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Add chrom regex filter #11

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Add chrom regex filter #11

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ca28b6a
add chromosome filtering regex
Lipastomies Apr 20, 2021
c4f081d
fix chrom regex
Lipastomies Apr 20, 2021
5f8084a
move regex to python script
Lipastomies Apr 20, 2021
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1 change: 1 addition & 0 deletions wdl/gwas/saige.json
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
"saige.test_combine.test.minmac": 5,
"saige.test_combine.test.logP": true,
"saige.test_combine.combine.logP": true,
"saige.test_combine.combine.chrom_regex": "^chr(([0-9]{1,2})|([XYM]))$",
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Not relevant for current functioning but while at this I would make chr optional in case this is used for data without a chr prefix. Also would add XYMT in case there's mitochondrial as MT

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Then, how about this:

Suggested change
"saige.test_combine.combine.chrom_regex": "^chr(([0-9]{1,2})|([XYM]))$",
"saige.test_combine.combine.chrom_regex": "^(chr)?(([0-9]{1,2})|([XYM]|MT))$",

Now chr is optional (matched 0 or 1 times) and chromosome can be 0-99, X,Y,M,MT


"saige.test_combine.combine.prefix": "finngen_R7_",
"saige.test_combine.combine.chrcol": "#chrom",
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8 changes: 6 additions & 2 deletions wdl/gwas/saige_sub.wdl
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Expand Up @@ -80,6 +80,7 @@ task combine {
String prefix
Boolean logP
String logPStr = if logP then "True" else "False"
String chrom_regex

command <<<
set -euxo pipefail
Expand All @@ -96,7 +97,7 @@ task combine {

echo "`date` converting results to ${prefix}${pheno}.gz"
python3 <<EOF | sort -k 1,1g -k 2,2g | bgzip > ${prefix}${pheno}.gz
import math, gzip
import math, gzip, re
from collections import OrderedDict
from functools import reduce

Expand All @@ -106,6 +107,8 @@ task combine {
def red(obj, func_list):
return "NA" if obj == "NA" else reduce(lambda o, func: func[0](o, *func[1]) if func[0] is not str.format else func[0](func[1], o), func_list, obj)

reg = re.compile("${chrom_regex}")

if "${traitType}" == "quantitative":
mapping = OrderedDict([
("#chrom", ("CHR", [(str.replace, ("chr", "")), (str.replace, ("X", "23")), (str.replace, ("Y", "24")), (str.replace, ("MT", "25")), (str.replace, ("M", "25"))])),
Expand Down Expand Up @@ -146,7 +149,8 @@ task combine {
print('\t'.join(mapping.keys()))
for line in f:
s = line.strip().split('\t')
print('\t'.join(str(red(s[header[v[0]]], v[1])) for v in mapping.values()))
if reg.match(s[0]):#match searches from the beginning of the string, which in this case is what we want
print('\t'.join(str(red(s[header[v[0]]], v[1])) for v in mapping.values()))
EOF
echo "`date` plotting qq and manha"
qqplot.R --file ${prefix}${pheno}.gz --bp_col "${bp_col}" --pval_col "${p_valcol}" --chrcol "${chrcol}" --loglog_pval ${loglog_pval}
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3 changes: 2 additions & 1 deletion wdl/gwas/saige_tests.json
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Expand Up @@ -12,10 +12,11 @@
"saige.test_combine.test.minmac": 5,
"saige.test_combine.test.logP": true,
"saige.test_combine.combine.logP": true,
"saige.test_combine.combine.chrom_regex": "^chr(([0-9]{1,2})|([XYM]))$",

"saige.test_combine.combine.prefix": "",
"saige.test_combine.combine.chrcol": "#chrom",
"saige.test_combine.combine.p_valcol": "pval",
"saige.test_combine.combine.bp_col": "pos",
"saige.test_combine.combine.loglog_pval": 10,
"saige.test_combine.combine.loglog_pval": 10
}