Mercurial > repos > cpt > cpt_gbk_to_gff
changeset 0:a68f32350196 draft
Uploaded
| author | cpt |
|---|---|
| date | Fri, 17 Jun 2022 12:46:43 +0000 |
| parents | |
| children | bb6332a85aa6 |
| files | cpt_gbk_to_gff/cpt-macros.xml cpt_gbk_to_gff/cpt_gbkToGff3.xml cpt_gbk_to_gff/gbk_to_gff3.py cpt_gbk_to_gff/macros.xml |
| diffstat | 4 files changed, 543 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_gbk_to_gff/cpt-macros.xml Fri Jun 17 12:46:43 2022 +0000 @@ -0,0 +1,115 @@ +<?xml version="1.0"?> +<macros> + <xml name="gff_requirements"> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package" version="1.65">biopython</requirement> + <requirement type="package" version="2.12.1">requests</requirement> + <yield/> + </requirements> + <version_command> + <![CDATA[ + cd $__tool_directory__ && git rev-parse HEAD + ]]> + </version_command> + </xml> + <xml name="citation/mijalisrasche"> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex">@unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-crr"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Ross}, + title = {CPT Galaxy Tools}, + year = {2020-}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-2020"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Criscione}, + title = {CPT Galaxy Tools}, + year = {2019-2021}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-2020-AJC-solo"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Criscione}, + title = {CPT Galaxy Tools}, + year = {2019-2021}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-clm"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Maughmer}, + title = {CPT Galaxy Tools}, + year = {2017-2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="sl-citations-clm"> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Maughmer}, + title = {CPT Galaxy Tools}, + year = {2017-2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_gbk_to_gff/cpt_gbkToGff3.xml Fri Jun 17 12:46:43 2022 +0000 @@ -0,0 +1,49 @@ +<?xml version="1.0"?> +<tool id="edu.tamu.cpt.gff3.customGbkToGff" name="(CPT) Genbank to GFF3: " version="20.1.0.0"> + <description> CPT made Biobython-based solution</description> + <macros> + <import>macros.xml</import> + <import>cpt-macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ +$__tool_directory__/gbk_to_gff3.py +$gbkIn +$makeMRNA +$makeGene +--identifier "$qualID" +--fastaFile $fastaOut +> $default]]></command> + <inputs> + <param label="GenBank file" name="gbkIn" type="data" format="genbank"/> + <param checked="true" label="Automatically generate any missing Gene features if CDS/RBS has none" name="makeGene" + type="boolean" truevalue="--makeGene" falsevalue=""/> + <param checked="true" label="Automatically generate missing mRNA features for genes" name="makeMRNA" + type="boolean" truevalue="--makeMRNA" falsevalue=""/> + <param label="Qualifier to derive GFF ID from" name="qualID" type="text" value="locus_tag"/> + </inputs> + <outputs> + <data format="gff3" hidden="false" name="default"/> + <data format="fasta" hidden="false" name="fastaOut"/> + </outputs> + <tests> + </tests> + <help><![CDATA[ +**What it does** + +A Biopython-based script to convert Genbank files to GFF3. Should resolve frame shift errors and other problems caused by the old Bioperl solution. + +Will also attempt to automatically parent RBS, CDS, and Exon features without a locus tag to an appropriate gene feature. +]]></help> + <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> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_gbk_to_gff/gbk_to_gff3.py Fri Jun 17 12:46:43 2022 +0000 @@ -0,0 +1,274 @@ +#!/usr/bin/env python + +import argparse +import sys + +from Bio import SeqIO +from Bio.SeqRecord import SeqRecord +from Bio.SeqFeature import FeatureLocation +from CPT_GFFParser import gffSeqFeature, gffWrite + +bottomFeatTypes = ["exon", "RBS", "CDS"] + +def makeGffFeat(inFeat, num, recName, identifier): + if inFeat.type == "RBS" or (inFeat.type == "regulatory" and "regulatory_class" in inFeat.qualifiers.keys() and inFeat.qualifiers["regulatory_class"][0] == "ribosome_binding_site"): + inFeat.type = "Shine_Dalgarno_sequence" + if "codon_start" in inFeat.qualifiers.keys(): + shift = int(inFeat.qualifiers["codon_start"][0]) - 1 + else: + shift = "." + if identifier in inFeat.qualifiers.keys(): + name = inFeat.qualifiers[identifier][0] + "." + inFeat.type + if num > 0: + name += "." + str(num) + else: + name = recName + "." + inFeat.type + "." + str(num) + + outFeat = gffSeqFeature(inFeat.location, inFeat.type, '', inFeat.strand, name, inFeat.qualifiers, None, None, None, shift, 0, "GbkToGff") + outFeat.qualifiers["ID"] = [name] + return outFeat + +def main(inFile, makeMRNA, makeGene, identifier, fastaFile, outFile): + + ofh = sys.stdout + if outFile: + ofh = outFile + + outRec = [] + failed = 0 + for rec in SeqIO.parse(inFile, "genbank"): + recID = rec.name + + if len(str(rec.seq)) > 0: + seqs_pending_writes = True + outSeq = str(rec.seq) + seqLen = len(outSeq) + + locBucket = {} + outFeats = [] + topTypeDict = {} + seekingParent = [] + geneNum = 0 + autoGeneNum = 0 + for feat in rec.features: + if identifier not in feat.qualifiers.keys(): #Allow metadata features and other features with no ID (Output warning?) - AJC + if feat.type in bottomFeatTypes: + seekingParent.append([feat, [], []]) # [Feature, all parent candidates, strongest parent candidates] + continue + elif feat.type not in topTypeDict.keys(): + topTypeDict[feat.type] = 1 + else: + topTypeDict[feat.type] += 1 + outFeats.append(makeGffFeat(feat, topTypeDict[feat.type], recID, identifier)) + continue + elif feat.qualifiers[identifier][0] not in locBucket.keys(): + locBucket[feat.qualifiers[identifier][0]] = [] + locBucket[feat.qualifiers[identifier][0]].append(feat) + + for locus in locBucket.keys(): + minLoc = locBucket[locus][0].location.start + maxLoc = locBucket[locus][0].location.end + for feat in locBucket[locus]: + minLoc = min(minLoc, feat.location.start) + maxLoc = max(maxLoc, feat.location.end) + for x in seekingParent: + if x[0].location.start >= minLoc and x[0].location.end <= maxLoc: + x[1].append(locus) + if x[0].location.start == minLoc or x[0].location.end == maxLoc: + x[2].append(locus) + + for x in seekingParent: #Reformat to [Feature, Locus, Unused/Free] + if len(x[2]) == 1: + finList = "" + if len(x[1]) > 1: + for loc in x[1]: + if loc != x[2][0]: + finList += loc + ", " + finList = str(x[0].type) + " had no locus tag set in .gbk file, automatically derived. Other, weaker candidate(s) were " + finList[0:-2] + "." + else: + finList = str(x[0].type) + " had no locus tag set in .gbk file, automatically derived." + if "Notes" not in x[0].qualifiers.keys(): + x[0].qualifiers["Notes"] = [] + x[0].qualifiers["Notes"].append(finList) + x[1] = x[2][0] + elif len(x[2]) > 1: + candidate = x[2][0] #Arbitrarily choose first one + finList = "" + strongList = "" + for loc in x[2]: + if loc != candidate: + finList += loc + ", " + strongList += loc + ", " + for loc in x[1]: + if loc not in x[2]: + finList += loc + ", " + finList = str(x[0].type) + " had no locus tag set in .gbk file, automatically derived. Other candidate(s) were " + finList[0:-2] + " (Equally strong candidate(s): " + strongList[0:-2] + ")." + if "Notes" not in x[0].qualifiers.keys(): + x[0].qualifiers["Notes"] = [] + x[0].qualifiers["Notes"].append(finList) + x[1] = candidate + elif len(x[1]) == 1: + x[1] = x[1][0] + if "Notes" not in x[0].qualifiers.keys(): + x[0].qualifiers["Notes"] = [] + finList = str(x[0].type) + " had no locus tag set in .gbk file, automatically derived." + x[0].qualifiers["Notes"].append(finList) + elif len(x[1]) > 1: + candidate = x[1][0] #Arbitrarily choose first one + finList = "" + for loc in x[1]: + if loc != candidate: + finList += loc + ", " + finList = str(x[0].type) + " had no locus tag set in .gbk file, automatically derived. Other candidates were " + finList[0:-2] + "." + if "Notes" not in x[0].qualifiers.keys(): + x[0].qualifiers["Notes"] = [] + x[0].qualifiers["Notes"].append(finList) + x[1] = candidate + else: + if makeGene: + sys.stderr.write("Warning: Unable to find potential parent for feature with no " + identifier + " of type " + str(x[0].type) + " at location [" + str(x[0].location.start + 1) + ", " + str(x[0].location.end) + "], creating standalone gene.\n") + autoGeneNum += 1 + x[0].source = "GbkToGff" + x[0].score = 0 + x[0].shift = 0 + if "ID" not in x[0].qualifiers.keys(): + x[0].qualifiers["ID"] = [recID + ".standalone_" + x[0].type + "." + str(autoGeneNum)] + tempName = recID + ".derived_Gene." + str(autoGeneNum) + tempQuals = {"ID" : [tempName], "Notes" : ["Gene feature automatically generated by Gbk to GFF conversion"]} + tempGene = gffSeqFeature(FeatureLocation(x[0].location.start, x[0].location.end, x[0].location.strand), 'gene', '', x[0].strand, tempName, tempQuals, None, None, None, ".", 0, "GbkToGff") + if makeMRNA: + tempName = recID + ".derived_mRNA." + str(autoGeneNum) + tempQuals = {"ID" : [tempName], "Notes" : ["mRNA feature automatically generated by Gbk to GFF conversion"]} + tempGene.sub_features.append(gffSeqFeature(FeatureLocation(x[0].location.start, x[0].location.end, x[0].location.strand), 'mRNA', '', x[0].strand, tempName, tempQuals, None, None, None, ".", 0, "GbkToGff")) + tempGene.sub_features[-1].sub_features.append(x[0]) + else: + tempGene.sub_features.append(x[0]) + + + outFeats.append(tempGene) + else: + sys.stderr.write("Warning: Unable to find potential parent for feature with no " + identifier + " of type " + str(x[0].type) + " at location [" + str(x[0].location.start + 1) + ", " + str(x[0].location.end) + "].\n") + if x[0].type not in topTypeDict.keys(): + topTypeDict[x[0].type] = 1 + else: + topTypeDict[x[0].type] += 1 + outFeats.append(makeGffFeat(x[0], topTypeDict[x[0].type], recID, identifier)) + + for locus in locBucket.keys(): + if len(locBucket[locus]) == 1: # No heirarchy to be made + outFeats.append(makeGffFeat(locBucket[locus][0], 0, recID, identifier)) + continue + topFeat = None + midFeat = None + bottomFeats = [] + typeDict = {} + minLoc = locBucket[locus][0].location.start + maxLoc = locBucket[locus][0].location.end + geneNum += 1 + for feat in locBucket[locus]: + # If we want to make our own top-level feat? + minLoc = min(minLoc, feat.location.start) + maxLoc = max(maxLoc, feat.location.end) + + # Gene->mRNA->CDS included as example, to add other feature-heirarchys in the appropriate slot + if feat.type in ['gene']: + if not topFeat: + topFeat = feat + # Else handle multiple top features + elif feat.type in ['mRNA', 'tRNA', 'rRNA']: + if not midFeat: + midFeat = feat + # Else handle multiple mid feats (May need another elif type-in-list statement if we actually expect a list of mid feats) + else: + if feat.type not in typeDict.keys(): + typeDict[feat.type] = 1 + else: + typeDict[feat.type] += 1 + bottomFeats.append(feat) + + for x in seekingParent: + if type(x[1]) != "list" and locus == x[1]: + x[0].qualifiers[identifier] = [locus] + bottomFeats.append(x[0]) + if x[0].type not in typeDict.keys(): + typeDict[x[0].type] = 1 + else: + typeDict[x[0].type] += 1 + + + + + + #if not topFeat: # Make our own top-level feature based off minLoc, maxLoc bounds + + for x in typeDict.keys(): # If only 1, set it to 0 so we don't append a number to the name + if typeDict[x] == 1: # Else, set to 1 so that we count up as we encounter the features + typeDict[x] = 0 + else: + typeDict[x] = 1 + + if not topFeat: + if makeGene: + if midFeat: + possibleStrand = midFeat.strand + else: + possibleStrand = bottomFeats[0].strand + tempName = recID + ".gene." + str(geneNum) + tempQuals = {identifier : [locus], "ID" : [tempName], "Notes" : ["Gene feature automatically generated by Gbk to GFF conversion"]} + topFeat = gffSeqFeature(FeatureLocation(minLoc, maxLoc, possibleStrand), 'gene', '', possibleStrand, tempName, tempQuals, None, None, None, ".", 0, "GbkToGff") + else: + sys.stderr.write("Unable to create a feature heirarchy at location [%d, %d] with features: \n" % (minLoc, maxLoc)) + for x in locBucket[locus]: + sys.stderr.write(str(x)) + sys.stderr.write('\n') + failed = 1 + continue + + outFeats.append(makeGffFeat(topFeat, 0, recID, identifier)) + if not midFeat and topFeat.type == "gene" and makeMRNA: + if identifier in topFeat.qualifiers.keys(): + tempName = topFeat.qualifiers[identifier][0] + ".mRNA" + tempQuals = {identifier : topFeat.qualifiers[identifier], "ID" : [tempName], "Notes" : ["mRNA feature automatically generated by Gbk to GFF conversion"]} + else: + tempName = outFeats[-1].ID + ".mRNA" + tempQuals = {identifier : topFeat.qualifiers[identifier], "ID" : [tempName], "Notes" : ["mRNA feature automatically generated by Gbk to GFF conversion"]} + midFeat = gffSeqFeature(FeatureLocation(minLoc, maxLoc, topFeat.strand), 'mRNA', '', topFeat.strand, tempName, tempQuals, None, None, None, ".", 0, "GbkToGff") + + if midFeat: # Again, need a new if statement if we want to handle multiple mid-tier features + outFeats[-1].sub_features.append(makeGffFeat(midFeat, 0, recID, identifier)) + outFeats[-1].sub_features[-1].qualifiers["Parent"] = [outFeats[-1].id] + for x in bottomFeats: + typeDict[x.type] += 1 + outFeats[-1].sub_features[-1].sub_features.append(makeGffFeat(x, typeDict[x.type], recID, identifier)) + outFeats[-1].sub_features[-1].sub_features[-1].qualifiers["Parent"] = [outFeats[-1].sub_features[-1].id] + else: # No midFeat, append bottom feats directly to top feats + for x in bottomFeats: + typeDict[x.type] += 1 + outFeats[-1].sub_features.append(makeGffFeat(x, typeDict[x.type], recID, identifier)) + outFeats[-1].sub_features[-1].qualifiers["Parent"] = [outFeats[-1].id] + + outRec.append(SeqRecord(rec.seq, recID, rec.name, rec.description, rec.dbxrefs, sorted(outFeats, key=lambda x: x.location.start), rec.annotations, rec.letter_annotations)) + SeqIO.write([outRec[-1]], fastaFile, "fasta") + gffWrite(outRec, ofh) + exit(failed) # 0 if all features handled, 1 if unable to handle some + + +if __name__ == '__main__': + parser = argparse.ArgumentParser( description='Biopython solution to Gbk to GFF conversion') + + parser.add_argument('inFile', type=argparse.FileType("r"), help='Path to an input GBK file' ) + parser.add_argument('--makeMRNA', action="store_true", required=False, help="Automatically create mRNA features") + parser.add_argument('--makeGene', action="store_true", required=False, help="Automatically create missing Gene features") + parser.add_argument('--identifier', type=str, default="locus_tag", required=False, help="Qualifier to derive ID property from") + parser.add_argument('--fastaFile', type=argparse.FileType("w"), help='Fasta output for sequences' ) + parser.add_argument('--outFile', type=argparse.FileType("w"), help='GFF feature output' ) + args = parser.parse_args() + main(**vars(args)) + + + + + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_gbk_to_gff/macros.xml Fri Jun 17 12:46:43 2022 +0000 @@ -0,0 +1,105 @@ +<?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="ldap_ref" + token_name="dn_ref" + token_label="Pick a DN" + token_fromfile="ldap_people.loc"> + <repeat name="repeat_@NAME@" title="@LABEL@"> + <param name="@NAME@" label="Select a @LABEL@" type="select"> + <options from_file="@FROMFILE@"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + </repeat> + </xml> + <xml name="ldap_ref_single" + token_name="dn_ref" + token_label="Pick a DN" + token_fromfile="ldap_people.loc"> + <param name="@NAME@" label="Select a @LABEL@" type="select"> + <options from_file="@FROMFILE@"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + </xml> + <xml name="gbk_feature_type" + token_label="Feature type to remove" + token_multiple="True" + token_optional="False" + token_name="positional_2"> + <param label="@LABEL@" optional="@TOKEN_OPTIONAL" multiple="@MULTIPLE@" name="feature_type" type="select"> + <option value="-10_signal">-10_signal</option> + <option value="-35_signal">-35_signal</option> + <option value="3'UTR">3'UTR</option> + <option value="5'UTR">5'UTR</option> + <option value="CAAT_signal">CAAT_signal</option> + <option selected="true" value="CDS">CDS</option> + <option value="C_region">C_region</option> + <option value="D-loop">D-loop</option> + <option value="D_segment">D_segment</option> + <option value="GC_signal">GC_signal</option> + <option value="J_segment">J_segment</option> + <option value="LTR">LTR</option> + <option value="N_region">N_region</option> + <option value="RBS">RBS</option> + <option value="STS">STS</option> + <option value="S_region">S_region</option> + <option value="TATA_signal">TATA_signal</option> + <option value="V_region">V_region</option> + <option value="V_segment">V_segment</option> + <option value="all">all</option> + <option value="assembly_gap">assembly_gap</option> + <option value="attenuator">attenuator</option> + <option value="enhancer">enhancer</option> + <option value="exon">exon</option> + <option value="gap">gap</option> + <option value="gene">gene</option> + <option value="iDNA">iDNA</option> + <option value="intron">intron</option> + <option value="mRNA">mRNA</option> + <option value="mat_peptide">mat_peptide</option> + <option value="misc_RNA">misc_RNA</option> + <option value="misc_binding">misc_binding</option> + <option value="misc_difference">misc_difference</option> + <option value="misc_feature">misc_feature</option> + <option value="misc_recomb">misc_recomb</option> + <option value="misc_signal">misc_signal</option> + <option value="misc_structure">misc_structure</option> + <option value="mobile_element">mobile_element</option> + <option value="modified_base">modified_base</option> + <option value="ncRNA">ncRNA</option> + <option value="old_sequence">old_sequence</option> + <option value="operon">operon</option> + <option value="oriT">oriT</option> + <option value="polyA_signal">polyA_signal</option> + <option value="polyA_site">polyA_site</option> + <option value="precursor_RNA">precursor_RNA</option> + <option value="prim_transcript">prim_transcript</option> + <option value="primer_bind">primer_bind</option> + <option value="promoter">promoter</option> + <option value="protein_bind">protein_bind</option> + <option value="rRNA">rRNA</option> + <option value="rep_origin">rep_origin</option> + <option value="repeat_region">repeat_region</option> + <option value="sig_peptide">sig_peptide</option> + <option value="source">source</option> + <option value="stem_loop">stem_loop</option> + <option value="tRNA">tRNA</option> + <option value="terminator">terminator</option> + <option value="tmRNA">tmRNA</option> + <option value="transit_peptide">transit_peptide</option> + <option value="unsure">unsure</option> + <option value="variation">variation</option> + </param> + </xml> +</macros>