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#71 Equivalent functionality with new gff3 parser by Uli Kohler
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| @@ -0,0 +1,93 @@ | ||
| #!/usr/bin/env python3 | ||
| """ | ||
| Author: Uli Köhler | ||
| Source: https://techoverflow.net/2013/11/30/a-simple-gff3-parser-in-python/ | ||
| A simple parser for the GFF3 format. | ||
| Test with transcripts.gff3 from | ||
| http://www.broadinstitute.org/annotation/gebo/help/gff3.html. | ||
| Format specification source: | ||
| http://www.sequenceontology.org/gff3.shtml | ||
| Version 1.1: Python3 ready | ||
| """ | ||
| from collections import namedtuple | ||
| import gzip | ||
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| ulrlib_available = False | ||
| try: | ||
| from urllib import parse | ||
| except ImportError: | ||
| from urllib2 import parse # for python 2.7 | ||
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| __author__ = "Uli Köhler" | ||
| __license__ = "Apache License v2.0" | ||
| __version__ = "1.1" | ||
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| # Initialized GeneInfo named tuple. Note: namedtuple is immutable | ||
| gffInfoFields = ["seqid", "source", "type", "start", "end", "score", "strand", "phase", "attributes"] | ||
| GFFRecord = namedtuple("GFFRecord", gffInfoFields) | ||
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| def parseGFFAttributes(attributeString): | ||
| """Parse the GFF3 attribute column and return a dict""" # | ||
| if attributeString == ".": return {} | ||
| ret = {} | ||
| for attribute in attributeString.split(";"): | ||
| key, value = attribute.split("=") | ||
| ret[parse.unquote(key)] = parse.unquote(value) | ||
| return ret | ||
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| def parseGFF3(filename): | ||
| """ | ||
| A minimalistic GFF3 format parser. | ||
| Yields objects that contain info about a single GFF3 feature. | ||
| Supports transparent gzip decompression. | ||
| """ | ||
| # Parse with transparent decompression | ||
| openFunc = gzip.open if filename.endswith(".gz") else open | ||
| with openFunc(filename) as infile: | ||
| for line in infile: | ||
| if line.startswith("#"): continue | ||
| parts = line.strip().split("\t") | ||
| # If this fails, the file format is not standard-compatible | ||
| assert len(parts) == len(gffInfoFields) | ||
| # Normalize data | ||
| normalizedInfo = { | ||
| "seqid": None if parts[0] == "." else parse.unquote(parts[0]), | ||
| "source": None if parts[1] == "." else parse.unquote(parts[1]), | ||
| "type": None if parts[2] == "." else parse.unquote(parts[2]), | ||
| "start": None if parts[3] == "." else int(parts[3]), | ||
| "end": None if parts[4] == "." else int(parts[4]), | ||
| "score": None if parts[5] == "." else float(parts[5]), | ||
| "strand": None if parts[6] == "." else parse.unquote(parts[6]), | ||
| "phase": None if parts[7] == "." else parse.unquote(parts[7]), | ||
| "attributes": parseGFFAttributes(parts[8]) | ||
| } | ||
| # Alternatively, you can emit the dictionary here, if you need mutability: | ||
| # yield normalizedInfo | ||
| yield GFFRecord(**normalizedInfo) | ||
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| if __name__ == "__main__": | ||
| import argparse | ||
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| parser = argparse.ArgumentParser() | ||
| parser.add_argument("file", help="The GFF3 input file (.gz allowed)") | ||
| parser.add_argument("--print-records", action="store_true", help="Print all GeneInfo objects, not only") | ||
| parser.add_argument("--filter-type", help="Ignore records not having the given type") | ||
| args = parser.parse_args() | ||
| # Execute the parser | ||
| recordCount = 0 | ||
| for record in parseGFF3(args.file): | ||
| # Apply filter, if any | ||
| if args.filter_type and record.type != args.filter_type: | ||
| continue | ||
| # Print record if specified by the user | ||
| if args.print_records: print(record) | ||
| # Access attributes like this: my_strand = record.strand | ||
| recordCount += 1 | ||
| print("Total records: %d" % recordCount) |
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