| Next changeset 1:0b22a90c660e (2022-05-20) |
|
Commit message:
Uploaded |
|
added:
cpt_fix_aragorn/cpt-macros.xml cpt_fix_aragorn/fix-aragorn-gff3.py cpt_fix_aragorn/fix-aragorn-gff3.xml cpt_fix_aragorn/gff3.py cpt_fix_aragorn/macros.xml cpt_fix_aragorn/test-data/FixAra_In.gff3 cpt_fix_aragorn/test-data/FixAra_Out.gff3 |
| b |
| diff -r 000000000000 -r 8e124760f3cc cpt_fix_aragorn/cpt-macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_fix_aragorn/cpt-macros.xml Fri May 13 17:59:38 2022 +0000 |
| [ |
| @@ -0,0 +1,115 @@ +<?xml version="1.0"?> +<macros> + <xml name="gff_requirements"> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package" version="1.65">biopython</requirement> + <requirement type="package" version="2.12.1">requests</requirement> + <yield/> + </requirements> + <version_command> + <![CDATA[ + cd $__tool_directory__ && git rev-parse HEAD + ]]> + </version_command> + </xml> + <xml name="citation/mijalisrasche"> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex">@unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-crr"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Ross}, + title = {CPT Galaxy Tools}, + year = {2020-}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-2020"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Criscione}, + title = {CPT Galaxy Tools}, + year = {2019-2021}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-2020-AJC-solo"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Criscione}, + title = {CPT Galaxy Tools}, + year = {2019-2021}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-clm"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Maughmer}, + title = {CPT Galaxy Tools}, + year = {2017-2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="sl-citations-clm"> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Maughmer}, + title = {CPT Galaxy Tools}, + year = {2017-2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r 8e124760f3cc cpt_fix_aragorn/fix-aragorn-gff3.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_fix_aragorn/fix-aragorn-gff3.py Fri May 13 17:59:38 2022 +0000 |
| [ |
| @@ -0,0 +1,65 @@ +#!/usr/bin/env python +import sys +import logging +import argparse +from CPT_GFFParser import gffParse, gffWrite, gffSeqFeature +from Bio.SeqFeature import SeqFeature +from gff3 import feature_lambda, feature_test_type + +logging.basicConfig(level=logging.INFO) +log = logging.getLogger(__name__) + + +def fixed_feature(rec): + for idx, feature in enumerate( + feature_lambda( + rec.features, feature_test_type, {"types": ["tRNA", "tmRNA"]}, subfeatures=True + ) + ): + + fid = "%s-%03d" % (feature.type, 1 + idx) + try: + name = [feature.type + "-" + feature.qualifiers["Codon"][0]] + except KeyError: + name = [feature.qualifiers['product'][0]] + try: + origSource = feature.qualifiers["source"][0] + except: + origSource = "." + gene = gffSeqFeature( + location=feature.location, + type="gene", + qualifiers={"ID": [fid + ".gene"], "source": [origSource], "Name": name}, + ) + feature.qualifiers["Name"] = name + # Below that we have an mRNA + exon = gffSeqFeature( + location=feature.location, + type="exon", + qualifiers={"source": [origSource], "ID": ["%s.exon" % fid], "Name": name}, + ) + feature.qualifiers["ID"] = [fid] + exon.qualifiers["Parent"] = [fid] + feature.qualifiers["Parent"] = [fid + ".gene"] + # gene -> trna -> exon + feature.sub_features = [exon] + gene.sub_features = [feature] + yield gene + + +def gff_filter(gff3): + found_gff = False + for rec in gffParse(gff3): + found_gff = True + rec.features = sorted(list(fixed_feature(rec)), key=lambda x: x.location.start) + rec.annotations = {} + gffWrite([rec], sys.stdout) + if not found_gff: + print("##gff-version 3") + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="add parent gene features to CDSs") + parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 annotations") + args = parser.parse_args() + gff_filter(**vars(args)) |
| b |
| diff -r 000000000000 -r 8e124760f3cc cpt_fix_aragorn/fix-aragorn-gff3.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_fix_aragorn/fix-aragorn-gff3.xml Fri May 13 17:59:38 2022 +0000 |
| [ |
| @@ -0,0 +1,33 @@ +<?xml version="1.0"?> +<tool id="edu.tamu.cpt.external.aragorn-gff3" name="Fix tRNA model" version="19.1.0.0"> + <description></description> + <macros> + <import>macros.xml</import> + <import>cpt-macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ +$__tool_directory__/fix-aragorn-gff3.py +@INPUT_GFF@ +> $default]]></command> + <inputs> + <expand macro="gff3_input" /> + </inputs> + <outputs> + <data format="gff3" name="default"/> + </outputs> + <tests> + <test> + <param name="gff3_data" value="FixAra_In.gff3"/> + <output name="default" file="FixAra_Out.gff3"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +For an input GFF3 file with tRNAs from the Aragorn or converted from the tRNAscan-SE tools, this tool modifies +the gene model to reflect a gene-tRNA-exon hierarchy. That change is needed +to allow for creation of proper tRNA features in Apollo. + ]]></help> + <expand macro="citations" /> +</tool> |
| b |
| diff -r 000000000000 -r 8e124760f3cc cpt_fix_aragorn/gff3.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_fix_aragorn/gff3.py Fri May 13 17:59:38 2022 +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_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' |
| b |
| diff -r 000000000000 -r 8e124760f3cc cpt_fix_aragorn/macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_fix_aragorn/macros.xml Fri May 13 17:59:38 2022 +0000 |
| b |
| @@ -0,0 +1,66 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.7">python</requirement> + <requirement type="package" version="1.77">biopython</requirement> + <requirement type="package" version="1.1.3">cpt_gffparser</requirement> + <yield/> + </requirements> + </xml> + <xml name="genome_selector"> + <conditional name="reference_genome"> + <param name="reference_genome_source" type="select" label="Reference Genome"> + <option value="history" selected="True">From History</option> + <option value="cached">Locally Cached</option> + </param> + <when value="cached"> + <param name="fasta_indexes" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"/> + </param> + </when> + <when value="history"> + <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> + </when> + </conditional> + </xml> + <xml name="gff3_input"> + <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> + </xml> + <xml name="input/gff3+fasta"> + <expand macro="gff3_input" /> + <expand macro="genome_selector" /> + </xml> + <token name="@INPUT_GFF@"> + "$gff3_data" + </token> + <token name="@INPUT_FASTA@"> +#if str($reference_genome.reference_genome_source) == 'cached': + "${reference_genome.fasta_indexes.fields.path}" +#else if str($reference_genome.reference_genome_source) == 'history': + genomeref.fa +#end if + </token> + <token name="@GENOME_SELECTOR_PRE@"> +#if $reference_genome.reference_genome_source == 'history': + ln -s $reference_genome.genome_fasta genomeref.fa; +#end if + </token> + <token name="@GENOME_SELECTOR@"> +#if str($reference_genome.reference_genome_source) == 'cached': + "${reference_genome.fasta_indexes.fields.path}" +#else if str($reference_genome.reference_genome_source) == 'history': + genomeref.fa +#end if + </token> + <xml name="input/fasta"> + <param label="Fasta file" name="sequences" type="data" format="fasta"/> + </xml> + + <token name="@SEQUENCE@"> + "$sequences" + </token> + <xml name="input/fasta/protein"> + <param label="Protein fasta file" name="sequences" type="data" format="fasta"/> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r 8e124760f3cc cpt_fix_aragorn/test-data/FixAra_In.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_fix_aragorn/test-data/FixAra_In.gff3 Fri May 13 17:59:38 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +##gff-version-3 +Phriendly aragorn tRNA 48610 48685 . - . Anticodon="tcc";Codon="Gly" |
| b |
| diff -r 000000000000 -r 8e124760f3cc cpt_fix_aragorn/test-data/FixAra_Out.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_fix_aragorn/test-data/FixAra_Out.gff3 Fri May 13 17:59:38 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +##gff-version 3 +Phriendly feature gene 48610 48685 . - . ID=tRNA-001.gene;source=.;Name=tRNA-"Gly"; +Phriendly aragorn tRNA 48610 48685 . - . Anticodon="tcc";Codon="Gly";Name=tRNA-"Gly";ID=tRNA-001;Parent=tRNA-001.gene; +Phriendly feature exon 48610 48685 . - . source=.;ID=tRNA-001.exon;Name=tRNA-"Gly";Parent=tRNA-001; |