def main(argv=None): if not argv: argv = sys.argv parser = E.ArgumentParser(description=__doc__) parser.add_argument("--version", action='version', version="1.0") parser.add_argument("-g", "--genome-file", dest="genome_file", type=str, help="filename with genome.") parser.add_argument("-i", "--ignore-missing", dest="ignore_missing", action="store_true", help="Ignore transcripts on contigs that are not " "in the genome-file.") parser.add_argument("-s", "--restrict-source", dest="restrict_source", type=str, choices=("protein_coding", "pseudogene", "lncRNA"), help="restrict input by source.") parser.add_argument("-m", "--method", dest="method", type=str, choices=( "full", "genome", "exons", "promotors", "tts", "regulons", "tts-regulons", "genes", "territories", "tss-territories", "great-domains", ), help="method for defining segments.") parser.add_argument("-r", "--territory-extension", dest="radius", type=int, help="radius of a territory.") parser.add_argument("-f", "--flank-size", dest="flank", type=int, help="size of the flanking region next to a gene.") parser.add_argument( "--flank-increment-size", dest="increment", type=int, help="size of increment in flank in genestructure annotation ") parser.add_argument("-p", "--promotor-size", dest="promotor", type=int, help="size of a promotor region.") parser.add_argument("-u", "--upstream-extension", dest="upstream", type=int, help="size of region upstream of tss.") parser.add_argument("-d", "--downstream-extension", dest="downstream", type=int, help="size of region downstream of tss.") parser.add_argument("--gene-detail", dest="detail", type=str, choices=("introns+exons", "exons", "introns"), help="level of detail for gene structure annotation ") parser.add_argument("--merge-overlapping-promotors", dest="merge_promotors", action="store_true", help="merge overlapping promotors.") parser.add_argument( "--min-intron-length", dest="min_intron_length", type=int, help="minimum intron length. If the distance between two " "consecutive exons is smaller, the region will be marked " "'unknown'.") parser.add_argument( "--is-unsorted", dest="is_sorted", action="store_false", help="sort input before processing. Otherwise, the input is assumed " "to be sorted.") parser.set_defaults( genome_file=None, flank=1000, increment=1000, max_frameshift_length=4, min_intron_length=30, ignore_missing=False, restrict_source=None, method="genome", radius=50000, promotor=5000, merge_promotors=False, upstream=5000, downstream=5000, detail="exons", is_sorted=True, ) (args) = E.start(parser) if args.genome_file: fasta = IndexedFasta.IndexedFasta(args.genome_file) else: raise ValueError("please specify a --genome-file") if not args.restrict_source: iterator = GTF.iterator(args.stdin) elif args.restrict_source: iterator = GTF.iterator_filtered(GTF.iterator(args.stdin), source=args.restrict_source) # elif options.method in ("promotors", "tts", "regulons"): # iterator = GTF.iterator_filtered( GTF.iterator(options.stdin), source = "protein_coding") # else: # iterator = GTF.iterator(options.stdin) if not args.is_sorted: iterator = GTF.iterator_sorted(iterator, sort_order="position") if args.method == "full" or args.method == "genome": segmentor = annotateGenome(iterator, fasta, args) elif args.method == "territories": segmentor = buildTerritories(iterator, fasta, 'gene', args) elif args.method == "tss-territories": segmentor = buildTerritories(iterator, fasta, 'tss', args) elif args.method == "exons": segmentor = annotateExons(iterator, fasta, args) elif args.method == "promotors": segmentor = annotatePromoters(iterator, fasta, args) elif args.method == "regulons": segmentor = annotateRegulons(iterator, fasta, True, args) elif args.method == "tts-regulons": segmentor = annotateRegulons(iterator, fasta, False, args) elif args.method == "tts": segmentor = annotateTTS(iterator, fasta, args) elif args.method == "genes": segmentor = annotateGenes(iterator, fasta, args) elif args.method == "great-domains": segmentor = annotateGREATDomains(iterator, fasta, args) E.stop()
def main(argv=None): if argv is None: argv = sys.argv parser = E.ArgumentParser(description=__doc__) parser.add_argument("--version", action='version', version="1.0") parser.add_argument( "-m", "--method", dest="method", type=str, choices=("add-flank", "add-upstream-flank", "add-downstream-flank", "crop", "crop-unique", "complement-groups", "combine-groups", "filter-range", "join-features", "merge-features", "sanitize", "to-forward-coordinates", "to-forward-strand", "rename-chr"), help="method to apply ") parser.add_argument("--ignore-strand", dest="ignore_strand", help="ignore strand information.", action="store_true") parser.add_argument("--is-gtf", dest="is_gtf", action="store_true", help="input will be treated as gtf.") parser.add_argument("-c", "--contigs-tsv-file", dest="input_filename_contigs", type=str, help="filename with contig lengths.") parser.add_argument( "--agp-file", dest="input_filename_agp", type=str, help="agp file to map coordinates from contigs to scaffolds.") parser.add_argument("-g", "--genome-file", dest="genome_file", type=str, help="filename with genome.") parser.add_argument("--crop-gff-file", dest="filename_crop_gff", type=str, help="GFF/GTF file to crop against.") parser.add_argument( "--group-field", dest="group_field", type=str, help="""gff field/attribute to group by such as gene_id, " "transcript_id, ... .""") parser.add_argument( "--filter-range", dest="filter_range", type=str, help="extract all elements overlapping a range. A range is " "specified by eithor 'contig:from..to', 'contig:+:from..to', " "or 'from,to' .") parser.add_argument("--sanitize-method", dest="sanitize_method", type=str, choices=("ucsc", "ensembl", "genome"), help="method to use for sanitizing chromosome names. " ".") parser.add_argument( "--flank-method", dest="flank_method", type=str, choices=("add", "extend"), help="method to use for adding flanks. ``extend`` will " "extend existing features, while ``add`` will add new features. " ".") parser.add_argument("--skip-missing", dest="skip_missing", action="store_true", help="skip entries on missing contigs. Otherwise an " "exception is raised .") parser.add_argument( "--contig-pattern", dest="contig_pattern", type=str, help="a comma separated list of regular expressions specifying " "contigs to be removed when running method sanitize .") parser.add_argument( "--assembly-report", dest="assembly_report", type=str, help="path to assembly report file which allows mapping of " "ensembl to ucsc contigs when running method sanitize .") parser.add_argument( "--assembly-report-hasids", dest="assembly_report_hasIDs", type=int, help="path to assembly report file which allows mapping of " "ensembl to ucsc contigs when running method sanitize .") parser.add_argument( "--assembly-report-ucsccol", dest="assembly_report_ucsccol", type=int, help="column in the assembly report containing ucsc contig ids" ".") parser.add_argument( "--assembly-report-ensemblcol", dest="assembly_report_ensemblcol", type=int, help="column in the assembly report containing ensembl contig ids") parser.add_argument( "--assembly-extras", dest="assembly_extras", type=str, help="additional mismatches between gtf and fasta to fix when" "sanitizing the genome .") parser.add_argument("--extension-upstream", dest="extension_upstream", type=float, help="extension for upstream end .") parser.add_argument("--extension-downstream", dest="extension_downstream", type=float, help="extension for downstream end .") parser.add_argument("--min-distance", dest="min_distance", type=int, help="minimum distance of features to merge/join .") parser.add_argument("--max-distance", dest="max_distance", type=int, help="maximum distance of features to merge/join .") parser.add_argument("--min-features", dest="min_features", type=int, help="minimum number of features to merge/join .") parser.add_argument("--max-features", dest="max_features", type=int, help="maximum number of features to merge/join .") parser.add_argument( "--rename-chr-file", dest="rename_chr_file", type=str, help="mapping table between old and new chromosome names." "TAB separated 2-column file.") parser.set_defaults(input_filename_contigs=False, filename_crop_gff=None, input_filename_agp=False, genome_file=None, rename_chr_file=None, add_up_flank=None, add_down_flank=None, complement_groups=False, crop=None, crop_unique=False, ignore_strand=False, filter_range=None, min_distance=0, max_distance=0, min_features=1, max_features=0, extension_upstream=1000, extension_downstream=1000, sanitize_method="ucsc", flank_method="add", output_format="%06i", skip_missing=False, is_gtf=False, group_field=None, contig_pattern=None, assembly_report=None, assembly_report_hasIDs=1, assembly_report_ensemblcol=4, assembly_report_ucsccol=9, assembly_extras=None) (args) = E.start(parser, argv=argv) contigs = None genome_fasta = None chr_map = None if args.input_filename_contigs: contigs = Genomics.readContigSizes( iotools.open_file(args.input_filename_contigs, "r")) if args.genome_file: genome_fasta = IndexedFasta.IndexedFasta(args.genome_file) contigs = genome_fasta.getContigSizes() if args.rename_chr_file: chr_map = {} with open(args.rename_chr_file, 'r') as filein: reader = csv.reader(filein, delimiter='\t') for row in reader: if len(row) != 2: raise ValueError( "Mapping table must have exactly two columns") chr_map[row[0]] = row[1] if not len(chr_map.keys()) > 0: raise ValueError("Empty mapping dictionnary") if args.assembly_report: df = pd.read_csv(args.assembly_report, comment="#", header=None, sep="\t") # fixes naming inconsistency in assembly report: ensembl chromosome # contigs found in columnn 0, ensembl unassigned contigs found in # column 4. if args.assembly_report_hasIDs == 1: ucsccol = args.assembly_report_ucsccol ensemblcol = args.assembly_report_ensemblcol df.loc[df[1] == "assembled-molecule", ensemblcol] = df.loc[df[1] == "assembled-molecule", 0] if args.sanitize_method == "ucsc": assembly_dict = df.set_index(ensemblcol)[ucsccol].to_dict() elif args.sanitize_method == "ensembl": assembly_dict = df.set_index(ucsccol)[ensemblcol].to_dict() else: raise ValueError(''' When using assembly report, please specify sanitize method as either "ucsc" or "ensembl" to specify direction of conversion ''') else: assembly_dict = {} if args.assembly_extras is not None: assembly_extras = args.assembly_extras.split(",") for item in assembly_extras: item = item.split("-") assembly_dict[item[0]] = item[1] if args.method in ("forward_coordinates", "forward_strand", "add-flank", "add-upstream-flank", "add-downstream-flank") \ and not contigs: raise ValueError("inverting coordinates requires genome file") if args.input_filename_agp: agp = AGP.AGP() agp.readFromFile(iotools.open_file(args.input_filename_agp, "r")) else: agp = None gffs = GTF.iterator(args.stdin) if args.method in ("add-upstream-flank", "add-downstream-flank", "add-flank"): add_upstream_flank = "add-upstream-flank" == args.method add_downstream_flank = "add-downstream-flank" == args.method if args.method == "add-flank": add_upstream_flank = add_downstream_flank = True upstream_flank = int(args.extension_upstream) downstream_flank = int(args.extension_downstream) extend_flank = args.flank_method == "extend" if args.is_gtf: iterator = GTF.flat_gene_iterator(gffs) else: iterator = GTF.joined_iterator(gffs, args.group_field) for chunk in iterator: is_positive = Genomics.IsPositiveStrand(chunk[0].strand) chunk.sort(key=lambda x: (x.contig, x.start)) lcontig = contigs[chunk[0].contig] if extend_flank: if add_upstream_flank: if is_positive: chunk[0].start = max(0, chunk[0].start - upstream_flank) else: chunk[-1].end = min(lcontig, chunk[-1].end + upstream_flank) if add_downstream_flank: if is_positive: chunk[-1].end = min(lcontig, chunk[-1].end + downstream_flank) else: chunk[0].start = max(0, chunk[0].start - downstream_flank) else: if add_upstream_flank: gff = GTF.Entry() if is_positive: gff.copy(chunk[0]) gff.end = gff.start gff.start = max(0, gff.start - upstream_flank) chunk.insert(0, gff) else: gff.copy(chunk[-1]) gff.start = gff.end gff.end = min(lcontig, gff.end + upstream_flank) chunk.append(gff) gff.feature = "5-Flank" gff.mMethod = "gff2gff" if add_downstream_flank: gff = GTF.Entry() if is_positive: gff.copy(chunk[-1]) gff.start = gff.end gff.end = min(lcontig, gff.end + downstream_flank) chunk.append(gff) else: gff.copy(chunk[0]) gff.end = gff.start gff.start = max(0, gff.start - downstream_flank) chunk.insert(0, gff) gff.feature = "3-Flank" gff.mMethod = "gff2gff" if not is_positive: chunk.reverse() for gff in chunk: args.stdout.write(str(gff) + "\n") elif args.method == "complement-groups": iterator = GTF.joined_iterator(gffs, group_field=args.group_field) for chunk in iterator: if args.is_gtf: chunk = [x for x in chunk if x.feature == "exon"] if len(chunk) == 0: continue chunk.sort(key=lambda x: (x.contig, x.start)) x = GTF.Entry() x.copy(chunk[0]) x.start = x.end x.feature = "intron" for c in chunk[1:]: x.end = c.start args.stdout.write(str(x) + "\n") x.start = c.end elif args.method == "combine-groups": iterator = GTF.joined_iterator(gffs, group_field=args.group_field) for chunk in iterator: chunk.sort(key=lambda x: (x.contig, x.start)) x = GTF.Entry() x.copy(chunk[0]) x.end = chunk[-1].end x.feature = "segment" args.stdout.write(str(x) + "\n") elif args.method == "join-features": for gff in combineGFF(gffs, min_distance=args.min_distance, max_distance=args.max_distance, min_features=args.min_features, max_features=args.max_features, merge=False, output_format=args.output_format): args.stdout.write(str(gff) + "\n") elif args.method == "merge-features": for gff in combineGFF(gffs, min_distance=args.min_distance, max_distance=args.max_distance, min_features=args.min_features, max_features=args.max_features, merge=True, output_format=args.output_format): args.stdout.write(str(gff) + "\n") elif args.method == "crop": for gff in cropGFF(gffs, args.filename_crop_gff): args.stdout.write(str(gff) + "\n") elif args.method == "crop-unique": for gff in cropGFFUnique(gffs): args.stdout.write(str(gff) + "\n") elif args.method == "filter-range": contig, strand, interval = None, None, None try: contig, strand, start, sep, end = re.match( "(\S+):(\S+):(\d+)(\.\.|-)(\d+)", args.filter_range).groups() except AttributeError: pass if not contig: try: contig, start, sep, end = re.match("(\S+):(\d+)(\.\.|-)(\d+)", args.filter_range).groups() strand = None except AttributeError: pass if not contig: try: start, end = re.match("(\d+)(\.\.|\,|\-)(\d+)", args.filter_range).groups() except AttributeError: raise "can not parse range %s" % args.filter_range contig = None strand = None if start: interval = (int(start), int(end)) else: interval = None E.debug("filter: contig=%s, strand=%s, interval=%s" % (str(contig), str(strand), str(interval))) for gff in GTF.iterator_filtered(gffs, contig=contig, strand=strand, interval=interval): args.stdout.write(str(gff) + "\n") elif args.method == "sanitize": def assemblyReport(id): if id in assembly_dict.keys(): id = assembly_dict[id] # if not in dict, the contig name is forced # into the desired convention, this is helpful user # modified gff files that contain additional contigs elif args.sanitize_method == "ucsc": if not id.startswith("contig") and not id.startswith("chr"): id = "chr%s" % id elif args.sanitize_method == "ensembl": if id.startswith("contig"): return id[len("contig"):] elif id.startswith("chr"): return id[len("chr"):] return id if args.sanitize_method == "genome": if genome_fasta is None: raise ValueError("please specify --genome-file= when using " "--sanitize-method=genome") f = genome_fasta.getToken else: if args.assembly_report is None: raise ValueError( "please specify --assembly-report= when using " "--sanitize-method=ucsc or ensembl") f = assemblyReport skipped_contigs = collections.defaultdict(int) outofrange_contigs = collections.defaultdict(int) filtered_contigs = collections.defaultdict(int) for gff in gffs: try: gff.contig = f(gff.contig) except KeyError: if args.skip_missing: skipped_contigs[gff.contig] += 1 continue else: raise if genome_fasta: lcontig = genome_fasta.getLength(gff.contig) if lcontig < gff.end: outofrange_contigs[gff.contig] += 1 continue if args.contig_pattern: to_remove = [ re.compile(x) for x in args.contig_pattern.split(",") ] if any([x.search(gff.contig) for x in to_remove]): filtered_contigs[gff.contig] += 1 continue args.stdout.write(str(gff) + "\n") if skipped_contigs: E.info("skipped %i entries on %i contigs: %s" % (sum(skipped_contigs.values()), len(list(skipped_contigs.keys())), str(skipped_contigs))) if outofrange_contigs: E.warn( "skipped %i entries on %i contigs because they are out of range: %s" % (sum(outofrange_contigs.values()), len(list( outofrange_contigs.keys())), str(outofrange_contigs))) if filtered_contigs: E.info("filtered out %i entries on %i contigs: %s" % (sum(filtered_contigs.values()), len(list(filtered_contigs.keys())), str(filtered_contigs))) elif args.method == "rename-chr": if not chr_map: raise ValueError("please supply mapping file") for gff in renameChromosomes(gffs, chr_map): args.stdout.write(str(gff) + "\n") else: for gff in gffs: if args.method == "forward_coordinates": gff.invert(contigs[gff.contig]) if args.method == "forward_strand": gff.invert(contigs[gff.contig]) gff.strand = "+" if agp: # note: this works only with forward coordinates gff.contig, gff.start, gff.end = agp.mapLocation( gff.contig, gff.start, gff.end) args.stdout.write(str(gff) + "\n") E.stop()
def main(argv=None): """script main. parses command line options in sys.argv, unless *argv* is given. """ if argv is None: argv = sys.argv parser = E.OptionParser( version="%prog version: $Id: gff2psl.py 2781 2009-09-10 11:33:14Z andreas $", usage=globals()["__doc__"]) parser.add_option("--is-gtf", dest="is_gtf", action="store_true", help="input is gtf.") parser.add_option("--no-header", dest="with_header", action="store_false", help="do not output BLAT header [default=%default].") parser.add_option("-g", "--genome-file", dest="genome_file", type="string", help="filename with genome.") parser.add_option("--queries-tsv-file", dest="input_filename_queries", type="string", help="fasta filename with queries [default=%default].") parser.add_option("--allow-duplicates", dest="allow_duplicates", action="store_true", help="""permit duplicate entries. Adjacent exons of a transcript will still be merged [default=%default].""" ) parser.set_defaults(is_gtf=False, genome_file=None, with_header=True, allow_duplicates=False, test=None) (options, args) = E.start(parser, add_pipe_options=True) if options.genome_file: genome_fasta = IndexedFasta.IndexedFasta(options.genome_file) else: genome_fasta = None if options.input_filename_queries: queries_fasta = IndexedFasta.IndexedFasta( options.input_filename_queries) else: queries_fasta = None ninput, noutput, nskipped = 0, 0, 0 if options.is_gtf: iterator = GTF.transcript_iterator(GTF.iterator_filtered(GTF.iterator(sys.stdin), feature="exon"), strict=not options.allow_duplicates) else: iterator = GTF.joined_iterator(GTF.iterator(sys.stdin)) if options.with_header: options.stdout.write(Blat.Match().getHeader() + "\n") for gffs in iterator: if options.test and ninput >= options.test: break ninput += 1 result = alignlib_lite.py_makeAlignmentBlocks() xstart = 0 intervals = Intervals.combine([(gff.start, gff.end) for gff in gffs]) for start, end in intervals: xend = xstart + end - start result.addDiagonal(xstart, xend, start - xstart) xstart = xend entry = Blat.Match() entry.mQueryId = gffs[0].transcript_id entry.mSbjctId = gffs[0].contig entry.strand = gffs[0].strand if genome_fasta: if entry.mSbjctId in genome_fasta: entry.mSbjctLength = genome_fasta.getLength(entry.mSbjctId) else: entry.mSbjctLength = result.getColTo() if queries_fasta: if entry.mQueryId in queries_fasta: entry.mQueryLength = queries_fasta.getLength(entry.mQueryId) else: entry.mQueryLength = result.getRowTo() entry.fromMap(result) options.stdout.write(str(entry) + "\n") noutput += 1 E.info("ninput=%i, noutput=%i, nskipped=%i" % (ninput, noutput, nskipped)) E.stop()