#!/usr/bin/env python

import sqlite3

import numpy as np

import zlib

import re

import os

import cPickle

import gemini_utils as util

from GeminiQuery import GeminiQuery

def get_variants(c, args):

"""

Report all columns in the variant table, except for the

genotype vectors.

"""

query = "SELECT * FROM variants \

ORDER BY chrom, start"

c.execute(query)

# build a list of all the column indices that are NOT

# gt_* columns. These will be the columns reported

(col_names, non_gt_idxs) = \

util.get_col_names_and_indices(c.description, ignore_gt_cols=True)

if args.use_header:

print args.separator.join(col for col in col_names)

for row in c:

print args.separator.join(str(row[i]) if row[i] is not None else "." \

for i in non_gt_idxs )

def get_genotypes(c, args):

"""For each variant, report each sample's genotype

on a separate line.

"""

idx_to_sample = util.map_indicies_to_samples(c)

query = "SELECT v.chrom, v.start, v.end, \

v.ref, v.alt, \

v.type, v.sub_type, \

v.aaf, v.in_dbsnp, v.gene, \

v.gts \

FROM variants v \

ORDER BY chrom, start"

c.execute(query)

# build a list of all the column indices that are NOT

# gt_* columns. These will be the columns reported

(col_names, non_gt_idxs) = \

util.get_col_names_and_indices(c.description, ignore_gt_cols=True)

col_names.append('sample')

col_names.append('genotype')

if args.use_header:

print args.separator.join(col for col in col_names)

for row in c:

gts = np.array(cPickle.loads(zlib.decompress(row['gts'])))

for idx, gt in enumerate(gts):

# xrange(len(row)-1) to avoid printing v.gts

print args.separator.join(str(row[i]) for i in xrange(len(row)-1)),

print args.separator.join([idx_to_sample[idx], gt])

def get_samples(c, args):

"""

Report all of the information about the samples in the DB

"""

query = "SELECT * FROM samples"

c.execute(query)

(col_names, col_idxs) = util.get_col_names_and_indices(c.description)

if args.use_header:

print args.separator.join(col_names)

for row in c:

print args.separator.join(str(row[i]) if row[i] is not None else "." \

for i in xrange(len(row)) )

def tfam(args):

"""

Report the information about the samples in the DB in TFAM format:

http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml

"""

query = ("select family_id, name, paternal_id, maternal_id, "

"sex, phenotype from samples")

gq = GeminiQuery(args.db)

gq.run(query)

for row in gq:

print " ".join(map(str, [row['family_id'], row['name'], row['paternal_id'],

row['maternal_id'], row['sex'], row['phenotype']]))

def dump(parser, args):

if os.path.exists(args.db):

conn = sqlite3.connect(args.db)

conn.isolation_level = None

conn.row_factory = sqlite3.Row

c = conn.cursor()

if args.variants:

get_variants(c, args)

elif args.genotypes:

get_genotypes(c, args)

elif args.samples:

get_samples(c, args)

elif args.tfam:

tfam(args)