Install mm10 LCR input file along with other variation resources. Tha…

…nks to @brentp

cloudbio/biodata/dbsnp.py

@@ -39,6 +39,7 @@ def download_dbsnp(genomes, bundle_version, dbsnp_version):
  _dbsnp_human(env, gid, manager, bundle_version, dbsnp_version)
  elif gid in ["mm10", "canFam3"]:
  _dbsnp_custom(env, gid)
+ _download_lcrs_custom(env, gid)
 
 def _dbsnp_custom(env, gid):
  """Retrieve resources for dbsnp builds from custom S3 biodata bucket.
@@ -157,8 +158,7 @@ def _download_ancestral(env, gid, gconfig):
  if not env.safe_exists(outfile):
  env.safe_run("ln -sf ../../GRCh37/variation/%s %s" % (outfile, outfile))
 
-
-def _download_qsignature(env,gid,gconfig):
+def _download_qsignature(env, gid, gconfig):
  """Download qsignature position file to detect samples problems
 
  :param env
@@ -171,17 +171,17 @@ def _download_qsignature(env,gid,gconfig):
  if gid == "GRCh37":
  outfile = "qsignature.vcf"
  if not env.safe_exists(outfile):
- zipfile = shared._remote_fetch(env, base_url , samedir=True)
- outdir = "qsignature" 
+ zipfile = shared._remote_fetch(env, base_url, samedir=True)
+ outdir = "qsignature"
  env.safe_run("mkdir -p %s" % outdir)
  env.safe_run("tar -jxf %s -C %s" % (zipfile, outdir))
  env.safe_run("mv %s/qsignature_positions.txt %s" % (outdir, outfile))
  env.safe_run("rm -rf %s" % outdir)
  env.safe_run("rm -rf %s" % zipfile)
- elif gid == "hg19": # symlink to GRCh37 download 
- outfile = os.path.basename(base_url) 
+ elif gid == "hg19": # symlink to GRCh37 download
+ outfile = os.path.basename(base_url)
  if not env.safe_exists(outfile):
- env.safe_run("ln -sf ../../GRCh37/variation/%s %s" % (outfile, outfile)) 
+ env.safe_run("ln -sf ../../GRCh37/variation/%s %s" % (outfile, outfile))
 
 
 def _download_background_vcf(gid):
@@ -229,3 +229,18 @@ def _fix_chrom_names(env, orig_file):
  return out_file
  shared._remote_fetch(env, lcr_url, fix_fn=_fix_chrom_names)
  env.safe_run("tabix -p vcf -f %s" % out_file)
+
+def _download_lcrs_custom(env, gid):
+ """Retrieve low complexity regions from other sources.
+
+ mm10 from Brent Pedersen: http://figshare.com/articles/LCR_mm10_bed_gz/1180124
+ """
+ urls = {"mm10": "http://files.figshare.com/1688228/LCR_mm10.bed.gz"}
+ out_file = "LCR.bed.gz"
+ cur_url = urls.get(gid)
+ if cur_url and not env.safe_exists(out_file):
+ def _bgzip_file(env, orig_file):
+ env.safe_run("zcat %s | bgzip -c > %s" % (orig_file, out_file))
+ return out_file
+ shared._remote_fetch(env, cur_url, fix_fn=_bgzip_file)
+ env.safe_run("tabix -p vcf -f %s" % out_file)