comparison allele-counts.py @ 14:e5d39283fe4d

allele-counts.py: Document output columns.

13:df1fb577db0d

COLUMNS = ['sample', 'chr', 'pos', 'A', 'C', 'G', 'T', 'coverage', 'alleles',
  'major', 'minor', 'freq', 'bias']
COLUMN_LABELS = ['SAMPLE', 'CHR',  'POS', 'A', 'C', 'G', 'T', 'CVRG', 'ALLELES',
  'MAJOR', 'MINOR', 'MAF', 'BIAS']
CANONICAL_VARIANTS = ['A', 'C', 'G', 'T']
USAGE = """Usage: %prog [options] -i variants.vcf -o alleles.csv
       cat variants.vcf | %prog [options] > alleles.csv"""
OPT_DEFAULTS = {'infile':'-', 'outfile':'-', 'freq_thres':1.0, 'covg_thres':100,
  'print_header':False, 'stdin':False, 'stranded':False, 'no_filter':False,
  'debug_loc':'', 'seed':''}
DESCRIPTION = """This will parse the VCF output of the "Naive Variant Caller"
(aka "BAM Coverage") Galaxy tool. For each position reported, it counts the
number of reads of each base, determines the major allele, minor allele (second
most frequent variant), and number of alleles above a threshold. So currently
it only considers SNVs (ACGT), including in the coverage figure. By default it
reads from stdin and prints to stdout."""
EPILOG = """Requirements:
The input VCF must report the variants for each strand.
The variants should be case-sensitive (e.g. all capital base letters).
Strand bias: Both strands must show the same bases passing the frequency
threshold (but not necessarily in the same order). If the site fails this test,

14:e5d39283fe4d

COLUMNS = ['sample', 'chr', 'pos', 'A', 'C', 'G', 'T', 'coverage', 'alleles',
  'major', 'minor', 'freq', 'bias']
COLUMN_LABELS = ['SAMPLE', 'CHR',  'POS', 'A', 'C', 'G', 'T', 'CVRG', 'ALLELES',
  'MAJOR', 'MINOR', 'MAF', 'BIAS']
CANONICAL_VARIANTS = ['A', 'C', 'G', 'T']
USAGE = """Usage: %prog [options] -i variants.vcf -o alleles.tsv
       cat variants.vcf | %prog [options] > alleles.tsv"""
OPT_DEFAULTS = {'infile':'-', 'outfile':'-', 'freq_thres':1.0, 'covg_thres':100,
  'print_header':False, 'stdin':False, 'stranded':False, 'no_filter':False,
  'debug_loc':'', 'seed':''}
DESCRIPTION = """This will parse the VCF output of the "Naive Variant Caller"
(aka "BAM Coverage") Galaxy tool. For each position reported, it counts the
number of reads of each base, determines the major allele, minor allele (second
most frequent variant), and number of alleles above a threshold. So currently
it only considers SNVs (ACGT), including in the coverage figure. By default it
reads from stdin and prints to stdout.
Prints a tab-delimited set of statistics to stdout.
To print output column labels, run "$ echo -n | ./allele-counts.py -H".
The columns are: 1:SAMPLE 2:CHR 3:POS 4:A 5:C 6:G 7:T 8:CVRG 9:ALLELES 10:MAJOR
11:MINOR 12:MAF 13:BIAS,
unless the --stranded option is used, in which case they are:
1:SAMPLE 2:CHR 3:POS 4:+A 5:+C 6:+G 7:+T 8:-A 9:-C 10:-G 11:-T 12:CVRG
13:ALLELES 14:MAJOR 15:MINOR 16:MAF 17:BIAS.
"""
EPILOG = """Requirements:
The input VCF must report the variants for each strand.
The variants should be case-sensitive (e.g. all capital base letters).
Strand bias: Both strands must show the same bases passing the frequency
threshold (but not necessarily in the same order). If the site fails this test,