delly-ready pipeline

snakecnv/Snakefile

@@ -155,7 +155,7 @@ rule parsing:
         unpack(snakemake_utils.getToolOuputFile),
         reference = REFERENCE
     output:
-        parseoutput = "{tool}/{tool}_{chrom}_{svtype}_parsed.vcf.gz"
+        parseoutput = "parse/{tool}/{tool}_{chrom}_{svtype}_parsed.vcf.gz"
     params:
         filterbed = FILTERBED
     threads:

snakecnv/bin/delly.py

@@ -10,54 +10,62 @@ from subprocess import run
 
 import pysam
 
-from extractDiscSplitReads import extractDiscSplitReads
-from insert_size_distro import insertsizes
 
 def eprint(*args, **kwargs):
     ''' A simple to sys.stderr printer wrapper '''
     print(*args, file=sys.stderr, **kwargs)
 
-def abs_file_path(f):
+
+def existing_file_abs_path(f):
     try:
-        my_real_path = Path(f).resolve()
+        Path(f).resolve()
     except FileNotFoundError:
         print("File %s is not an existing and valid file" % f)
+        exit(1)
     else:
         my_abs_path = os.path.abspath(f)
     return my_abs_path
 
+
+def file_abs_path(f):
+    return os.path.abspath(f)
+
+
 def get_bamfiles(bamlist):
     with open(bamlist, "r") as fin:
-        bamfiles = [abs_file_path(f.strip()) for f in fin]
+        bamfiles = [existing_file_abs_path(f.strip()) for f in fin]
     return bamfiles
 
+
 def get_all_chromosomes(bamfile):
     with pysam.AlignmentFile(bamfile, "rb") as samfile:
-        header = samfile.header
         chromosomes = [contig['SN'] for contig in samfile.header['SQ']]
     return chromosomes
 
+
 def get_unwanted_chroms(chroms_all, chromosome):
     if chromosome not in chroms_all:
         eprint("Selected chromosome is not a valid chromosome")
     chroms_all.remove(chromosome)
     return chroms_all
 
+
 def append_chroms_to_exclude(exclusion_file, unwanted_chromosomes, odir="."):
-    new_exclusion = os.path.join(odir,"excluded.tsv")
+    new_exclusion = os.path.join(odir, "excluded.tsv")
     copyfile(exclusion_file, new_exclusion)
     with open(new_exclusion,  "a") as fout:
         for chrom in unwanted_chromosomes:
             fout.write(chrom+"\n")
     return new_exclusion
 
+
 def runDelly(args):
     bamlist = args.bamlist
     genome = args.genome
-    excluded = abs_file_path(args.excluded)
     chrom = args.chrom
     svtype = args.svtype
-    output = args.output
+    excluded = existing_file_abs_path(args.excluded)
+    output = file_abs_path(args.output)
 
     bamfiles = get_bamfiles(bamlist)
 
@@ -85,17 +93,16 @@ def runDelly(args):
     # construct delly string
     delly_filter_str = "delly filter "
     delly_filter_str += "-f germline "
+    delly_filter_str += "-m 100 "
     delly_filter_str += "-t %s " % svtype
     delly_filter_str += "-o %s " % output
     delly_filter_str += "delly_raw.bcf "
     completed = run(delly_filter_str, shell=True)
 
-#delly filter -f germline  -m 100 -t ${svtype} -o ${outputfile} delly_raw.bcf
-
     os.chdir(oldir)
-    #rmtree(tempdir)
+    rmtree(tempdir)
 
-    #return completed.returncode
+    return completed.returncode
 
 def parse_arguments():
     parser = argparse.ArgumentParser(

snakecnv/lib/svsnakemake_utils.py

@@ -61,7 +61,7 @@ class SnakemakeUtils:
         inputs = []
         for tool in self.tools:
             if wildcards.svtype in self.tools_sv_types[tool]:
-                inputs.append("{tool}/{tool}_{chrom}_{svtype}_parsed.vcf.gz".format(
+                inputs.append("parse/{tool}/{tool}_{chrom}_{svtype}_parsed.vcf.gz".format(
                     tool=tool, chrom=wildcards.chrom, svtype=wildcards.svtype
                 ))
         return inputs

snakecnv/tools/lumpy.snk

@@ -2,7 +2,6 @@ lumpy_sv = ['DEL', 'INV', 'DUP']
 
 rule lumpy:
     input:
-        bams = expand("extraction/{{chrom}}/{sample}.bam", sample=samples),
         bamlist = "bamlist.txt",
         excluded = "exclusion/excluded.bed"
     output:
@@ -16,4 +15,4 @@ rule lumpy:
         stderr = "logs/lumpy/{chrom}.e"
     shell:
         "lumpy.py -b {input.bamlist} -c {wildcards.chrom}"
-        " -r {params.readlength -t {threads} | bgzip -c > {output}"
+        " -r {params.readlength} -t {threads} | bgzip -c > {output}"