transcript-transformer
Advanced tools
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| 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 |
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| [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) |
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