levseq 1.3.1__tar.gz → 1.3.2__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {levseq-1.3.1/levseq.egg-info → levseq-1.3.2}/PKG-INFO +1 -1
- {levseq-1.3.1 → levseq-1.3.2}/levseq/__init__.py +1 -1
- {levseq-1.3.1 → levseq-1.3.2}/levseq/utils.py +1 -2
- {levseq-1.3.1 → levseq-1.3.2/levseq.egg-info}/PKG-INFO +1 -1
- {levseq-1.3.1 → levseq-1.3.2}/LICENSE +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/MANIFEST.in +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/README.md +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/IO_processor.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/barcoding/__init__.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/barcoding/demultiplex +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/barcoding/demultiplex-arm64 +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/barcoding/demultiplex-x86 +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/barcoding/minion_barcodes.fasta +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/basecaller.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/cmd.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/coordinates.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/globals.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/interface.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/parser.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/run_levseq.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/screen.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/seqfit.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/simulation.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/user.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/variantcaller.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq/visualization.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq.egg-info/SOURCES.txt +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq.egg-info/dependency_links.txt +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq.egg-info/entry_points.txt +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq.egg-info/requires.txt +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/levseq.egg-info/top_level.txt +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/setup.cfg +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/setup.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/tests/test_demultiplex_docker.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/tests/test_deploy.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/tests/test_opligopools.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/tests/test_seqfitvis.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/tests/test_seqs.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/tests/test_statistics.py +0 -0
- {levseq-1.3.1 → levseq-1.3.2}/tests/test_variant_calling.py +0 -0
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@@ -18,7 +18,7 @@
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__title__ = 'levseq'
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__description__ = 'LevSeq nanopore sequencing'
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__url__ = 'https://github.com/fhalab/levseq/'
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__version__ = '1.3.
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__version__ = '1.3.2'
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__author__ = 'Yueming Long, Ariane Mora, Francesca-Zhoufan Li, Emre Gursoy'
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__author_email__ = 'ylong@caltech.edu'
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__license__ = 'GPL3'
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@@ -248,7 +248,6 @@ def alignment_from_cigar(cigar: str, alignment: str, ref: str, query_qualities:
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pos += op_len
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ref_pos += op_len
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elif op == 1: # insertion to the reference
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insertion_updates
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inserts[ref_pos - 1] = alignment[pos - 1:pos + op_len]
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new_seq = new_seq[:-1] + 'I' # Set the previous position to be an insertion
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pos += op_len
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@@ -501,4 +500,4 @@ def get_variant_label_for_well(seq_df, threshold):
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combined_p_value = float("nan")
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# Return also the mean mutation rate for the well
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mean_mutation_rate = np.mean([1 - x for x in non_refs['freq_non_ref'].values])
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return label, probability, combined_p_value, mixed_well, mean_mutation_rate
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return label, probability, combined_p_value, mixed_well, mean_mutation_rate
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