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Remove label dtype/depend on BED row format #48

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Remove label dtype/depend on BED row format #48

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19 changes: 4 additions & 15 deletions kipoiseq/dataloaders/sequence.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,6 @@ class BedDataset(object):
bed_columns: number of columns corresponding to the bed file. All the columns
after that will be parsed as targets
num_chr: if specified, 'chr' in the chromosome name will be dropped
label_dtype: specific data type for labels, Example: `float` or `np.float32`
ambiguous_mask: if specified, rows containing only ambiguous_mask values will be skipped
incl_chromosomes: exclusive list of chromosome names to include in the final dataset.
if not None, only these will be present in the dataset
Expand All @@ -65,7 +64,6 @@ class BedDataset(object):
int] # blockStarts

def __init__(self, tsv_file,
label_dtype=None,
bed_columns=3,
num_chr=False,
ambiguous_mask=None,
Expand All @@ -76,7 +74,6 @@ def __init__(self, tsv_file,
self.tsv_file = tsv_file
self.bed_columns = bed_columns
self.num_chr = num_chr
self.label_dtype = label_dtype
self.ambiguous_mask = ambiguous_mask
self.incl_chromosomes = incl_chromosomes
self.excl_chromosomes = excl_chromosomes
Expand All @@ -95,8 +92,7 @@ def __init__(self, tsv_file,
self.df = pd.read_table(self.tsv_file,
header=None,
dtype={i: d
for i, d in enumerate(self.bed_types[:self.bed_columns] +
[self.label_dtype] * self.n_tasks)},
for i, d in enumerate(self.bed_types[:found_columns])},
sep='\t')
if self.num_chr and self.df.iloc[0][0].startswith("chr"):
self.df[0] = self.df[0].str.replace("^chr", "")
Expand All @@ -122,14 +118,14 @@ def __getitem__(self, idx):
if self.ignore_targets or self.n_tasks == 0:
labels = {}
else:
labels = row.iloc[self.bed_columns:].values.astype(self.label_dtype)
labels = row.iloc[self.bed_columns:].values
return interval, labels

def __len__(self):
return len(self.df)

def get_targets(self):
return self.df.iloc[:, self.bed_columns:].values.astype(self.label_dtype)
return self.df.iloc[:, self.bed_columns:].values


@kipoi_dataloader(override={"dependencies": deps, 'info.authors': package_authors})
Expand All @@ -153,8 +149,6 @@ class StringSeqIntervalDl(Dataset):
md5: 01320157a250a3d2eea63e89ecf79eba
num_chr_fasta:
doc: True, the the dataloader will make sure that the chromosomes don't start with chr.
label_dtype:
doc: None, datatype of the task labels taken from the intervals_file. Example - str, int, float, np.float32
auto_resize_len:
doc: None, required sequence length.
# max_seq_len:
Expand Down Expand Up @@ -189,7 +183,6 @@ def __init__(self,
intervals_file,
fasta_file,
num_chr_fasta=False,
label_dtype=None,
auto_resize_len=None,
# max_seq_len=None,
# use_strand=False,
Expand All @@ -213,7 +206,6 @@ def __init__(self,
self.bed = BedDataset(self.intervals_file,
num_chr=self.num_chr_fasta,
bed_columns=3,
label_dtype=parse_dtype(label_dtype),
ignore_targets=ignore_targets)
self.fasta_extractors = None

Expand Down Expand Up @@ -281,8 +273,6 @@ class SeqIntervalDl(Dataset):
md5: 01320157a250a3d2eea63e89ecf79eba
num_chr_fasta:
doc: True, the the dataloader will make sure that the chromosomes don't start with chr.
label_dtype:
doc: 'None, datatype of the task labels taken from the intervals_file. Example: str, int, float, np.float32'
auto_resize_len:
doc: None, required sequence length.
# use_strand:
Expand Down Expand Up @@ -324,7 +314,6 @@ def __init__(self,
intervals_file,
fasta_file,
num_chr_fasta=False,
label_dtype=None,
auto_resize_len=None,
# max_seq_len=None,
# use_strand=False,
Expand All @@ -335,7 +324,7 @@ def __init__(self,
dtype=None):
# core dataset, not using the one-hot encoding params
self.seq_dl = StringSeqIntervalDl(intervals_file, fasta_file, num_chr_fasta=num_chr_fasta,
label_dtype=label_dtype, auto_resize_len=auto_resize_len,
auto_resize_len=auto_resize_len,
# use_strand=use_strand,
ignore_targets=ignore_targets)

Expand Down