Merge branch 'main' of github.com:seqcode/seqchromloader into main

Author: yztxwd

seqchromloader/loader.py

@@ -29,7 +29,7 @@ class SeqChromLoader():
     def __init__(self, SeqChromDataset):
         self.SeqChromDataset = SeqChromDataset
 
-    def __call__(self, *args, dataloader_kws:dict=None, **kwargs):
+    def __call__(self, *args, dataloader_kws:dict={}, **kwargs):
         # default dataloader kws
         if dataloader_kws is not None:
             wif = dataloader_kws.pop("worker_init_fn", worker_init_fn)
@@ -268,4 +268,4 @@ def val_dataloader(self):
         return wds.WebLoader(self.val_loader, num_workers=self.num_workers, batch_size=self.batch_size_per_rank)
 
     def test_dataloader(self):
-        return wds.WebLoader(self.test_loader, num_workers=self.num_workers, batch_size=self.batch_size_per_rank)
+        return wds.WebLoader(self.test_loader, num_workers=self.num_workers, batch_size=self.batch_size_per_rank)

seqchromloader/utils.py

@@ -300,7 +300,7 @@ def rev_comp(inp_str):
 
 class BigWigInaccessible(Exception):
     def __init__(self, chrom, start, end, *args):
-        super.__init__(*args)
+        super().__init__(*args)
         self.chrom = chrom
         self.start = start
         self.end = end
@@ -348,4 +348,4 @@ def extract_info(chrom, start, end, label, genome_pyfasta, bigwigs, target_bam,
 
 if __name__ == "__main__":
     chip_seq_coordinates = load_chipseq_data("Bichrom/sample_data/Ascl1.peaks", genome_sizes_file="Bichrom/sample_data/mm10.info",
-                                                    to_keep=None, to_filter=['chr17', 'chr11', 'chrM', 'chrUn'])
+                                                    to_keep=None, to_filter=['chr17', 'chr11', 'chrM', 'chrUn'])