From 9a450c94bd9203056bafe1385bb870189d125e3e Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Wed, 6 Jun 2018 17:52:21 +0200
Subject: [PATCH] Add align after build_pop
---
cnvpipelines.py | 22 +++++++++++++++++++---
snakecnv/align.snk | 6 +++---
snakecnv/popsim.snk | 12 +++++++-----
3 files changed, 29 insertions(+), 11 deletions(-)
diff --git a/cnvpipelines.py b/cnvpipelines.py
index da873d2..b0e8fc5 100755
--- a/cnvpipelines.py
+++ b/cnvpipelines.py
@@ -705,13 +705,13 @@ class CnvPipeline:
raise FileExistsError(file + "already exists but is not a link")
os.symlink(file, final_link)
- final_sample_file = os.path.join(self.wdir, "samples.list")
+ final_sample_file = os.path.join(self.wdir, "samples.yml")
self.parse_align_sample_file(samples, final_sample_file)
config = {
"wdir": self.wdir,
"reference": os.path.join(ref_dir, os.path.basename(reference)),
- "sample_file": final_sample_file
+ "sample_file_align": final_sample_file
}
with open(self.config_file, "w") as config_file:
@@ -753,6 +753,17 @@ class CnvPipeline:
if not os.path.exists(dest):
os.symlink(source, dest)
+ @staticmethod
+ def _create_samples_fastq_simulaton(nb_inds, smple_file):
+ samples = {}
+ for i in range(1, nb_inds+1):
+ samples["indiv%d" % i] = {
+ "reads1": os.path.join("pop", "indiv%d_1.fq.gz" % i),
+ "reads2": os.path.join("pop", "indiv%d_2.fq.gz" % i)
+ }
+ with open(smple_file, "w") as samples_f:
+ yaml.dump(samples, samples_f, default_flow_style=False)
+
def run_simulation(self, nb_inds, reference, nstretches, sv_list, coverage, force_polymorphism,
haploid, proba_del, proba_inv, read_len, insert_len_mean, insert_len_sd, min_deletions,
min_inversions, max_try, genotypes, force_wdir=False, **kwargs):
@@ -799,6 +810,10 @@ class CnvPipeline:
ref_final = os.path.join(self.wdir, os.path.basename(reference))
self._link(reference, ref_final)
+ # Create sample file for fastq files:
+ samples_file_fq = os.path.join(self.wdir, "samples.yml")
+ self._create_samples_fastq_simulaton(nb_inds, samples_file_fq)
+
config = {
"wdir": self.wdir,
"nb_inds": nb_inds,
@@ -813,7 +828,8 @@ class CnvPipeline:
"insert_len_sd": insert_len_sd,
"min_deletions": min_deletions,
"min_inversions": min_inversions,
- "max_try": max_try
+ "max_try": max_try,
+ "sample_file_align": samples_file_fq
}
nstretches_final = None
diff --git a/snakecnv/align.snk b/snakecnv/align.snk
index c051364..eaba3ab 100644
--- a/snakecnv/align.snk
+++ b/snakecnv/align.snk
@@ -13,7 +13,7 @@ from align_snakemake_utils import SnakemakeUtils
# Get from config:
-samples = get_samples_align(config['sample_file'])
+samples = get_samples_align(config['sample_file_align'])
reference = config['reference']
wdir = config['wdir']
@@ -23,10 +23,10 @@ snakemake_utils = SnakemakeUtils(samples)
include: "tools/threads.snk"
-localrules: all
+localrules: all_align
-rule all:
+rule all_align:
input:
expand("bams/{sample}.bam", sample=samples.keys()),
expand("bams/{sample}.bam.bai", sample=samples.keys())
diff --git a/snakecnv/popsim.snk b/snakecnv/popsim.snk
index 7458e7d..3a41aef 100644
--- a/snakecnv/popsim.snk
+++ b/snakecnv/popsim.snk
@@ -54,7 +54,7 @@ def buildpop_inputs():
def buildpop_outputs():
outputs = []
for n in range(1, NB_INDS+1):
- outputs += [os.path.join("pop", "indiv%d_1.fq.gz" % n), os.path.join("pop", "indiv%d_2.fq.gz" % n)]
+ outputs += [os.path.abspath(os.path.join("pop", "indiv%d_1.fq.gz" % n)), os.path.abspath(os.path.join("pop", "indiv%d_2.fq.gz" % n))]
return outputs
bp_inputs, bp_params = buildpop_inputs()
@@ -62,12 +62,14 @@ bp_outputs = buildpop_outputs()
include: "tools/threads.snk"
+include: "align.snk"
-localrules: all
+localrules: all_popsim
-rule all:
+rule all_popsim:
input:
- *bp_outputs
+ expand("bams/{sample}.bam", sample=["indiv%d" % i for i in range(1, NB_INDS+1)])
+ #*bp_outputs
rule buildpop:
input:
@@ -118,4 +120,4 @@ rule buildpop:
command.append("-f")
if params.haploid:
command.append("-a")
- shell(" ".join(command) + " 1> %s 2> %s" % (log.stdout, log.stderr))
\ No newline at end of file
+ shell(" ".join(command) + " 1> %s 2> %s" % (log.stdout, log.stderr))
--
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