levseq 1.2.9__tar.gz → 1.3.1__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.
Files changed (40) hide show
  1. {levseq-1.2.9/levseq.egg-info → levseq-1.3.1}/PKG-INFO +2 -2
  2. {levseq-1.2.9 → levseq-1.3.1}/levseq/__init__.py +2 -2
  3. {levseq-1.2.9 → levseq-1.3.1}/levseq/barcoding/minion_barcodes.fasta +6 -6
  4. {levseq-1.2.9 → levseq-1.3.1}/levseq/run_levseq.py +1 -1
  5. {levseq-1.2.9 → levseq-1.3.1}/levseq/utils.py +2 -1
  6. {levseq-1.2.9 → levseq-1.3.1/levseq.egg-info}/PKG-INFO +2 -2
  7. {levseq-1.2.9 → levseq-1.3.1}/LICENSE +0 -0
  8. {levseq-1.2.9 → levseq-1.3.1}/MANIFEST.in +0 -0
  9. {levseq-1.2.9 → levseq-1.3.1}/README.md +0 -0
  10. {levseq-1.2.9 → levseq-1.3.1}/levseq/IO_processor.py +0 -0
  11. {levseq-1.2.9 → levseq-1.3.1}/levseq/barcoding/__init__.py +0 -0
  12. {levseq-1.2.9 → levseq-1.3.1}/levseq/barcoding/demultiplex +0 -0
  13. {levseq-1.2.9 → levseq-1.3.1}/levseq/barcoding/demultiplex-arm64 +0 -0
  14. {levseq-1.2.9 → levseq-1.3.1}/levseq/barcoding/demultiplex-x86 +0 -0
  15. {levseq-1.2.9 → levseq-1.3.1}/levseq/basecaller.py +0 -0
  16. {levseq-1.2.9 → levseq-1.3.1}/levseq/cmd.py +0 -0
  17. {levseq-1.2.9 → levseq-1.3.1}/levseq/coordinates.py +0 -0
  18. {levseq-1.2.9 → levseq-1.3.1}/levseq/globals.py +0 -0
  19. {levseq-1.2.9 → levseq-1.3.1}/levseq/interface.py +0 -0
  20. {levseq-1.2.9 → levseq-1.3.1}/levseq/parser.py +0 -0
  21. {levseq-1.2.9 → levseq-1.3.1}/levseq/screen.py +0 -0
  22. {levseq-1.2.9 → levseq-1.3.1}/levseq/seqfit.py +0 -0
  23. {levseq-1.2.9 → levseq-1.3.1}/levseq/simulation.py +0 -0
  24. {levseq-1.2.9 → levseq-1.3.1}/levseq/user.py +0 -0
  25. {levseq-1.2.9 → levseq-1.3.1}/levseq/variantcaller.py +0 -0
  26. {levseq-1.2.9 → levseq-1.3.1}/levseq/visualization.py +0 -0
  27. {levseq-1.2.9 → levseq-1.3.1}/levseq.egg-info/SOURCES.txt +0 -0
  28. {levseq-1.2.9 → levseq-1.3.1}/levseq.egg-info/dependency_links.txt +0 -0
  29. {levseq-1.2.9 → levseq-1.3.1}/levseq.egg-info/entry_points.txt +0 -0
  30. {levseq-1.2.9 → levseq-1.3.1}/levseq.egg-info/requires.txt +0 -0
  31. {levseq-1.2.9 → levseq-1.3.1}/levseq.egg-info/top_level.txt +0 -0
  32. {levseq-1.2.9 → levseq-1.3.1}/setup.cfg +0 -0
  33. {levseq-1.2.9 → levseq-1.3.1}/setup.py +0 -0
  34. {levseq-1.2.9 → levseq-1.3.1}/tests/test_demultiplex_docker.py +0 -0
  35. {levseq-1.2.9 → levseq-1.3.1}/tests/test_deploy.py +0 -0
  36. {levseq-1.2.9 → levseq-1.3.1}/tests/test_opligopools.py +0 -0
  37. {levseq-1.2.9 → levseq-1.3.1}/tests/test_seqfitvis.py +0 -0
  38. {levseq-1.2.9 → levseq-1.3.1}/tests/test_seqs.py +0 -0
  39. {levseq-1.2.9 → levseq-1.3.1}/tests/test_statistics.py +0 -0
  40. {levseq-1.2.9 → levseq-1.3.1}/tests/test_variant_calling.py +0 -0
{levseq-1.2.9/levseq.egg-info → levseq-1.3.1}/PKG-INFO RENAMED
@@ -1,8 +1,8 @@
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  Metadata-Version: 2.1
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  Name: levseq
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- Version: 1.2.9
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+ Version: 1.3.1
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  Home-page: https://github.com/fhalab/levseq/
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- Author: Yueming Long, Emreay Gursoy, Ariane Mora, Francesca-Zhoufan Li
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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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  Project-URL: Bug Tracker, https://github.com/fhalab/levseq/
{levseq-1.2.9 → levseq-1.3.1}/levseq/__init__.py RENAMED
@@ -18,8 +18,8 @@
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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__ = '1.2.9'
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- __author__ = 'Yueming Long, Emreay Gursoy, Ariane Mora, Francesca-Zhoufan Li'
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+ __version__ = '1.3.1'
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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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{levseq-1.2.9 → levseq-1.3.1}/levseq/barcoding/minion_barcodes.fasta RENAMED
@@ -267,9 +267,9 @@ GCTTGCGATTGATGCTTAGTATCA
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  >RB38
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  ACCACAGGAGGACGATACAGAGAA
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  >RB39
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- TCTGCCACACACTCGTAAGTCCTT
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+ CCACAGTGTCAACTAGAGCCTCTC
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  >RB40
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- GTCGATACTGGACCTATCCCTTGG
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+ TAGTTTGGATGACCAAGGATAGCC
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  >RB41
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  GGAGTTCGTCCAGAGAAGTACACG
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  >RB42
@@ -285,7 +285,7 @@ GCTGTGTTCCACTTCATTCTCCTG
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  >RB47
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  GTGCAACTTTCCCACAGGTAGTTC
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  >RB48
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- GAGTCCGTGACAACTTCTGAAAGC
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+ CATCTGGAACGTGGTACACCTGTA
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  >RB49
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  ACTGGTGCAGCTTTGAACATCTAG
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  >RB50
@@ -297,7 +297,7 @@ TGAGAGACAAGATTGTTCGTGGAC
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  >RB53
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  AGATTCAGACCGTCTCATGCAAAG
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  >RB54
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- GGGTGCCAACTACATACCAAACCT
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+ CAAGAGCTTTGACTAAGGAGCATG
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  >RB55
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  TGGAAGATGAGACCCTGATCTACG
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  >RB56
@@ -309,7 +309,7 @@ CAGGTTACTCCTCCGTGAGTCTGA
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  >RB59
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  TCAATCAAGAAGGGAAAGCAAGGT
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  >RB60
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- GAACCCTACTTTGGACAGACACCT
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+ CATGTTCAACCAAGGCTTCTATGG
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  >RB61
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  AGAGGGTACTATGTGCCTCAGCAC
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  >RB62
@@ -381,4 +381,4 @@ GATTGTCCTCAAACTGCCACCTAC
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  >RB95
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  CCTGTCTGGAAGAAGAATGGACTT
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  >RB96
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- CTGAACGGTCATAGAGTCCACCAT
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+ CTGAACGGTCATAGAGTCCACCAT
{levseq-1.2.9 → levseq-1.3.1}/levseq/run_levseq.py RENAMED
@@ -364,7 +364,7 @@ def create_nc_variant(variant, refseq):
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  return refseq
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  elif "DEL" in variant:
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  return "#DEL#"
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- elif variant == '+':
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+ elif "INS" in variant:
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  return "#INS#"
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  else:
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  mutations = variant.split("_")
{levseq-1.2.9 → levseq-1.3.1}/levseq/utils.py RENAMED
@@ -248,6 +248,7 @@ 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
@@ -500,4 +501,4 @@ 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
{levseq-1.2.9 → levseq-1.3.1/levseq.egg-info}/PKG-INFO RENAMED
@@ -1,8 +1,8 @@
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  Metadata-Version: 2.1
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  Name: levseq
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- Version: 1.2.9
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+ Version: 1.3.1
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  Home-page: https://github.com/fhalab/levseq/
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- Author: Yueming Long, Emreay Gursoy, Ariane Mora, Francesca-Zhoufan Li
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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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  Project-URL: Bug Tracker, https://github.com/fhalab/levseq/
{levseq-1.2.9 → levseq-1.3.1}/LICENSE RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/MANIFEST.in RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/README.md RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/levseq/IO_processor.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/levseq/basecaller.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/levseq/cmd.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/levseq/coordinates.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/levseq/globals.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/levseq/interface.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/levseq/parser.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/levseq/screen.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/levseq/seqfit.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/levseq/simulation.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/levseq/user.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/levseq/variantcaller.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/levseq/visualization.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/setup.cfg RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/setup.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/tests/test_deploy.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/tests/test_opligopools.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/tests/test_seqfitvis.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/tests/test_seqs.py RENAMED
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{levseq-1.2.9 → levseq-1.3.1}/tests/test_statistics.py RENAMED
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