Add virAnnot tool

tools/virAnnot/.shed.yml

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+categories:
+- Metagenomics
+description: virAnnot wrappers
+homepage_url: https://github.com/marieBvr/virAnnot
+type: unrestricted
+long_description: VirAnnot was build to ease the assembly, blast search, taxonomic
+  annotation and OTUs assignation of viral metagenomic NGS data. It is designed to
+  identify viruses in plant metagenomic data but it can be used to assemble and annotate
+  any sequences with the NCBI taxonomy.
+name: virannot
+owner: melefebvre
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for the anndata tool suite: {{ tool_name }}"
+suite:
+  name: "suite_virannot"
+  description: "Add taxonomic info to HTS data and assign viral OTUs"
+  long_description: "VirAnnot was build to ease the assembly, blast search, taxonomic
+  annotation and OTUs assignation of viral metagenomic NGS data. It is designed to
+  identify viruses in plant metagenomic data but it can be used to assemble and annotate
+  any sequences with the NCBI taxonomy."

tools/virAnnot/blast2tsv.py

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+#!/usr/bin/env python3
+
+
+# Name: blast2tsv
+# Author(s): Sebastien Theil, Marie Lefebvre - INRAE
+# Aims: Convert blast xml output to tsv and add taxonomy
+
+
+import argparse
+import csv
+import logging as log
+import os
+
+from Bio import Entrez
+from Bio import SeqIO
+from Bio.Blast import NCBIXML
+from ete3 import NCBITaxa
+
+ncbi = NCBITaxa()
+
+
+def main():
+    options = _set_options()
+    _set_log_level(options.verbosity)
+    hits = _read_xml(options)
+    _write_tsv(options, hits)
+
+
+def _guess_database(accession):
+    """Guess the correct database for querying based off the format of the accession"""
+    database_mappings_refseq = {'AC_': 'nuccore', 'NC_': 'nuccore', 'NG_': 'nuccore',
+                                'NT_': 'nuccore', 'NW_': 'nuccore', 'NZ_': 'nuccore',
+                                'AP_': 'protein', 'NP_': 'protein', 'YP_': 'protein',
+                                'XP_': 'protein', 'WP_': 'protein'}
+    return database_mappings_refseq[accession[0:3]]
+
+
+def _read_xml(options):
+    """
+    Parse XML blast results file
+    Keep only the first hit
+    """
+    log.info("Read XML file.")
+    results = open(options.xml_file, 'r')
+    records = NCBIXML.parse(results)
+    xml_results = {}
+    for blast_record in records:
+        for aln in blast_record.alignments:
+            hit_count = 1
+            for hit in aln.hsps:
+                hsp = {}
+                if hit_count == 1:
+                    first_hit_frame = hit.frame[1] if len(hit.frame) > 0 else 0  # strand
+                    cumul_hit_identity = hit.identities if hit.identities else 0
+                    cumul_hit_score = hit.bits  # hit score
+                    cumul_hit_evalue = hit.expect  # evalue
+                    cumul_hit_length = hit.align_length if hit.align_length is not None else 0
+                    hit_count = hit_count + 1
+                else:
+                    # all HSPs in different strand than 1st HSPs will be discarded.
+                    if (first_hit_frame > 0 and hit.frame[1] > 0) or (first_hit_frame < 0 and hit.frame[1] < 0):
+                        cumul_hit_identity = cumul_hit_identity + hit.identities
+                        cumul_hit_length = cumul_hit_length + hit.align_length
+                        cumul_hit_evalue = cumul_hit_evalue + hit.expect
+                        cumul_hit_score = cumul_hit_score + hit.bits
+                        hit_count = hit_count + 1
+            if hit_count == 1:
+                final_hit_count = hit_count
+            elif hit_count > 1:
+                final_hit_count = hit_count - 1
+            hsp["evalue"] = cumul_hit_evalue / final_hit_count  # The smaller the E-value, the better the match
+            hsp["query_id"] = blast_record.query_id
+            hsp["query_length"] = blast_record.query_length  # length of the query
+            hsp["accession"] = aln.accession.replace("ref|", "")
+            hsp["description"] = aln.hit_def
+            hsp["hit_length"] = aln.length  # length of the hit
+            hsp["hsp_length"] = hit.align_length  # length of the hsp alignment
+            hsp["queryOverlap"] = _get_overlap_value(options.algo, hsp, 'hsp', hsp["query_length"])[0]
+            if cumul_hit_length == 0:
+                hsp["percentIdentity"] = round(cumul_hit_identity, 1)  # identity percentage
+            else:
+                hsp["percentIdentity"] = round(cumul_hit_identity / cumul_hit_length * 100, 1)  # identity percentage
+            hsp["score"] = cumul_hit_score  # The higher the bit-score, the better the sequence similarity
+            hsp["num_hsps"] = final_hit_count
+            hsp["hit_cumul_length"] = cumul_hit_length
+            hsp["hitOverlap"] = _get_overlap_value(options.algo, hsp, 'hit', hsp["query_length"])[1]
+            db = _guess_database(hsp["accession"])
+            try:
+                handle = Entrez.esummary(db=db, id=hsp["accession"])
+                taxid = str(int(Entrez.read(handle)[0]['TaxId']))
+                handle.close()
+                log.info("Taxid found for " + hsp["accession"])
+                lineage = ncbi.get_lineage(taxid)
+                names = ncbi.get_taxid_translator(lineage)
+                ordered = [names[tid] for tid in lineage]
+                taxonomy = ordered[1:]
+                hsp["tax_id"] = taxid
+                hsp["taxonomy"] = ';'.join(taxonomy)
+                hsp["organism"] = taxonomy[-1]
+            except RuntimeError:
+                hsp["tax_id"] = ""
+                hsp["taxonomy"] = ""
+                hsp["organism"] = ""
+                log.warning("RuntimeError - Taxid not found for " + hsp["accession"])
+            if hsp["evalue"] <= options.max_evalue and hsp["queryOverlap"] >= options.min_qov and \
+                    hsp["hitOverlap"] >= options.min_hov and hsp["score"] >= options.min_score:
+                xml_results[hsp["query_id"]] = hsp
+            else:
+                xml_results[hsp["query_id"]] = [hsp["query_length"]]
+
+    return xml_results
+
+
+def _get_overlap_value(algo, hsp, type, qlength):
+    """
+    Set hsp or hit overlap values for hit and query
+    Return array [query_overlap, hit_overlap]
+    """
+    if type == 'hsp':
+        q_align_len = qlength
+        h_align_len = hsp["hsp_length"]
+    else:
+        q_align_len = qlength
+        h_align_len = hsp["hit_cumul_length"]
+
+    if algo == 'BLASTX':
+        if q_align_len:
+            query_overlap = (q_align_len * 3 / q_align_len) * 100
+        if hsp["hit_length"]:
+            hit_overlap = (h_align_len / hsp["hit_length"]) * 100
+    elif algo == 'TBLASTN':
+        if q_align_len:
+            query_overlap = (q_align_len / q_align_len) * 100
+        if hsp["hit_length"]:
+            hit_overlap = (h_align_len * 3 / hsp["hit_length"]) * 100
+    elif algo == 'TBLASTX':
+        if q_align_len:
+            query_overlap = (q_align_len * 3 / hsp["hsp_length"]) * 100
+        if hsp["hit_length"]:
+            hit_overlap = (h_align_len * 3 / hsp["hit_length"]) * 100
+    else:
+        if q_align_len:
+            query_overlap = (q_align_len / q_align_len) * 100
+        if hsp["hit_length"]:
+            hit_overlap = (h_align_len / hsp["hit_length"]) * 100
+    if query_overlap is None:
+        query_overlap = 0
+    if query_overlap > 100:
+        query_overlap = 100
+    if 'hit_overlap' not in locals():
+        hit_overlap = 0
+    if hit_overlap > 100:
+        hit_overlap = 100
+
+    return [round(query_overlap, 0), round(hit_overlap, 0)]
+
+
+def _write_tsv(options, hits):
+    """
+    Write output
+    """
+    # get a list of contig without corresponding number of mapped reads
+    if options.rn_file is not None:
+        with open(options.rn_file) as rn:
+            rows = (line.split('\t') for line in rn)
+            rn_list = {row[0]: row[1:] for row in rows}
+    fasta = SeqIO.to_dict(SeqIO.parse(open(options.fasta_file), 'fasta'))
+    headers = "#algo\tquery_id\tnb_reads\tquery_length\taccession\tdescription\torganism\tpercentIdentity\tnb_hsps\tqueryOverlap\thitOverlap\tevalue\tscore\ttax_id\ttaxonomy\tsequence\n"
+    if not os.path.exists(options.output):
+        os.mkdir(options.output)
+    tsv_file = options.output + "/blast2tsv_output.tab"
+    log.info("Write output file: " + tsv_file)
+    f = open(tsv_file, "w+")
+    f.write(headers)
+    for h in hits:
+        if options.rn_file is not None:
+            read_nb = ''.join(rn_list[h]).replace("\n", "")
+        else:
+            read_nb = ''
+        if len(hits[h]) > 1:
+            f.write(options.algo + "\t" + h + "\t" + read_nb + "\t" + str(hits[h]["query_length"]) + "\t")
+            f.write(hits[h]["accession"] + "\t" + hits[h]["description"] + "\t")
+            f.write(hits[h]["organism"] + "\t" + str(hits[h]["percentIdentity"]) + "\t")
+            f.write(str(hits[h]["num_hsps"]) + "\t" + str(hits[h]["queryOverlap"]) + "\t")
+            f.write(str(hits[h]["hitOverlap"]) + "\t" + str(hits[h]["evalue"]) + "\t")
+            f.write(str(hits[h]["score"]) + "\t" + str(hits[h]["tax_id"]) + "\t")
+            if h in fasta:
+                f.write(hits[h]["taxonomy"] + "\t" + str(fasta[h].seq))
+            else:
+                f.write(hits[h]["taxonomy"] + "\t\"\"")
+            f.write("\n")
+        else:
+            f.write(options.algo + "\t" + h + "\t" + read_nb + "\t" + str(hits[h])[1:-1] + "\t")
+            f.write("\n")
+    f.close()
+    _create_abundance(options, tsv_file)
+
+
+def _create_abundance(options, tsv_file):
+    """
+    extract values from tsv files
+    and create abundance files
+    """
+    log.info("Calculating abundance.")
+    file_path = tsv_file
+    abundance = dict()
+    with open(tsv_file, 'r') as current_file:
+        log.debug("Reading " + file_path)
+        csv_reader = csv.reader(current_file, delimiter='\t')
+        line_count = 0
+        for row in csv_reader:
+            if line_count == 0:
+                # headers
+                line_count += 1
+            else:
+                # no annotation
+                if len(row) == 16:
+                    if row[14] != "":
+                        nb_reads = row[2]
+                        if nb_reads == "":
+                            current_reads_nb = 0
+                            log.debug("No reads number for " + row[1])
+                        else:
+                            current_reads_nb = int(nb_reads)
+                        contig_id = row[14]
+                        if contig_id in abundance:
+                            # add reads
+                            abundance[contig_id]["reads_nb"] = abundance[row[14]]["reads_nb"] + current_reads_nb
+                            abundance[contig_id]["contigs_nb"] = abundance[row[14]]["contigs_nb"] + 1
+                        else:
+                            # init reads for this taxo
+                            abundance[contig_id] = {}
+                            abundance[contig_id]["reads_nb"] = current_reads_nb
+                            abundance[contig_id]["contigs_nb"] = 1
+                    else:
+                        log.debug("No annotations for contig " + row[1])
+                else:
+                    log.debug("No annotations for contig " + row[1])
+    log.debug(abundance)
+    reads_file = open(options.output + "/blast2tsv_reads.txt", "w+")
+    for taxo in abundance:
+        reads_file.write(str(abundance[taxo]["reads_nb"]))
+        reads_file.write("\t")
+        reads_file.write("\t".join(taxo.split(";")))
+        reads_file.write("\n")
+    reads_file.close()
+    log.info("Abundance file created " + options.output + "/blast2tsv_reads.txt")
+    contigs_file = open(options.output + "/blast2tsv_contigs.txt", "w+")
+    for taxo in abundance:
+        contigs_file.write(str(abundance[taxo]["contigs_nb"]))
+        contigs_file.write("\t")
+        contigs_file.write("\t".join(taxo.split(";")))
+        contigs_file.write("\n")
+    contigs_file.close()
+    log.info("Abundance file created " + options.output + "/blast2tsv_contigs.txt")
+
+
+def _set_options():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-x', '--xml', help='XML files with results of blast', action='store', required=True, dest='xml_file')
+    parser.add_argument('-rn', '--read-count', help='Tab-delimited file associating seqID with read number.', action='store', dest='rn_file')
+    parser.add_argument('-c', '--contigs', help='FASTA file with contigs sequence.', action='store', required=True, dest='fasta_file')
+    parser.add_argument('-me', '--max_evalue', help='Max evalue', action='store', type=float, default=0.0001, dest='max_evalue')
+    parser.add_argument('-qov', '--min_query_overlap', help='Minimum query overlap', action='store', type=int, default=5, dest='min_qov')
+    parser.add_argument('-mhov', '--min_hit_overlap', help='Minimum hit overlap', action='store', type=int, default=5, dest='min_hov')
+    parser.add_argument('-s', '--min_score', help='Minimum score', action='store', type=int, default=30, dest='min_score')
+    parser.add_argument('-a', '--algo', help='Blast type detection (BLASTN|BLASTP|BLASTX|TBLASTX|TBLASTN|DIAMONDX).', action='store', type=str, default='BLASTX', dest='algo')
+    parser.add_argument('-o', '--out', help='The output file (.csv).', action='store', type=str, default='./blast2tsv', dest='output')
+    parser.add_argument('-v', '--verbosity', help='Verbose level', action='store', type=int, choices=[1, 2, 3, 4], default=1)
+    args = parser.parse_args()
+    return args
+
+
+def _set_log_level(verbosity):
+    if verbosity == 1:
+        log_format = '%(asctime)s %(levelname)-8s %(message)s'
+        log.basicConfig(level=log.INFO, format=log_format)
+    elif verbosity == 3:
+        log_format = '%(filename)s:%(lineno)s - %(asctime)s %(levelname)-8s %(message)s'
+        log.basicConfig(level=log.DEBUG, format=log_format)
+
+
+if __name__ == "__main__":
+    main()

tools/virAnnot/macros.xml

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+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.83">biopython</requirement>
+            <requirement type="package" version="3.1.3">ete3</requirement>
+            <requirement type="package" version="1.2.4">clustalo</requirement>
+            <requirement type="package" version="8.5.0">curl</requirement>
+            <requirement type="package" version="4.3.2">r-base</requirement>
+            <requirement type="package" version="23.12.0">pyaml</requirement>
+            <requirement type="package" version="3.1.2">openpyxl</requirement>
+            <requirement type="package" version="3.1.9">xlsxwriter</requirement>
+            <requirement type="package" version="2.0.1">xlrd</requirement>
+            <requirement type="package" version="2.2.0">pandas</requirement>
+            <requirement type="package" version="2.8.1">krona</requirement>
+            <requirement type="package" version="3.0">zip</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <token name="@HEADLESS@"><![CDATA[export QT_QPA_PLATFORM='offscreen' &&]]></token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1094/PBIOMES-07-19-0037-A</citation>
+        </citations>
+    </xml>
+</macros>