Add version to downloaded Manta, move vcftobedpe from manta folder

sngyngl · Feb 28, 2017 · 8e037f7 · 8e037f7
1 parent 5a376f8
commit 8e037f7
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Showing 5 changed files with 6 additions and 5 deletions.
diff --git a/quast_libs/manta/__init__.py → quast_libs/ra_utils/__init__.py b/quast_libs/manta/__init__.py → quast_libs/ra_utils/__init__.py
diff --git a/quast_libs/ra_utils.py → quast_libs/ra_utils/misc.py b/quast_libs/ra_utils.py → quast_libs/ra_utils/misc.py
@@ -18,8 +18,9 @@
 bedtools_dirpath = join(qconfig.LIBS_LOCATION, 'bedtools')
 bedtools_bin_dirpath = join(qconfig.LIBS_LOCATION, 'bedtools', 'bin')
 
-config_manta_relpath = join('build', 'bin', 'configManta.py')
+manta_version = '0.29.6'
 manta_dirpath = None
+config_manta_relpath = join('build', 'bin', 'configManta.py')
 
 manta_external_dirpath = join(qconfig.QUAST_HOME, 'external_tools/manta')
 manta_ext_linux_fpath = join(manta_external_dirpath, 'manta_linux.tar.bz2')
@@ -104,7 +105,7 @@ def compile_bedtools(logger, only_clean=False):
 
 def download_manta(logger, bed_fpath=None, only_clean=False):
     global manta_dirpath
-    manta_dirpath = get_dir_for_download('manta', 'Manta', [config_manta_relpath], logger)
+    manta_dirpath = get_dir_for_download('manta' + manta_version, 'Manta', [config_manta_relpath], logger)
     if not manta_dirpath:
         return False
 

diff --git a/quast_libs/manta/vcfToBedpe.py → quast_libs/ra_utils/vcfToBedpe.py b/quast_libs/manta/vcfToBedpe.py → quast_libs/ra_utils/vcfToBedpe.py
diff --git a/quast_libs/reads_analyzer.py b/quast_libs/reads_analyzer.py
@@ -16,7 +16,7 @@
 from quast_libs import qconfig, qutils
 from quast_libs.ca_utils.misc import ref_labels_by_chromosomes
 from quast_libs.fastaparser import create_fai_file, get_chr_lengths_from_fastafile
-from quast_libs.ra_utils import compile_reads_analyzer_tools, get_manta_fpath, sambamba_fpath, \
+from quast_libs.ra_utils.misc import compile_reads_analyzer_tools, get_manta_fpath, sambamba_fpath, \
     bwa_fpath, bedtools_fpath, paired_reads_names_are_equal, download_manta
 from .qutils import is_non_empty_file, add_suffix, get_chr_len_fpath, correct_name, is_python2
 
@@ -142,7 +142,7 @@ def process_one_ref(cur_ref_fpath, output_dirpath, err_path, bed_fpath=None):
         cmd = 'gunzip -c %s' % found_SV_fpath
         qutils.call_subprocess(shlex.split(cmd), stdout=open(unpacked_SV_fpath, 'w'),
                                stderr=open(err_path, 'a'), logger=logger)
-    from quast_libs.manta import vcfToBedpe
+    from quast_libs.ra_utils import vcfToBedpe
     vcfToBedpe.vcfToBedpe(open(unpacked_SV_fpath), open(ref_bed_fpath, 'w'))
     return ref_bed_fpath
 

diff --git a/setup.py b/setup.py
@@ -38,7 +38,7 @@
 from quast_libs.glimmer import compile_glimmer
 from quast_libs.gage import compile_gage
 from quast_libs.ca_utils.misc import compile_aligner, compile_gnuplot
-from quast_libs.ra_utils import compile_reads_analyzer_tools, download_manta, compile_bwa, compile_bedtools
+from quast_libs.ra_utils.misc import compile_reads_analyzer_tools, download_manta, compile_bwa, compile_bedtools
 
 name = 'quast'
 quast_package = qconfig.PACKAGE_NAME