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transcript-transformer

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transcript-transformer - pypi Package Compare versions

Comparing version
0.9.5
to
0.9.6
+1
-1
PKG-INFO
Metadata-Version: 2.4
Name: transcript-transformer
Version: 0.9.5
Version: 0.9.6
Summary: Transformers for Transcripts

@@ -5,0 +5,0 @@ Home-page: https://github.com/jdcla/transcript_transformer

[metadata]
name = transcript-transformer
version = 0.9.5
version = 0.9.6
author = Jim Clauwaert

@@ -5,0 +5,0 @@ description = Transformers for Transcripts

Metadata-Version: 2.4
Name: transcript-transformer
Version: 0.9.5
Version: 0.9.6
Summary: Transformers for Transcripts

@@ -5,0 +5,0 @@ Home-page: https://github.com/jdcla/transcript_transformer

@@ -84,11 +84,11 @@ import os

read_lims = [20, 41]
f = h5py.File(h5_path, "r")
tr_ids = (
pl.from_numpy(np.array(f["transcript/transcript_id"])).to_series().cast(pl.Utf8)
)
tr_lens = pl.from_numpy(np.array(f["transcript/transcript_len"])).to_series()
ribo_to_parse = deepcopy(ribo_paths)
# load from hdf5 file
with h5py.File(h5_path, "r") as f:
tr_ids = pl.Series(np.array(f["transcript/transcript_id"]), dtype=pl.Utf8)
tr_lens = pl.from_numpy(np.array(f["transcript/transcript_len"])).to_series()
f_keys = f.keys()
samples = {}
for group_samples in ribo_paths.values():
samples.update(group_samples)
samples_to_process = deepcopy(samples)
for sample_id, path in samples.items():

@@ -101,3 +101,3 @@ cond_1 = (

cond_2 = not (parallel or overwrite) and (
f"transcript/riboseq/{sample_id}" in f.keys()
f"transcript/riboseq/{sample_id}" in f_keys
)

@@ -109,5 +109,4 @@ if cond_1 or cond_2:

)
ribo_to_parse.pop(sample_id)
f.close()
for sample_id, path in samples.items():
samples_to_process.pop(sample_id)
for sample_id, path in samples_to_process.items():
print(f"Loading in {sample_id}...")

@@ -114,0 +113,0 @@ riboseq_data = parse_ribo_reads(path, read_lims, tr_ids, tr_lens)