--- /dev/null
+[comment]: # Copyright (C) The Lightning Authors. All rights reserved.
+[comment]: # ()
+[comment]: # SPDX-License-Identifier: AGPL-3.0
+gVCF Regions
+========
+
+gVCF Regions is a command line tool that output the called regions of a gVCF file in BED format.
+It handles four main types of gVCFs (Complete Genomics, Freebayes, GATK), with the capability
+to customize the settings of 'called regions'.
+
+### gVCF Regions Command
+```
+gvcf_regions.py [-h] [--unreported_is_called]
+ [--ignore_phrases IGNORE_PHRASES [IGNORE_PHRASES ...]]
+ [--min_GQ MIN_GQ] [--min_QUAL MIN_QUAL]
+ [--pass_phrases PASS_PHRASES [PASS_PHRASES ...]]
+ [--gvcf_type {complete_genomics,freebayes,gatk}]
+ GVCF
+
+Output the called regions of a gvcf file to stdout in bed format.
+
+positional arguments:
+ GVCF input gvcf file, accept gzipped and unzipped files, or
+ "-" for stream
+
+optional arguments:
+ -h, --help show this help message and exit
+ --unreported_is_called
+ use this flag to treat unreported sites as called
+ --ignore_phrases IGNORE_PHRASES [IGNORE_PHRASES ...]
+ list of phrases considered as discarded, e.g., CNV,
+ ME. A line that contains any of the ignore phrases is
+ discarded.
+ --min_GQ MIN_GQ minimum GQ (Genotype Quality) considered as called
+ --min_QUAL MIN_QUAL minimum QUAL considered as called
+ --pass_phrases PASS_PHRASES [PASS_PHRASES ...]
+ list of phrases considered as called, e.g., PASS,
+ REFCALL. A line must contain any of the pass phrases
+ to be considered as called.
+ --gvcf_type {complete_genomics,freebayes,gatk}
+ type of gvcf output. [unreported_is_called,
+ ignore_phrases, min_GQ, min_QUAL, pass_phrases]
+ presets: complete_genomics: [True, ['CNV', 'INS:ME'],
+ None, None, ['PASS']]. freebayes: [False, None, None,
+ None, ['PASS']]. gatk: [False, None, 5, None, None].
+```
--- /dev/null
+# Copyright (C) The Lightning Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+#!/usr/bin/env python
+
+import argparse
+import gzip
+import sys
+
+def is_header(line):
+ """Check if a line is header."""
+
+ return line.startswith('#')
+
+def has_END(line):
+ """Check if a line has the 'END=' tag."""
+
+ return 'END=' in line
+
+# FIELD index
+# CHROM 0, POS 1, REF 3, QUAL 5, INFO 7, FORMAT 8, sample 9
+
+def get_END(line):
+ """Extract the END position of a line from the 'END=' tag under INFO."""
+
+ INFO = line.strip().split('\t')[7]
+ INFO_fields = INFO.split(';')
+ for INFO_field in INFO_fields:
+ if INFO_field.split('=')[0] == 'END':
+ END = int(INFO_field.split('=')[1])
+ return END
+
+def get_bed_region(line):
+ """Extract the bed region of a line.
+
+ Return:
+ tuple: (line_start, line_end)"""
+
+ fields = line.strip().split('\t')
+ POS = int(fields[1])
+ REF = fields[3]
+
+ # vcf: 1 index, inclusive start, inclusive end
+ # bed: 0 index, inclusive start, exlusive end
+
+ # starting postion of the line in bed index
+ if POS == 0:
+ line_start = 0
+ else:
+ line_start = POS - 1
+ # ending position of the line in bed index
+ if has_END(line):
+ line_end = get_END(line)
+ else:
+ line_end = POS - 1 + len(REF)
+ return (line_start, line_end)
+
+def get_GQ(line):
+ """Extract the GQ (Genotype Quality) of a line."""
+
+ fields = line.strip().split('\t')
+ FORMAT, sample = fields[8], fields[9]
+ FORMAT_fields = FORMAT.split(':')
+ sample_fields = sample.split(':')
+
+ # No genotype quality present in gVCF. Happens in some lines of GATK gVCF output.
+ try:
+ GQ_index = FORMAT_fields.index('GQ')
+ GQ = int(sample_fields[GQ_index])
+ except ValueError:
+ GQ = 0
+ return GQ
+
+def get_GT(line):
+ """Extract the GT (Genotype) of a line."""
+
+ fields = line.strip().split('\t')
+ FORMAT, sample = fields[8], fields[9]
+ FORMAT_fields = FORMAT.split(':')
+ sample_fields = sample.split(':')
+
+ try:
+ GT_index = FORMAT_fields.index('GT')
+ GT = sample_fields[GT_index]
+ except ValueError:
+ GT = None
+ return GT
+
+
+def is_considered(line, ignore_phrases):
+ """Check if a line should be considered. A line that contains any of the
+ ignore phrases is discarded. E.g., to discard CNV and ME lines of Complete Genomics
+ gvcf, set ignore_phrases = ['CNV', 'INS:ME'].
+
+ Args:
+ ignore_phrases (None or non-empty list)"""
+
+ if ignore_phrases != None:
+ for ignore_phrase in ignore_phrases:
+ if ignore_phrase in line:
+ return False
+ return True
+
+def is_called(line, min_GQ, min_QUAL, pass_phrases):
+ """Check if a line is considered as 'called', i.e., if its GQ is at least
+ min_GQ, if its QUAL is at least min_QUAL, if it contains any of the
+ pass phrases, E.g., for freebayes gvcf, set pass_phrases = ['PASS'],
+ and if the GT field has no '.' (no call).
+
+ Args:
+ min_GQ (None or int)
+ min_QUAL (None or float)
+ pass_phrases (None or non-empty list)"""
+
+ fields = line.strip().split('\t')
+ GQ_passes = (min_GQ == None or get_GQ(line) >= min_GQ)
+ QUAL_passes = (min_QUAL == None or float(fields[5]) >= min_QUAL)
+
+ line_has_pass_phrases = True
+ if pass_phrases != None:
+ for pass_phrase in pass_phrases:
+ if pass_phrase in line:
+ line_has_pass_phrases = True
+ break
+ else:
+ line_has_pass_phrases = False
+
+ GT = get_GT(line)
+ if GT:
+ GT_without_nocall = not ('.' in GT)
+ else:
+ GT_without_nocall = True
+
+ return GQ_passes and QUAL_passes and line_has_pass_phrases and GT_without_nocall
+
+def gvcf_regions(gvcf, unreported_is_called, ignore_phrases,
+ min_GQ, min_QUAL, pass_phrases):
+ """Generate the called regions of a gvcf as a bed file.
+
+ Args:
+ unreported_is_called (bool): whether an unreported site is considered
+ as called. E.g., in Complete Genomics gvcf, an unreported site
+ is hom-ref (called), whereas in freebayes/gatk gvcf, it is no-call.
+ ignore_phrases (None or non-empty list)
+ min_GQ (None or int)
+ min_QUAL (None or float)
+ pass_phrases (None or non-empty list)"""
+
+ if gvcf == "-":
+ g = sys.stdin
+ elif gvcf.endswith(".gz"):
+ g = gzip.open(gvcf)
+ else:
+ g = open(gvcf)
+
+ region_CHROM = ''
+ for line in g:
+ if isinstance(line, bytes):
+ line = line.decode("utf-8")
+ # filter out header and lines with ignore phrases
+ if not is_header(line) and is_considered(line, ignore_phrases):
+ fields = line.strip().split('\t')
+ CHROM = fields[0]
+ is_line_called = is_called(line, min_GQ, min_QUAL, pass_phrases)
+ (line_start, line_end) = get_bed_region(line)
+ assert line_end is not None, line
+
+ # handle cases depending on if the previous block is called,
+ # if the current line is called, and if the previous block
+ # and the current line have a gap
+
+ # when chromosome changes
+ if region_CHROM != CHROM:
+ # when chromosome changes from one to another,
+ # write the previous region
+ if region_CHROM != '':
+ # we assume a chromosome ends with a string of 'N's
+ if is_previous_block_called:
+ region_end = previous_block_end
+ print('\t'.join([region_CHROM,
+ str(region_start), str(region_end)]))
+ region_CHROM = CHROM
+ if is_line_called:
+ region_start = line_start
+ is_previous_block_called = True
+ else:
+ # we assume a chromosome starts with a string of 'N's
+ is_previous_block_called = False
+ # update previous_block_end
+ previous_block_end = line_end
+ # when line and previous block are on the same chromosome and
+ # they have a gap
+ elif line_start > previous_block_end:
+ if is_previous_block_called:
+ if unreported_is_called:
+ if not is_line_called:
+ region_end = line_start
+ print('\t'.join([region_CHROM,
+ str(region_start), str(region_end)]))
+ is_previous_block_called = False
+ else:
+ region_end = previous_block_end
+ print('\t'.join([region_CHROM,
+ str(region_start), str(region_end)]))
+ if is_line_called:
+ region_start = line_start
+ else:
+ is_previous_block_called = False
+ else:
+ if unreported_is_called:
+ region_start = previous_block_end
+ if is_line_called:
+ is_previous_block_called = True
+ else:
+ region_end = line_start
+ print('\t'.join([region_CHROM,
+ str(region_start), str(region_end)]))
+ else:
+ if is_line_called:
+ region_start = line_start
+ is_previous_block_called = True
+ # update previous_block_end
+ previous_block_end = line_end
+ # when line and previous block are on the same chromosome and
+ # they are back to back without gap
+ elif line_start == previous_block_end:
+ if is_previous_block_called:
+ if not is_line_called:
+ region_end = line_start
+ print('\t'.join([region_CHROM,
+ str(region_start), str(region_end)]))
+ is_previous_block_called = False
+ else:
+ if is_line_called:
+ region_start = line_start
+ is_previous_block_called = True
+ # update previous_block_end
+ previous_block_end = line_end
+ # when line and previous block overlap
+ else:
+ if (is_previous_block_called and is_line_called and
+ line_end > previous_block_end):
+ previous_block_end = line_end
+ # at the end of file, write the previous region
+ else:
+ # we assume a chromosome ends with a string of 'N's
+ if is_previous_block_called:
+ region_end = previous_block_end
+ print('\t'.join([region_CHROM,
+ str(region_start), str(region_end)]))
+
+ if g != "-":
+ g.close()
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser(description='Output the called regions \
+ of a gvcf file to stdout in bed format.')
+ parser.add_argument('gvcf', metavar='GVCF', help='input gvcf file, \
+ accept gzipped and unzipped files, or "-" for stream')
+
+ parser.add_argument('--unreported_is_called', action='store_true',
+ help='use this flag to treat unreported sites as called')
+ parser.add_argument('--ignore_phrases', nargs='+',
+ help='list of phrases considered as discarded, e.g., CNV, ME. \
+ A line that contains any of the ignore phrases is discarded.')
+ parser.add_argument('--min_GQ', type=int,
+ help='minimum GQ (Genotype Quality) considered as called')
+ parser.add_argument('--min_QUAL', type=float,
+ help='minimum QUAL considered as called')
+ parser.add_argument('--pass_phrases', nargs='+',
+ help='list of phrases considered as called, e.g., PASS, REFCALL. \
+ A line must contain any of the pass phrases to be considered as called.')
+
+ # presets of unreported_is_called, ignore_phrases, min_GQ, min_QUAL, pass_phrases
+ complete_genomics_preset = [True, ['CNV', 'INS:ME'], None, None, ['PASS']]
+ freebayes_preset = [False, None, None, None, ['PASS']]
+ gatk_preset = [False, None, 5, None, None]
+
+ gvcf_type_help = '''type of gvcf output.
+ [unreported_is_called, ignore_phrases, min_GQ, min_QUAL, pass_phrases] presets:
+ complete_genomics: %s.
+ freebayes: %s.
+ gatk: %s.''' % (complete_genomics_preset,
+ freebayes_preset, gatk_preset)
+
+ parser.add_argument("--gvcf_type",
+ choices=['complete_genomics', 'freebayes', 'gatk'], help=gvcf_type_help)
+ args = parser.parse_args()
+
+ par = [args.unreported_is_called, args.ignore_phrases,
+ args.min_GQ, args.min_QUAL, args.pass_phrases]
+
+ if args.gvcf_type == 'complete_genomics':
+ par = complete_genomics_preset
+ elif args.gvcf_type == 'freebayes':
+ par = freebayes_preset
+ elif args.gvcf_type == 'gatk':
+ par = gatk_preset
+
+ all_par = [args.gvcf] + par
+ gvcf_regions(*all_par)
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