bug fix that backend is not used

Author: yztxwd

seqchromloader/loader.py

@@ -139,7 +139,7 @@ def initialize(self):
         # create the stream handler after child processes spawned to enable parallel reading
         # this function will be called by worker_init_function in DataLoader
         self.genome_pyfaidx = pyfaidx.Fasta(self.genome_fasta)
-        self.bigwigs = [utils.BigWig(bw_path) for bw_path in self.bigwig_filelist] if self.bigwig_filelist is not None else None
+        self.bigwigs = [utils.BigWig(bw_path, backend=config.BIGWIG_BACKEND) for bw_path in self.bigwig_filelist] if self.bigwig_filelist is not None else None
         if self.target_bam is not None:
             if isinstance(self.target_bam, list):
                 self.target_pysam = [pysam.AlignmentFile(b) for b in self.target_bam]

seqchromloader/utils.py

@@ -461,7 +461,7 @@ def compute_mean_std_bigwig(bigwig):
     :type bigwig: str
     :rtype: (mean, stddev)
     """
-    bw = BigWig(bigwig)
+    bw = BigWig(bigwig, backend=config.BIGWIG_BACKEND)
 
     # get chrom length list
     chroms = bw.chroms()

seqchromloader/writer.py

@@ -16,7 +16,7 @@
 import pysam
 import webdataset as wds
 
-from seqchromloader import utils
+from seqchromloader import utils, config
 from seqchromloader.loader import _SeqChromDatasetByWds
 
 logger = logging.getLogger(__name__)
@@ -147,17 +147,17 @@ def dump_data_webdataset_worker(coords,
                                 ):
     #get handlers
     genome_pyfaidx = pyfaidx.Fasta(fasta)
-    bigwigs = [utils.BigWig(bw) for bw in bigwig_files] if bigwig_files is not None else None
+    bigwigs = [utils.BigWig(bw, backend=config.BIGWIG_BACKEND) for bw in bigwig_files] if bigwig_files is not None else None
     if target_bam is not None:
         if isinstance(target_bam, list):
             target = [pysam.AlignmentFile(b) for b in target_bam]
         else:
             target = pysam.AlignmentFile(target_bam)
     elif target_bw is not None:
         if isinstance(target_bw, list):
-            target = [utils.BigWig(b) for b in target_bw]
+            target = [utils.BigWig(b, backend=config.BIGWIG_BACKEND) for b in target_bw]
         else:
-            target = utils.BigWig(target_bw)
+            target = utils.BigWig(target_bw, backend=config.BIGWIG_BACKEND)
     else:
         target = None