Mercurial > repos > nick > allele_counts_1
changeset 14:e5d39283fe4d
allele-counts.py: Document output columns.
| author | nicksto <nmapsy@gmail.com> |
|---|---|
| date | Wed, 09 Dec 2015 11:03:33 -0500 |
| parents | df1fb577db0d |
| children | 2aa561f29da4 |
| files | allele-counts.py |
| diffstat | 1 files changed, 11 insertions(+), 3 deletions(-) [+] |
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--- a/allele-counts.py Tue Dec 03 13:45:16 2013 -0500 +++ b/allele-counts.py Wed Dec 09 11:03:33 2015 -0500 @@ -23,8 +23,8 @@ 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""" +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':''} @@ -33,7 +33,15 @@ 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.""" +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).