAATTTAACATTTACAACCTTTTTAAGTC\n+CTTTTATTAACACGGTGTTATCGTTTTCTAACACGATGTGAATATTATCTGTGGCTAGAT\n+AGTAAATATAATGTGAGACGTTGTGACGTTTTAGTTCAGAATAAAACAATTCACAGTCTA\n+AATCTTTTCGCACTTGATCGAATATTTCTTTAAAAATGGCAACCTGAGCCATTGGTAAAA\n+CCTTCCATGTGATACGAGGGCGCGTAGTTTGCATTATCGTTTTTATCGTTTCAATCTGGT\n+CTGACCTCCTTGTGTTTTGTTGATGATTTATGTCAAATATTAGGAATGTTTTCACTTAAT\n+AGTATTGGTTGCGTAACAAAGTGCGGTCCTGCTGGCATTCTGGAGGGAAATACAACCGAC\n+AGATGTATGTAAGGCCAACGTGCTCAAATCTTCATACAGAAAGATTTGAAGTAATATTTT\n+AACCGCTAGATGAAGAGCAAGCGCATGGAGCGACAAAATGAATAAAGAACAATCTGCTGA\n+TGATCCCTCCGTGGATCTGATTCGTGTAAAAAATATGCTTAATAGCACCATTTCTATGAG\n+TTACCCTGATGTTGTAATTGCATGTATAGAACATAAGGTGTCTCTGGAAGCATTCAGAGC\n+AATTGAGGCAGCGTTGGTGAAGCACGATAATAATATGAAGGATTATTCCCTGGTGGTTGA\n+CTGATCACCATAACTGCTAATCATTCAAACTATTTAGTCTGTGACAGAGCCAACACGCAG\n+TCTGTCACTGTCAGGAAAGTGGTAAAACTGCAACTCAATTACTGCAATGCCCTCGTAATT\n+AAGTGAATTTACAATATCGTCCTGTTCGGAGGGAAGAACGCGGGATGTTCATTCTTCATC\n+ACTTTTAATTGATGTATATGCTCTCTTTTCTGACGTTAGTCTCCGACGGCAGGCTTCAAT\n+GACCCAGGCTGAGAAATTCCCGGACCCTTTTTGCTCAAGAGCGATGTTAATTTGTTCAAT\n+CATTTGGTTAGGAAAGCGGATGTTGCGGGTTGTTGTTCTGCGGGTTCTGTTCTTCGTTGA\n+CATGAGGTTGCCCCGTATTCAGTGTCGCTGATTTGTATTGTCTGAAGTTGTTTTTACGTT\n+AAGTTGATGCAGATCAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTT\n+GATGGCCTCCACGCACGTTGTGATATGTAGATGATAATCATTATCACTTTACGGGTCCTT\n+TCCGGTGATCCGACAGGTTACG\n' |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c test-data/NC_001416_Table_In.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_001416_Table_In.gff3 Wed Apr 26 03:42:32 2023 +0000 |
| b |
| b'@@ -0,0 +1,476 @@\n+##gff-version 3\n+##sequence-region NC_001416.1_phage_lambda 1 48502\n+NC_001416.1_phage_lambda\t.\tgene\t14261\t14875\t.\t+\t.\towner=jolenerr@tamu.edu;ID=cdb58372-2440-4e07-bcc4-739e0aba461f;date_last_modified=2020-05-27;Name=tail tip assembly protein K;date_creation=2020-05-13\n+NC_001416.1_phage_lambda\t.\tmRNA\t14261\t14875\t.\t+\t.\towner=jolenerr@tamu.edu;Parent=cdb58372-2440-4e07-bcc4-739e0aba461f;ID=c53587ff-12d9-4a3a-a7ac-e87e54c5232b;date_last_modified=2020-05-27;Name=tail tip assembly protein K;date_creation=2020-05-13\n+NC_001416.1_phage_lambda\t.\tCDS\t14276\t14875\t.\t+\t0\tParent=c53587ff-12d9-4a3a-a7ac-e87e54c5232b;ID=2d4171c3-93b5-4c30-afba-9a0969dd4a6f;Name=2d4171c3-93b5-4c30-afba-9a0969dd4a6f\n+NC_001416.1_phage_lambda\t.\texon\t14276\t14875\t.\t+\t.\tParent=c53587ff-12d9-4a3a-a7ac-e87e54c5232b;ID=782a319b-3988-4cb2-aedf-47242382005c;Name=782a319b-3988-4cb2-aedf-47242382005c\n+NC_001416.1_phage_lambda\t.\texon\t14261\t14265\t.\t+\t.\tParent=c53587ff-12d9-4a3a-a7ac-e87e54c5232b;ID=709a9728-db34-4010-bfc3-41b0687edb80;Name=709a9728-db34-4010-bfc3-41b0687edb80\n+###\n+NC_001416.1_phage_lambda\t.\tgene\t47727\t47944\t.\t+\t.\towner=jolenerr@tamu.edu;ID=e3d29177-18a8-4bc0-8d91-15e5760f3bd3;date_last_modified=2020-05-13;Name=NC_001416.1_phage_lambda.gene_60;date_creation=2020-05-13\n+NC_001416.1_phage_lambda\t.\tmRNA\t47727\t47944\t.\t+\t.\towner=jolenerr@tamu.edu;Parent=e3d29177-18a8-4bc0-8d91-15e5760f3bd3;ID=90e550aa-f463-46d2-bec4-87aa38e63ee2;date_last_modified=2020-05-13;Name=NC_001416.1_phage_lambda.gene_60-00001;date_creation=2020-05-13\n+NC_001416.1_phage_lambda\t.\tCDS\t47738\t47944\t.\t+\t0\tParent=90e550aa-f463-46d2-bec4-87aa38e63ee2;ID=586909d5-f3a6-44bb-8e9e-5a5230b2127a;Name=586909d5-f3a6-44bb-8e9e-5a5230b2127a\n+NC_001416.1_phage_lambda\t.\texon\t47727\t47730\t.\t+\t.\tParent=90e550aa-f463-46d2-bec4-87aa38e63ee2;ID=bf5e1837-0469-4372-9652-7677fee29843;Name=bf5e1837-0469-4372-9652-7677fee29843\n+NC_001416.1_phage_lambda\t.\texon\t47738\t47944\t.\t+\t.\tParent=90e550aa-f463-46d2-bec4-87aa38e63ee2;ID=14232a86-ebfe-4f10-aa28-2910207542f7;Name=14232a86-ebfe-4f10-aa28-2910207542f7\n+###\n+NC_001416.1_phage_lambda\t.\tgene\t13416\t14127\t.\t+\t.\towner=jolenerr@tamu.edu;ID=11a10b01-003c-4900-aae9-46139ae23652;date_last_modified=2020-05-27;Name=tail tip protein L;date_creation=2020-05-13\n+NC_001416.1_phage_lambda\t.\tmRNA\t13416\t14127\t.\t+\t.\towner=jolenerr@tamu.edu;Parent=11a10b01-003c-4900-aae9-46139ae23652;ID=07cc76d7-d0f4-447f-a851-3aeaee1b71ac;date_last_modified=2020-05-27;Name=tail tip protein L;date_creation=2020-05-13\n+NC_001416.1_phage_lambda\t.\tCDS\t13429\t14127\t.\t+\t0\tParent=07cc76d7-d0f4-447f-a851-3aeaee1b71ac;ID=37a2e1ad-d49c-43d3-b33b-727c848e2a38;Name=37a2e1ad-d49c-43d3-b33b-727c848e2a38\n+NC_001416.1_phage_lambda\t.\texon\t13429\t14127\t.\t+\t.\tParent=07cc76d7-d0f4-447f-a851-3aeaee1b71ac;ID=008fa66b-e5b3-489b-8d99-208103afde8f;Name=008fa66b-e5b3-489b-8d99-208103afde8f\n+NC_001416.1_phage_lambda\t.\texon\t13416\t13419\t.\t+\t.\tParent=07cc76d7-d0f4-447f-a851-3aeaee1b71ac;ID=0a4ad3d9-21dc-4fab-badb-a94e4493c397;Name=0a4ad3d9-21dc-4fab-badb-a94e4493c397\n+###\n+NC_001416.1_phage_lambda\t.\tgene\t19641\t20855\t.\t+\t.\towner=jolenerr@tamu.edu;ID=e7267f7d-4717-4e28-a1a0-564b10661248;date_last_modified=2020-05-27;Name=tail fiber protein stf;date_creation=2020-05-13\n+NC_001416.1_phage_lambda\t.\tmRNA\t19641\t20855\t.\t+\t.\towner=jolenerr@tamu.edu;Parent=e7267f7d-4717-4e28-a1a0-564b10661248;ID=b7a5dc48-88c5-4edc-9081-091ef39ff3ea;date_last_modified=2020-05-27;Name=tail fiber protein stf;date_creation=2020-05-13\n+NC_001416.1_phage_lambda\t.\texon\t19641\t19644\t.\t+\t.\tParent=b7a5dc48-88c5-4edc-9081-091ef39ff3ea;ID=e794f054-733e-4b10-99df-128b37cd80e8;Name=e794f054-733e-4b10-99df-128b37cd80e8\n+NC_001416.1_phage_lambda\t.\tCDS\t19650\t20855\t.\t+\t0\tParent=b7a5dc48-88c5-4edc-9081-091ef39ff3ea;ID=f1584714-9cc6-4209-8730-0d7c199cff35;Name=f1584714-9cc6-4209-8730-0d7c199cff35\n+NC_001416.1_phage_lambda\t.\texon\t19650\t20855\t.\t+\t.\tParent=b7a5dc48-88c5-4edc-9081-091ef39ff3ea;ID=b44a883e-e4e2-4432-b665-355a803943dc;Name=b44a883e-e4e2-4432-b665-35'..b'.\tgene\t38031\t38241\t.\t+\t.\towner=jason.gill@tamu.edu;Note=added by JJG;ID=d731b2bf-e9f9-484f-8851-814510c6a5ec;date_last_modified=2020-05-27;Name=regulatory protein cro;date_creation=2019-02-07\n+NC_001416.1_phage_lambda\t.\tmRNA\t38031\t38241\t.\t+\t.\towner=jason.gill@tamu.edu;Parent=d731b2bf-e9f9-484f-8851-814510c6a5ec;ID=5cfd706b-b814-43f9-b604-fc8c179f853a;date_last_modified=2020-05-27;Name=regulatory protein cro;date_creation=2019-02-07\n+NC_001416.1_phage_lambda\t.\texon\t38031\t38035\t.\t+\t.\tParent=5cfd706b-b814-43f9-b604-fc8c179f853a;ID=041be549-96a8-42a3-b5eb-258ebb4ffd5f;Name=041be549-96a8-42a3-b5eb-258ebb4ffd5f\n+NC_001416.1_phage_lambda\t.\tCDS\t38041\t38241\t.\t+\t0\tParent=5cfd706b-b814-43f9-b604-fc8c179f853a;ID=97688d3e-13d8-48fd-9e05-2d919293f914;Name=97688d3e-13d8-48fd-9e05-2d919293f914\n+NC_001416.1_phage_lambda\t.\texon\t38041\t38241\t.\t+\t.\tParent=5cfd706b-b814-43f9-b604-fc8c179f853a;ID=e6686b84-108a-4c8f-a5b9-64b92b6dc5b5;Name=e6686b84-108a-4c8f-a5b9-64b92b6dc5b5\n+###\n+NC_001416.1_phage_lambda\t.\tgene\t38345\t38653\t.\t+\t.\towner=jason.gill@tamu.edu;Note=added by JJG;ID=1b331cf3-0897-4489-aa55-b14669ea5998;date_last_modified=2020-05-27;Name=regulatory protein cII;date_creation=2019-02-07\n+NC_001416.1_phage_lambda\t.\tmRNA\t38345\t38653\t.\t+\t.\towner=jason.gill@tamu.edu;Parent=1b331cf3-0897-4489-aa55-b14669ea5998;ID=b970dd3f-9787-459c-84ed-5b839b85b9e7;date_last_modified=2020-05-27;Name=regulatory protein cII;date_creation=2019-02-07\n+NC_001416.1_phage_lambda\t.\tCDS\t38360\t38653\t.\t+\t0\tParent=b970dd3f-9787-459c-84ed-5b839b85b9e7;ID=c4ae3e6a-4e56-412d-8ece-0036053910ef;Name=c4ae3e6a-4e56-412d-8ece-0036053910ef\n+NC_001416.1_phage_lambda\t.\texon\t38360\t38653\t.\t+\t.\tParent=b970dd3f-9787-459c-84ed-5b839b85b9e7;ID=c29fe89e-348d-4da7-b313-85c362f92307;Name=c29fe89e-348d-4da7-b313-85c362f92307\n+NC_001416.1_phage_lambda\t.\texon\t38345\t38348\t.\t+\t.\tParent=b970dd3f-9787-459c-84ed-5b839b85b9e7;ID=b2199555-1cbb-443c-92d3-fa5a0a17670e;Name=b2199555-1cbb-443c-92d3-fa5a0a17670e\n+###\n+NC_001416.1_phage_lambda\t.\tgene\t30392\t30626\t.\t-\t.\towner=jolenerr@tamu.edu;Note=Contains InterPro domain IPR000962;ID=4fba3f9c-cbc0-4454-b278-efe088695fef;date_last_modified=2020-05-27;Name=DksA/TraR C4-type zinc finger domain-containing protein;date_creation=2020-05-13\n+NC_001416.1_phage_lambda\t.\tmRNA\t30392\t30626\t.\t-\t.\towner=jolenerr@tamu.edu;Parent=4fba3f9c-cbc0-4454-b278-efe088695fef;ID=7dfc2c2d-a50d-4e77-b673-2dcd16c2ef3b;date_last_modified=2020-05-27;Name=DksA/TraR C4-type zinc finger domain-containing protein;date_creation=2020-05-13\n+NC_001416.1_phage_lambda\t.\texon\t30624\t30626\t.\t-\t.\tParent=7dfc2c2d-a50d-4e77-b673-2dcd16c2ef3b;ID=cbf0bbe9-fdae-426f-a6ce-40926606c1ca;Name=cbf0bbe9-fdae-426f-a6ce-40926606c1ca\n+NC_001416.1_phage_lambda\t.\tCDS\t30392\t30613\t.\t-\t0\tParent=7dfc2c2d-a50d-4e77-b673-2dcd16c2ef3b;ID=1fa7e4a7-9200-45d9-b9fd-21e36b254897;Name=1fa7e4a7-9200-45d9-b9fd-21e36b254897\n+NC_001416.1_phage_lambda\t.\texon\t30392\t30613\t.\t-\t.\tParent=7dfc2c2d-a50d-4e77-b673-2dcd16c2ef3b;ID=529064a4-a072-48ec-bd67-0eb3011ae53c;Name=529064a4-a072-48ec-bd67-0eb3011ae53c\n+###\n+NC_001416.1_phage_lambda\t.\tgene\t46174\t46368\t.\t+\t.\towner=jolenerr@tamu.edu;ID=18e578e1-38cb-4846-96e8-0190a5a26369;date_last_modified=2020-05-13;Name=o-spanin Rz1;date_creation=2020-05-13\n+NC_001416.1_phage_lambda\t.\tmRNA\t46174\t46368\t.\t+\t.\towner=jolenerr@tamu.edu;Parent=18e578e1-38cb-4846-96e8-0190a5a26369;ID=b4c199b2-1838-43c0-a09d-77718a49dbe2;date_last_modified=2020-05-13;Name=o-spanin Rz1;date_creation=2020-05-13\n+NC_001416.1_phage_lambda\t.\tCDS\t46186\t46368\t.\t+\t0\tParent=b4c199b2-1838-43c0-a09d-77718a49dbe2;ID=7ac7bb1c-0d6d-4476-8a02-8ad963da6156;Name=7ac7bb1c-0d6d-4476-8a02-8ad963da6156\n+NC_001416.1_phage_lambda\t.\texon\t46174\t46178\t.\t+\t.\tParent=b4c199b2-1838-43c0-a09d-77718a49dbe2;ID=668e24d1-fcea-459e-bbf3-6132bbb9854e;Name=668e24d1-fcea-459e-bbf3-6132bbb9854e\n+NC_001416.1_phage_lambda\t.\texon\t46186\t46368\t.\t+\t.\tParent=b4c199b2-1838-43c0-a09d-77718a49dbe2;ID=f8d07a76-6f8d-4100-9ba6-cec0e3a033f9;Name=f8d07a76-6f8d-4100-9ba6-cec0e3a033f9\n' |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c test-data/PhageTable_Out.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PhageTable_Out.html Wed Apr 26 03:42:32 2023 +0000 |
| [ |
| b'@@ -0,0 +1,2124 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <meta http-equiv="X-UA-Compatible" content="IE=edge">\n+ <meta name="viewport" content="width=device-width, initial-scale=1">\n+ <!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <title>Annotation Table</title>\n+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.2/jquery.min.js"></script>\n+\t<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" crossorigin="anonymous">\n+\t<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap-theme.min.css" crossorigin="anonymous">\n+\t<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/js/bootstrap.min.js" crossorigin="anonymous"></script>\n+\n+ <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.11/css/jquery.dataTables.css">\n+ <script type="text/javascript" charset="utf8" src="https://cdn.datatables.net/1.10.11/js/jquery.dataTables.js"></script>\n+ <style type="text/css">\n+/*\n+ * Base structure\n+ */\n+\n+/* Move down content because we have a fixed navbar that is 50px tall */\n+body {\n+ padding-top: 50px;\n+}\n+\n+h3:before {\n+ display: block;\n+ content: " ";\n+ margin-top: -50px;\n+ height: 50px;\n+ visibility: hidden;\n+}\n+\n+/*\n+ * Global add-ons\n+ */\n+\n+.sub-header {\n+ padding-bottom: 10px;\n+ border-bottom: 1px solid #eee;\n+}\n+\n+/*\n+ * Top navigation\n+ * Hide default border to remove 1px line.\n+ */\n+.navbar-fixed-top {\n+ border: 0;\n+}\n+\n+/*\n+ * Sidebar\n+ */\n+\n+/* Hide for mobile, show later */\n+.sidebar {\n+ display: none;\n+}\n+@media (min-width: 768px) {\n+ .sidebar {\n+ position: fixed;\n+ top: 51px;\n+ bottom: 0;\n+ left: 0;\n+ z-index: 1000;\n+ display: block;\n+ padding: 20px;\n+ overflow-x: hidden;\n+ overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */\n+ background-color: #f5f5f5;\n+ border-right: 1px solid #eee;\n+ }\n+}\n+\n+/* Sidebar navigation */\n+.nav-sidebar {\n+ margin-right: -21px; /* 20px padding + 1px border */\n+ margin-bottom: 20px;\n+ margin-left: -20px;\n+}\n+.nav-sidebar > li > a {\n+ padding-right: 20px;\n+ padding-left: 20px;\n+}\n+.nav-sidebar > .active > a,\n+.nav-sidebar > .active > a:hover,\n+.nav-sidebar > .active > a:focus {\n+ color: #fff;\n+ background-color: #428bca;\n+}\n+\n+\n+/*\n+ * Main content\n+ */\n+\n+.main {\n+ padding: 20px;\n+}\n+@media (min-width: 768px) {\n+ .main {\n+ padding-right: 40px;\n+ padding-left: 40px;\n+ }\n+}\n+.main .page-header {\n+ margin-top: 0;\n+}\n+\n+\n+/*\n+ * Placeholder dashboard ideas\n+ */\n+\n+.placeholders {\n+ margin-bottom: 30px;\n+ text-align: center;\n+}\n+.placeholders h4 {\n+ margin-bottom: 0;\n+}\n+.placeholder {\n+ margin-bottom: 20px;\n+}\n+.placeholder img {\n+ display: inline-block;\n+ border-radius: 50%;\n+}\n+\n+td.moron {\n+ font-size: 150%;\n+ padding: 0px;\n+ color: gray;\n+}\n+.strand_emph {\n+ text-decoration: underline;\n+ color: black;\n+}\n+\n+ </style>\n+ <!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries -->\n+ <!--[if lt IE 9]>\n+ <script src="//oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>\n+ <script src="//oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>\n+ <![endif]-->\n+ </head>\n+ <body>\n+\n+ <nav class="navbar navbar-inverse navbar-fixed-top">\n+ <div class="container-fluid">\n+ <div class="navbar-header">\n+ <a class="navbar-brand" href="#">Annotation Table</a>\n+ </div>\n+ </div>\n+ </nav>\n+\n+ <div class="container-fluid">\n+ <div class="row">\n+ <div class="col-md-12 main" id="main">\n+ <ul class="nav nav-tabs" role="tablist" id="myTabs">\n+ <li role="presentation" class="active"><a href="#overview" role="tab" data-toggle="tab">Overview</a></li>\n+ '..b' <td>None</td>\n+ <td>None</td>\n+ <td>None</td>\n+ <td>None</td>\n+ </tr>\n+ <tr>\n+ <td>NC_001416-1_phage_lambda</td>\n+ <td>e3d29177-18a8-4bc0-8d91-15e5760f3bd3</td>\n+ <td>gene</td>\n+ <td>NC_001416.1_phage_lambda.gene_60</td>\n+ <td>47727..47944</td>\n+ <td>47727</td>\n+ <td>47944</td>\n+ <td>+</td>\n+ <td>68</td>\n+ <td>GGAG</td>\n+ <td>7</td>\n+ <td>ATG</td>\n+ <td>TGA</td>\n+ <td>74</td>\n+ <td>752f31a0-018a-4223-a7f9-72685604b7a3</td>\n+ <td>jolenerr@tamu.edu</td>\n+ <td>2020-05-13</td>\n+ <td>2020-05-13</td>\n+ <td>None</td>\n+ <td>None</td>\n+ <td>None</td>\n+ <td>None</td>\n+ </tr>\n+ <tr>\n+ <td>NC_001416-1_phage_lambda</td>\n+ <td>e0b009e4-729e-4d97-b818-ec0cbebcb1f4</td>\n+ <td>gene</td>\n+ <td>NC_001416.1_phage_lambda.orf00102</td>\n+ <td>48109..48314</td>\n+ <td>48109</td>\n+ <td>48314</td>\n+ <td>-</td>\n+ <td>64</td>\n+ <td>GGGG</td>\n+ <td>7</td>\n+ <td>ATG</td>\n+ <td>TGA</td>\n+ <td>None</td>\n+ <td>None</td>\n+ <td>jolenerr@tamu.edu</td>\n+ <td>2020-05-13</td>\n+ <td>2020-05-13</td>\n+ <td>None</td>\n+ <td>None</td>\n+ <td>None</td>\n+ <td>None</td>\n+ </tr>\n+ </tbody>\n+ </table>\n+ </div>\n+ </div>\n+ </div>\n+ </div>\n+ </div>\n+\n+ <script type="text/javascript">\n+ $(document).ready( function () {\n+\n+\n+\n+$(\'#myTabs a\').click(function (e) {\n+\te.preventDefault()\n+\t$(this).tab(\'show\')\n+})\n+\n+\n+\n+jQuery.fn.dataTable.ext.type.detect.unshift( function ( data ) {\n+ if ( typeof data !== \'string\' ) {\n+ return null;\n+ }\n+\n+ var matches = data.match(/^(\\d+)\\.\\.(\\d+)/);\n+ return matches ? \'genomic\' : null;\n+} );\n+\n+\n+\n+jQuery.extend( jQuery.fn.dataTableExt.oSort, {\n+ "genomic-pre": function ( a ) {\n+ var matches = a.match(/^(\\d+)\\.\\.(\\d+)/);\n+ console.log(a + " " + matches[1]);\n+ return parseInt(matches[1]);\n+ },\n+\n+ "genomic-asc": function ( a, b ) {\n+ return ((a < b) ? -1 : ((a > b) ? 1 : 0));\n+ },\n+\n+ "genomic-desc": function ( a, b ) {\n+ return ((a < b) ? 1 : ((a > b) ? -1 : 0));\n+ }\n+} );\n+\n+ $(\'table\').DataTable();\n+ });\n+ </script>\n+ </body>\n+</html>\n' |
| b |
| diff -r 6a4d1bd8ac1d -r 32e011fa615c test-data/PhageTable_Out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PhageTable_Out.tabular Wed Apr 26 03:42:32 2023 +0000 |
| b |
| b'@@ -0,0 +1,79 @@\n+# Organism ID\tID\tType\tName\tLocation\tBoundary\tBoundary\tStrand\tCDS Length (AA)\tShine-Dalgarno sequence\tShine-Dalgarno spacing\tStart Codon\tStop Codon\tDistance to next upstream gene on same strand\tNext gene upstream\tOwner\tCreated\tLast Modified\tUser entered Notes\tDescription\tProduct\tDBxrefs\t\n+NC_001416.1_phage_lambda\t1185c0aa-14c4-45c3-ab0d-889bbfdbf137\tgene\tterminase small subunit\t181..736\t181\t736\t+\t181\tGGA\t7\tATG\tTAA\tNone\tNone\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t6d452f5a-9508-40c1-9d43-d98831ca8919\tgene\tterminase large subunit\t701..2636\t701\t2636\t+\t641\tGGGT\t6\tGTG\tTGA\t-36\t1185c0aa-14c4-45c3-ab0d-889bbfdbf137\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t38175e36-b9e9-48ea-9d1c-7f115fae7194\tgene\thead completion protein\t2622..2839\t2622\t2839\t+\t68\tGGAG\t7\tATG\tTGA\t-15\t6d452f5a-9508-40c1-9d43-d98831ca8919\tjolenerr@tamu.edu\t2020-05-13\t2020-05-28\tInterPro domain IPR004174\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t0695da41-cce8-4f07-a27a-eb42ac82ae56\tgene\tportal protein B\t2824..4437\t2824\t4437\t+\t533\tAGGA\t8\tATG\tTAA\t-16\t38175e36-b9e9-48ea-9d1c-7f115fae7194\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t422aab41-ac49-4818-b87e-9331023dcacf\tgene\tcapsid assembly protein\t4406..5737\t4406\t5737\t+\t673\t"GGAG, AGGAGG"\t"-609, 6"\t"GTG (4417..5737:1), GTG (5035..5737:1)"\tTAA\t-32\t0695da41-cce8-4f07-a27a-eb42ac82ae56\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t274304d3-079e-4e08-aa11-219235e1aacb\tgene\tcapsid decoration protein\t5739..6079\t5739\t6079\t+\t110\tGGA\t5\tATG\tTAA\t1\t422aab41-ac49-4818-b87e-9331023dcacf\tjolenerr@tamu.edu\t2020-05-13\t2020-05-28\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t4f815f9e-5092-4db3-b722-0d912c116293\tgene\tmajor capsid protein\t6099..7160\t6099\t7160\t+\t350\tAGG\t6\tGTG\tTAA\t19\t274304d3-079e-4e08-aa11-219235e1aacb\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t4da662d1-028a-43e2-9b50-f48ad03bdd64\tgene\tDNA packaging protein FI\t7173..7600\t7173\t7600\t+\t136\tGGGG\t13\tGTG\tTAA\t12\t4f815f9e-5092-4db3-b722-0d912c116293\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t638d1ac5-aea4-4988-b46d-01cf79793dfb\tgene\thead-tail connector protein FII\t7603..7965\t7603\t7965\t+\t117\tGGAG\t5\tGTG\tTGA\t2\t4da662d1-028a-43e2-9b50-f48ad03bdd64\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\tb541056e-bf91-4113-bce7-86bab4d27f76\tgene\ttail completion protein Z\t7968..8555\t7968\t8555\t+\t192\tGGGG\t5\tATG\tTGA\t2\t638d1ac5-aea4-4988-b46d-01cf79793dfb\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\tfca8745c-c433-4845-9430-c8a9dd4dc37b\tgene\ttail tube terminator protein U\t8535..8947\t8535\t8947\t+\t131\tAGGA\t13\tATG\tTGA\t-21\tb541056e-bf91-4113-bce7-86bab4d27f76\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\td9ee7b0e-b4a7-48cf-8c4b-aa95ca8863e0\tgene\ttail tube protein V\t8946..9695\t8946\t9695\t+\t246\tGAGG\t5\tATG\tTAA\t-2\tfca8745c-c433-4845-9430-c8a9dd4dc37b\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t0b5a859a-39f6-4c49-91b7-0b2def466374\tgene\ttape measure chaperone GT\t9699..10133\t9699\t10133\t+\t275\t"GGAG, GGAG"\t"8, 8"\t"ATG (9710..10133:1), ATG (9710..10115:1)"\tTGA\t3\td9ee7b0e-b4a7-48cf-8c4b-aa95ca8863e0\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\tc6a11d3b-7b9d-446f-ba16-3a642f3f6fbd\tgene\ttape measure chaperone GT\t10115..10549\t10115\t10549\t+\t144\tNone\tNone\tGTG\tTGA\t-19\t0b5a859a-39f6-4c49-91b7-0b2def466374\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t7ef9ffad-d420-4a1c-9a8d-2312dc04b558\tgene\ttape measure protein H\t10528..13103\t10528\t13103\t+\t853\tAGGAGG\t8\tATG\tTGA\t-22\tc6a11d3b-7b9d-446f-ba16-3a642f3f6fbd\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t55fe46da-9e0e-4454-aff9-f'..b'002363577\t42080..42272\t42080\t42272\t+\t60\tAGGAG\t5\tGTG\tTGA\t-44\tc402b694-7971-451b-aa24-4e70550eef2d\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t49135134-fa86-4df5-a0d7-b629ff152305\tgene\tCDS.0.1596_0.0419290277112\t42230..42439\t42230\t42439\t+\t66\tGGA\t6\tGTG\tTAA\t-43\t61a0d8bd-5b58-4077-bc04-2bcf4dee8939\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\ta8c3d9d2-cc66-4394-a821-ec0db2e411de\tgene\tNC_001416.1_phage_lambda.gene_51\t42419..43043\t42419\t43043\t+\t204\tGAGG\t6\tATG\tTGA\t-21\t49135134-fa86-4df5-a0d7-b629ff152305\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t0cea2875-2757-4c9b-97f5-7b0ec545394a\tgene\tNC_001416.1_phage_lambda.gene_52\t43032..43246\t43032\t43246\t+\t68\tGAG\t5\tATG\tTGA\t-12\ta8c3d9d2-cc66-4394-a821-ec0db2e411de\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t8ce6427a-594a-4320-955b-be6dd71ab223\tgene\tNC_001416.1_phage_lambda.gene_53\t43135..43889\t43135\t43889\t+\t221\tGGAG\t8\tATG\tTGA\t-112\t0cea2875-2757-4c9b-97f5-7b0ec545394a\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t1653554c-4be1-453b-a377-86e20759321a\tgene\tlate gene regulator\t43875..44509\t43875\t44509\t+\t207\tGGAG\t7\tATG\tTAG\t-15\t8ce6427a-594a-4320-955b-be6dd71ab223\tjolenerr@tamu.edu\t2020-05-13\t2020-05-27\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t6c3ab9c5-a407-47b8-89df-fa997262a409\tgene\tCDS.0.1630_0.132755174165\t44612..44815\t44612\t44815\t+\t64\tGGT\t6\tATG\tTAA\t102\t1653554c-4be1-453b-a377-86e20759321a\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t94064736-88a6-4e82-8c89-8226f57526e8\tgene\tantiholin S107\t45175..45509\t45175\t45509\t+\t213\t"GGGGG, GGGGG"\t"6, 6"\t"ATG (45185..45509:1), ATG (45191..45509:1)"\tTAA\t359\t6c3ab9c5-a407-47b8-89df-fa997262a409\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\tf8ba23df-ca21-4307-8f5a-ef8243f01acc\tgene\tendolysin R\t45483..45969\t45483\t45969\t+\t158\tGGAG\t6\tATG\tTGA\t-27\t94064736-88a6-4e82-8c89-8226f57526e8\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t4795342c-7959-44d9-925a-781f17371e7a\tgene\ti-spanin Rz\t45953..46427\t45953\t46427\t+\t153\tGAG\t10\tATG\tTAG\t-17\tf8ba23df-ca21-4307-8f5a-ef8243f01acc\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t18e578e1-38cb-4846-96e8-0190a5a26369\tgene\to-spanin Rz1\t46174..46368\t46174\t46368\t+\t60\tAGGAG\t7\tATG\tTGA\t-254\t4795342c-7959-44d9-925a-781f17371e7a\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t6eedd5c5-3c44-404a-af31-acee26522035\tgene\tbor\t46459..46763\t46459\t46763\t-\t97\tGGA\t8\tATG\tTAA\t132\t2da1b434-7877-4aa2-b88b-24922f70988b\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t2da1b434-7877-4aa2-b88b-24922f70988b\tgene\tCDS.0.3497_0.36888415839\t46896..47029\t46896\t47029\t-\t32\tGGGG\t10\tATG\tTAA\t12\t5d4e2403-4389-497c-a220-9740cd9935cc\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t5d4e2403-4389-497c-a220-9740cd9935cc\tgene\tCDS.0.2625_0.768191840841\t47042..47463\t47042\t47463\t-\t136\tAGGT\t7\tATG\tTAA\t645\te0b009e4-729e-4d97-b818-ec0cbebcb1f4\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\t752f31a0-018a-4223-a7f9-72685604b7a3\tgene\tCDS.0.864_0.667986446525\t47518..47652\t47518\t47652\t+\t40\tGGT\t9\tTTG\tTAA\t1149\t18e578e1-38cb-4846-96e8-0190a5a26369\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\te3d29177-18a8-4bc0-8d91-15e5760f3bd3\tgene\tNC_001416.1_phage_lambda.gene_60\t47727..47944\t47727\t47944\t+\t68\tGGAG\t7\tATG\tTGA\t74\t752f31a0-018a-4223-a7f9-72685604b7a3\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n+NC_001416.1_phage_lambda\te0b009e4-729e-4d97-b818-ec0cbebcb1f4\tgene\tNC_001416.1_phage_lambda.orf00102\t48109..48314\t48109\t48314\t-\t64\tGGGG\t7\tATG\tTGA\tNone\tNone\tjolenerr@tamu.edu\t2020-05-13\t2020-05-13\tNone\tNone\tNone\tNone\t\n' |