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More fixes
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@llandsmeer
llandsmeer committed Jul 13, 2020
1 parent c99348c commit f816242
Showing 1 changed file with 47 additions and 17 deletions.
64 changes: 47 additions & 17 deletions SCRIPTS/gwas2cojo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,9 +42,10 @@
import sys
import argparse
import collections
import datetime
import gzip
import math
import time
import datetime

try:
import numpy as np
Expand All @@ -69,19 +70,19 @@ def LiftOver(*a):

# case insensitive
GWAS_H_CHR_AND_BP_COMB_OPTIONS = ['chr_pos_(b36)']
GWAS_H_CHR_OPTIONS = ['chr', 'chromosome', 'Chromosome', 'CHR', 'Chr']
GWAS_H_BP_OPTIONS = ['bp_hg18', 'bp_hg19', 'bp', 'pos', 'position', 'Position', 'BP', 'POS', 'Pos']
GWAS_H_REF_OPTIONS = ['reference_allele', 'effect_allele', 'riskallele', 'CODEDALLELE', 'EA']
GWAS_H_OTH_OPTIONS = ['other_allele', 'noneffect_allele', 'nonriskallele', 'OTHERALLELE', 'NEA']
GWAS_H_FREQ_OPTIONS = ['ref_allele_frequency', 'effect_allele_freq', 'eaf', 'raf', 'CAF', 'EAF', 'Freq.A1.1000G.EUR']
GWAS_H_BETA_OPTIONS = ['log_odds', 'logOR', 'beta', 'effect', 'BETA_FIXED', 'BETA', 'Beta', 'b', 'OR']
GWAS_H_CHR_OPTIONS = ['chr', 'chromosome', 'Chromosome', 'CHR', 'Chr', 'Chr(GCF1405.25)']
GWAS_H_BP_OPTIONS = ['bp_hg18', 'bp_hg19', 'bp', 'pos', 'position', 'Position', 'BP', 'POS', 'Pos', 'Start(GCF1405.25)']
GWAS_H_EFF_OPTIONS = ['A1', 'Allele1', 'reference_allele', 'effect_allele', 'riskallele', 'CODEDALLELE', 'EA']
GWAS_H_OTH_OPTIONS = ['A2', 'Allele2', 'other_allele', 'noneffect_allele', 'nonriskallele', 'OTHERALLELE', 'NEA']
GWAS_H_FREQ_OPTIONS = ['ref_allele_frequency', 'effect_allele_freq', 'eaf', 'raf', 'CAF', 'EAF', 'Freq1', 'freq(A1)', 'Freq.A1.1000G.EUR']
GWAS_H_BETA_OPTIONS = ['log_odds', 'logOR', 'beta', 'effect', 'BETA_FIXED', 'BETA', 'Beta', 'b', 'Effect']
GWAS_H_SE_OPTIONS = ['log_odds_se', 'se_gc', 'se', 'stderr', 'SE_FIXED', 'SE']
GWAS_H_PVALUE_OPTIONS = ['pvalue', 'p-value_gc', 'p-value', 'p.value', 'pval', 'p', 'P_FIXED', 'P', 'Pvalue']
GWAS_H_PVALUE_OPTIONS = ['pvalue', 'p-value_gc', 'p-value', 'p.value', 'pval', 'p', 'P_FIXED', 'P', 'Pvalue', 'P-value']
GWAS_H_NTOTAL_OPTIONS = ['n_samples', 'TotalSampleSize', 'n_eff', 'N_EFF', 'N', 'neff', 'Neff']
GWAS_H_NCONTROL_OPTIONS = ['N_control', 'N_controls', 'controls']
GWAS_H_NCASE_OPTIONS = ['N_case', 'N_cases', 'cases']
GWAS_H_NCONTROL_OPTIONS = ['N_control', 'N_controls', 'controls', 'TotalCases']
GWAS_H_NCASE_OPTIONS = ['N_case', 'N_cases', 'cases', 'TotalSampleSize']
GWAS_HG18_HINTS = ['hg18', 'b36']
GWAS_HG19_HINTS = ['hg19']
GWAS_HG19_HINTS = ['hg19', 'GCF1405.25']


def build_parser():
Expand Down Expand Up @@ -116,6 +117,7 @@ def build_parser():
gwas_header.add_argument('--gwas:other', metavar='COLUMN', help='Non-effect/Other/Major allele column name.')
gwas_header.add_argument('--gwas:freq', metavar='COLUMN', help='Effect/Risk/Coded/Minor allele frequency column name.')
gwas_header.add_argument('--gwas:beta', metavar='COLUMN', help='Log-odds column name [beta/effect], relative to effect/risk/coded/minor allele.')
gwas_header.add_argument('--gwas:or', metavar='COLUMN', help='Odds-ratio column name [OR], relative to effect/risk/coded/minor allele.')
gwas_header.add_argument('--gwas:se', metavar='COLUMN', help='Log-odds standard error column name.')
gwas_header.add_argument('--gwas:p', metavar='COLUMN', help='P-value column name.')
gwas_header.add_argument('--gwas:chr-bp', metavar='COLUMN', help='Position column name when encoded as chr:pos.')
Expand Down Expand Up @@ -292,7 +294,7 @@ def fopen(filename):

def read_gwas(args, filename, report=None):
liftover = None
float_conv_failed = yes = no = 0
wrong_column_count = float_conv_failed = yes = no = 0
desc = {}
default_p, default_std = args['gwas:default:p'], args['gwas:default:se']
default_n, default_chr = args['gwas:default:n'], args['gwas:default:chr']
Expand Down Expand Up @@ -342,12 +344,18 @@ def select(name, options, fail=True):
hpos_bp = select('bp', GWAS_H_BP_OPTIONS)
else:
postype_combined = True
href = select('effect', GWAS_H_REF_OPTIONS)
href = select('effect', GWAS_H_EFF_OPTIONS)
hoth = select('other', GWAS_H_OTH_OPTIONS)
hfreq = select('freq', GWAS_H_FREQ_OPTIONS)
hb = select('beta', GWAS_H_BETA_OPTIONS)
hse = select('se', GWAS_H_SE_OPTIONS)
hp = select('p', GWAS_H_PVALUE_OPTIONS)
if args['gwas:beta'] is not None:
hb = select('beta', GWAS_H_BETA_OPTIONS)
elif args['gwas:or'] is not None:
hb = None
hor = select('or', [])
else:
hb = select('beta', GWAS_H_BETA_OPTIONS) # select default or fail
if not args['gwas:n'] is None:
hn = [header.index(col) for col in args['gwas:n'].split(',')]
desc['n'] = '+'.join(args['gwas:n'].split(','))
Expand Down Expand Up @@ -384,6 +392,12 @@ def select(name, options, fail=True):
reporter = ReporterLine('Reading gwas data.')
continue
parts = line.split(args['gwas:sep'])
if len(parts) != len(header):
# MDD switches halfway to a different format for a small number of non-significant SNPs
if report:
log_error(report, 'wrong_column_count', gwas=parts)
wrong_column_count += 1
continue
if postype_combined:
ch, bp, *_ = parts[hpos].split(':', 2) # Some append :<SNP>/:<INDEL>, just ignore
if default_chr:
Expand All @@ -405,9 +419,18 @@ def select(name, options, fail=True):
except ValueError:
n = 'NA'
gwas_freq = parts[hfreq]
gwas_beta = default_beta or parts[hb]
try:
gwas_freq, gwas_beta = float(gwas_freq), float(gwas_beta)
if default_beta:
gwas_beta = default_beta
elif hb is None:
or_ = float(parts[hor])
if or_ < 0:
print('negative ODDS ratio. is this a beta?')
exit(1)
gwas_beta = math.log(or_)
else:
gwas_beta = float(parts[hb])
gwas_freq = float(gwas_freq)
except ValueError:
row = GWASRow(parts[href].upper(), parts[hoth].upper(),
gwas_freq, gwas_beta,
Expand Down Expand Up @@ -446,11 +469,18 @@ def select(name, options, fail=True):
reporter.update(lineno, f.fileno())
except KeyboardInterrupt:
print('Aborted reading gwas data at line', lineno)
except UnicodeDecodeError:
# IBD turns into gibberish after 95%, we can probably discard that
print('UnicodeDecodeError, aborted reading gwas data at line', lineno)
if liftover:
print('Successfully', desc['build'], '->', args['gen:build'], 'converted', yes, 'rows')
print('Build conversion failed for', no, 'rows (reported as gwas_build_conv_failed).')
if float_conv_failed:
print('Numeric conversion failed for', float_conv_failed, 'rows (reported as gwas_float_conv_failed).')
if wrong_column_count:
print('Invalid number of columns for', wrong_column_count, 'rows (reported as wrong_column_count).')
print()
print()


def update_read_stats(args, gwas, stats_filename, output=None, report=None):
Expand All @@ -462,7 +492,7 @@ def update_read_stats(args, gwas, stats_filename, output=None, report=None):
freq_comp = np.zeros((40000, 2)) if np else None
converted = discarded = 0
stopped = False
rsids_seen = {} # some summary stat files have duplicate rsids...
rsids_seen = set() # some summary stat files have duplicate rsids...
def select(name, options, can_fail=False):
option_name = 'gen:' + name
option_val = getattr(args, option_name)
Expand Down

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