morrislab · amcpherson · Jan 25, 2017
diff --git a/README.md b/README.md
@@ -73,7 +73,7 @@ Running PhyloWGS
 
 2. Compile the C++ file.
 
-        g++ -o mh.o -O3 mh.cpp  util.cpp `gsl-config --cflags --libs`
+        g++ -o phylowgs_mh -O3 mh.cpp  util.cpp `gsl-config --cflags --libs`
 
 3. Run PhyloWGS. Minimum invocation on sample data set:
 

diff --git a/conda/phylowgs/build.sh b/conda/phylowgs/build.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+mkdir -p $PREFIX/bin
+
+g++ -g -o phylowgs_mh -O3 mh.cpp  util.cpp `gsl-config --cflags --libs`
+
+cp phylowgs_mh $PREFIX/bin/phylowgs_mh
+
+$PYTHON setup.py install
+
diff --git a/conda/phylowgs/cnv_data.txt b/conda/phylowgs/cnv_data.txt
@@ -0,0 +1,2 @@
+cnv	a	d	ssms	physical_cnvs
+c0	66023,50883,62757,36056,58777	126755,100469,121941,71263,115417	s2,1,2;s4,0,1	chrom=1,start=1234,end=5678,major_cn=2,minor_cn=1,cell_prev=0.8;chrom=X,start=15,end=10000,major_cn=2,minor_cn=0,cell_prev=0.8;chrom=22,start=123,end=456,major_cn=1,minor_cn=0,cell_prev=0.8
diff --git a/conda/phylowgs/meta.yaml b/conda/phylowgs/meta.yaml
@@ -0,0 +1,27 @@
+package:
+  name: phylowgs
+  version: 'smchet5'
+
+source:
+  git_url: https://github.com/morrislab/phylowgs.git
+  git_rev: smchet5
+
+requirements:
+  build:
+    - python
+    - gsl
+  run:
+    - python
+    - numpy
+    - scipy
+    - ete2
+    - gsl
+
+build:
+  number: 1
+
+about:
+  home: https://github.com/morrislab/phylowgs.git
+  license: GPL
+  summary: Application for inferring subclonal composition and evolution from whole-genome sequencing data.
+
diff --git a/conda/phylowgs/run_test.sh b/conda/phylowgs/run_test.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+phylowgs_evolve -B 10 -s 10 -i 10 $RECIPE_DIR/ssm_data.txt $RECIPE_DIR/cnv_data.txt
diff --git a/conda/phylowgs/ssm_data.txt b/conda/phylowgs/ssm_data.txt
@@ -0,0 +1,12 @@
+id	gene	a	d	mu_r	mu_v
+s0	a	66023,50883,62757,36056,58777	126755,100469,121941,71263,115417	0.999	0.5
+s1	b	71532,50933,64719,52048,83311	135031,97485,120826,101788,157737	0.999	0.5
+s2	c	93057,61406,72640,61648,54961	106716,83179,83799,86440,84607	0.999	0.5
+s3	GOLGA7B	31531,40281,18089,34256,36473	72221,84463,37410,73050,76869	0.999	0.5
+s4	KHNYN	94954,74636,67529,42328,59678	116386,106518,83271,66152,94465	0.999	0.5
+s5	NPHP4	9653,2300,4506,3559,3695	112775,79087,84707,92076,95849	0.999	0.5
+s6	NPM1	9072,2953,4140,5150,5270	127079,112052,86626,137055,185970	0.999	0.5
+s7	OLFM2	36288,28055,26648,35692,26492	74007,58150,56286,76579,54844	0.999	0.5
+s8	PYHIN1	75935,106216,153378,115054,112006	76826,111139,155389,123305,119960	0.999	0.5
+s9	RHCG	28543,31070,57616,34454,40929	51929,64677,116465,68393,79788	0.999	0.5
+s10	SMC1A	54447,39896,60454,63950,48658	82781,73370,92894,120384,89511	0.999	0.5
diff --git a/mh.cpp b/mh.cpp
@@ -13,8 +13,8 @@
 
 using namespace std;
 
-//  g++ -o mh.o  mh.cpp  util.cpp `gsl-config --cflags --libs`
-// ./mh.o 5000 100 11 1 8 4 ssm_data.txt cnv_data.txt c_tree_ssm_data_1.txt c_data_states_ssm_data_1.txt c_params.txt 5
+//  g++ -o phylowgs_mh mh.cpp  util.cpp `gsl-config --cflags --libs`
+// ./phylowgs_mh 5000 100 11 1 8 4 ssm_data.txt cnv_data.txt c_tree_ssm_data_1.txt c_data_states_ssm_data_1.txt c_params.txt 5
 //https://www.gnu.org/software/gsl/manual/html_node/Shared-Libraries.html
 
 

diff --git a/phylowgs/__init__.py b/phylowgs/__init__.py
diff --git a/alleles.py → phylowgs/alleles.py b/alleles.py → phylowgs/alleles.py
diff --git a/cc.py → phylowgs/cc.py b/cc.py → phylowgs/cc.py
diff --git a/data.py → phylowgs/data.py b/data.py → phylowgs/data.py
diff --git a/evolve.py → phylowgs/evolve.py b/evolve.py → phylowgs/evolve.py
diff --git a/node.py → phylowgs/node.py b/node.py → phylowgs/node.py
diff --git a/params.py → phylowgs/params.py b/params.py → phylowgs/params.py
@@ -57,8 +57,7 @@ def metropolis(tssb,iters=1000,std=0.01,burnin=0,n_ssms=0,n_cnvs=0,fin1='',fin2=
 	NNODES = str(len(nodes))
 	TREE_HEIGHT = str(max([node.ht for node in nodes])+1)
 
-	script_dir = os.path.dirname(os.path.realpath(__file__))
-	sp.check_call(['%s/mh.o' % script_dir, MH_ITR, MH_STD, N_SSM_DATA, N_CNV_DATA, NNODES, TREE_HEIGHT, FNAME_SSM_DATA, FNAME_CNV_DATA, FNAME_C_TREE, FNAME_C_DATA_STATES, FNAME_C_PARAMS,FNAME_C_MH_ARATIO, NTPS])
+	sp.check_call(['phylowgs_mh', MH_ITR, MH_STD, N_SSM_DATA, N_CNV_DATA, NNODES, TREE_HEIGHT, FNAME_SSM_DATA, FNAME_CNV_DATA, FNAME_C_TREE, FNAME_C_DATA_STATES, FNAME_C_PARAMS,FNAME_C_MH_ARATIO, NTPS])
 	ar = str(loadtxt(FNAME_C_MH_ARATIO,dtype='string'))
 	update_tree_params(tssb,FNAME_C_PARAMS) # update the tree with the new parameters sampled using the c++ code
 

diff --git a/parser/README.md → phylowgs/parser/README.md b/parser/README.md → phylowgs/parser/README.md
diff --git a/phylowgs/parser/__init__.py b/phylowgs/parser/__init__.py
diff --git a/parser/cnvs.txt.example → phylowgs/parser/cnvs.txt.example b/parser/cnvs.txt.example → phylowgs/parser/cnvs.txt.example
diff --git a/parser/create_phylowgs_inputs.py → phylowgs/parser/create_phylowgs_inputs.py b/parser/create_phylowgs_inputs.py → phylowgs/parser/create_phylowgs_inputs.py
diff --git a/parser/parse_cnvs.py → phylowgs/parser/parse_cnvs.py b/parser/parse_cnvs.py → phylowgs/parser/parse_cnvs.py
diff --git a/...r/test/inputs/mutect_tcga/mutect_tcga.vcf → ...r/test/inputs/mutect_tcga/mutect_tcga.vcf b/...r/test/inputs/mutect_tcga/mutect_tcga.vcf → ...r/test/inputs/mutect_tcga/mutect_tcga.vcf
diff --git a/...puts/mutect_tcga/mutect_tcga_with_ids.vcf → ...puts/mutect_tcga/mutect_tcga_with_ids.vcf b/...puts/mutect_tcga/mutect_tcga_with_ids.vcf → ...puts/mutect_tcga/mutect_tcga_with_ids.vcf
diff --git a/parser/test/inputs/strelka/strelka.vcf → ...gs/parser/test/inputs/strelka/strelka.vcf b/parser/test/inputs/strelka/strelka.vcf → ...gs/parser/test/inputs/strelka/strelka.vcf
diff --git a/parser/test/inputs/vardict/vardict.vcf → ...gs/parser/test/inputs/vardict/vardict.vcf b/parser/test/inputs/vardict/vardict.vcf → ...gs/parser/test/inputs/vardict/vardict.vcf
diff --git a/...nputs/vardict/vardict.vcf.intact_comments → ...nputs/vardict/vardict.vcf.intact_comments b/...nputs/vardict/vardict.vcf.intact_comments → ...nputs/vardict/vardict.vcf.intact_comments
diff --git a/.../test/outputs/mutect_tcga/mutect_tcga.ssm → .../test/outputs/mutect_tcga/mutect_tcga.ssm b/.../test/outputs/mutect_tcga/mutect_tcga.ssm → .../test/outputs/mutect_tcga/mutect_tcga.ssm
diff --git a/...puts/mutect_tcga/mutect_tcga_with_ids.ssm → ...puts/mutect_tcga/mutect_tcga_with_ids.ssm b/...puts/mutect_tcga/mutect_tcga_with_ids.ssm → ...puts/mutect_tcga/mutect_tcga_with_ids.ssm
diff --git a/parser/test/outputs/strelka/strelka.ssm → ...s/parser/test/outputs/strelka/strelka.ssm b/parser/test/outputs/strelka/strelka.ssm → ...s/parser/test/outputs/strelka/strelka.ssm
diff --git a/parser/test/outputs/vardict/vardict.ssm → ...s/parser/test/outputs/vardict/vardict.ssm b/parser/test/outputs/vardict/vardict.ssm → ...s/parser/test/outputs/vardict/vardict.ssm
diff --git a/parser/test/run_tests.py → phylowgs/parser/test/run_tests.py b/parser/test/run_tests.py → phylowgs/parser/test/run_tests.py
diff --git a/parser/test/util/munge_ids.py → phylowgs/parser/test/util/munge_ids.py b/parser/test/util/munge_ids.py → phylowgs/parser/test/util/munge_ids.py
diff --git a/parser/test/util/munge_positions.py → phylowgs/parser/test/util/munge_positions.py b/parser/test/util/munge_positions.py → phylowgs/parser/test/util/munge_positions.py
diff --git a/posterior_trees.py → phylowgs/posterior_trees.py b/posterior_trees.py → phylowgs/posterior_trees.py
diff --git a/printo.py → phylowgs/printo.py b/printo.py → phylowgs/printo.py
diff --git a/redo_ids.py → phylowgs/redo_ids.py b/redo_ids.py → phylowgs/redo_ids.py
diff --git a/tssb.py → phylowgs/tssb.py b/tssb.py → phylowgs/tssb.py
diff --git a/util.py → phylowgs/util.py b/util.py → phylowgs/util.py
diff --git a/util2.py → phylowgs/util2.py b/util2.py → phylowgs/util2.py
diff --git a/write_results.py → phylowgs/write_results.py b/write_results.py → phylowgs/write_results.py
diff --git a/pwgsresults/result_generator.py b/pwgsresults/result_generator.py
@@ -4,12 +4,12 @@
 import sys
 import os
 sys.path.append(os.path.join(os.path.dirname(os.path.realpath(__file__)), '..'))
-import util2
+import phylowgs.util2
 import json
 
 class ResultGenerator(object):
   def generate(self, tree_file, include_ssm_names):
-    reader = util2.TreeReader(tree_file)
+    reader = phylowgs.util2.TreeReader(tree_file)
     first_tree = next(reader.load_trees())
     cnv_logical_physical_mapping = json.loads(reader.read_extra_file('cnv_logical_physical_mapping.json'))
     try:
@@ -35,7 +35,7 @@ def generate(self, tree_file, include_ssm_names):
     return summaries, mutlist, all_mutass, params
 
   def _summarize_all_pops(self, tree_file):
-    reader = util2.TreeReader(tree_file)
+    reader = phylowgs.util2.TreeReader(tree_file)
     for idx, llh, tree in reader.load_trees_and_metadata(remove_empty_vertices = True):
       yield (idx, llh) + self._summarize_pops(tree)
     reader.close()

diff --git a/setup.py b/setup.py
@@ -0,0 +1,18 @@
+from setuptools import setup, find_packages
+
+setup(
+    name='phylowgs',
+    packages=find_packages(),
+    description='Application for inferring subclonal composition and evolution from whole-genome sequencing data.',
+    keywords=[],
+    classifiers=[],
+    entry_points={
+        'console_scripts': [
+            'phylowgs_evolve = phylowgs.evolve:main',
+            'phylowgs_write_results = phylowgs.write_results:main',
+            'phylowgs_create_inputs = phylowgs.parser.create_phylowgs_inputs:main',
+            'phylowgs_parse_cnvs = phylowgs.parser.parse_cnvs:main',
+        ],
+    },
+)
+
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		cnv a d ssms physical_cnvs
		c0 66023,50883,62757,36056,58777 126755,100469,121941,71263,115417 s2,1,2;s4,0,1 chrom=1,start=1234,end=5678,major_cn=2,minor_cn=1,cell_prev=0.8;chrom=X,start=15,end=10000,major_cn=2,minor_cn=0,cell_prev=0.8;chrom=22,start=123,end=456,major_cn=1,minor_cn=0,cell_prev=0.8
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		#!/bin/bash

		phylowgs_evolve -B 10 -s 10 -i 10 $RECIPE_DIR/ssm_data.txt $RECIPE_DIR/cnv_data.txt