From 1507cadf4e4137cd3dd1f5f5d54fd4d993aa9ce3 Mon Sep 17 00:00:00 2001
From: Jody Phelan <jody.phelan@lshmt.ac.uk>
Date: Fri, 12 Apr 2019 14:57:10 +0100
Subject: [PATCH] add get_bed_gt from VCF

---
 meta.yaml                 |  8 +++++---
 pathogenprofiler/utils.py |  7 +++----
 pathogenprofiler/vcf.py   | 26 +++++++++++++++++++++++++-
 scripts/splitchr.py       |  1 -
 4 files changed, 33 insertions(+), 9 deletions(-)

diff --git a/meta.yaml b/meta.yaml
index 7c59851..4fe0a83 100644
--- a/meta.yaml
+++ b/meta.yaml
@@ -13,7 +13,7 @@ source:
 build:
   script: python -m pip install --no-deps --ignore-installed .
   noarch: python
-  number: 0
+  number: 1
 
 requirements:
   host:
@@ -26,8 +26,8 @@ requirements:
     - bowtie2
     - minimap2
     - parallel
-    - samtools>=1.9
-    - bcftools>=1.9
+    - samtools
+    - bcftools
     - tqdm
     - delly
 
@@ -36,6 +36,8 @@ test:
     - pathogenprofiler
   commands:
     - splitchr.py -h
+    - samtools
+    - bcftools
 
 about:
   home: https://github.com/jodyphelan/{{ name }}
diff --git a/pathogenprofiler/utils.py b/pathogenprofiler/utils.py
index a1f399b..06957d6 100644
--- a/pathogenprofiler/utils.py
+++ b/pathogenprofiler/utils.py
@@ -59,12 +59,12 @@ def get_random_file(prefix = None,extension=None):
 	randint = rand_generator.randint(1,999999)
 	if prefix:
 		if extension:
-			return "%s.%s.%s" % (prefix,randint,extension)
+			return "%s.%s%s" % (prefix,randint,extension)
 		else:
 			return "%s.%s.txt" % (prefix,randint)
 	else:
 		if extension:
-			return "%s.tmp.%s" % (randint,extension)
+			return "%s.tmp%s" % (randint,extension)
 		else:
 			return "%s.tmp.txt" % (randint)
 
@@ -108,7 +108,6 @@ def load_bed(filename,columns,key1,key2=None,intasint=False):
 	return results
 
 def split_bed(bed_file,size,reformat=False):
-	bed_regions = {}
 	for l in open(filecheck(bed_file)):
 		row = l.rstrip().split()
 		chrom,start,end = row[0],int(row[1]),int(row[2])
@@ -292,7 +291,7 @@ def which(program):
 	def is_exe(fpath):
 		return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
 
-	fpath, fname = os.path.split(program)
+	fpath = os.path.split(program)[0]
 	if fpath:
 		if is_exe(program):
 			return program
diff --git a/pathogenprofiler/vcf.py b/pathogenprofiler/vcf.py
index 03e5335..483e6d4 100644
--- a/pathogenprofiler/vcf.py
+++ b/pathogenprofiler/vcf.py
@@ -165,7 +165,31 @@ def get_positions(self):
 			row = l.split()
 			results.append((row[0],int(row[1])))
 		return results
-
+	def get_bed_gt(self,bed_file,ref_file):
+		add_arguments_to_self(self,locals())
+		cmd = "bcftools convert --gvcf2vcf -f %(ref_file)s %(filename)s  | bcftools view -T %(bed_file)s  | bcftools query -f '%%CHROM\\t%%POS\\t%%REF\\t%%ALT[\\t%%GT\\t%%AD]\\n'" % vars(self)
+		results = defaultdict(lambda : defaultdict(dict))
+		for l in cmd_out(cmd):
+			#Chromosome	4348079	0/0	51
+			chrom,pos,ref,alt,gt,ad = l.rstrip().split()
+			pos =int(pos)
+			d = {}
+			alts = alt.split(",")
+			ad = [int(x) for x in ad.split(",")] if ad!="." else [100]
+			if gt=="0/0":
+				d[ref] = ad[0]
+			elif gt=="./.":
+				d[ref] = 0
+			else:
+				for i,a in enumerate([ref]+alts):
+					d[a] = ad[i]
+			results[chrom][pos] = d
+		bed = load_bed(bed_file,[1,3,5],1,3)
+		for chrom in bed:
+			for pos in bed[chrom]:
+				if int(pos) not in results[chrom]:
+					results[chrom][int(pos)] = {bed[chrom][pos][2]:50}
+		return results
 
 class delly_bcf(bcf):
 	def __init__(self,filename):
diff --git a/scripts/splitchr.py b/scripts/splitchr.py
index 3346f48..63428b9 100755
--- a/scripts/splitchr.py
+++ b/scripts/splitchr.py
@@ -1,5 +1,4 @@
 #! /usr/bin/env python
-import sys
 import pathogenprofiler as pp
 import argparse