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Possibly get rid of sqt dependency #85

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marcelm opened this issue Nov 9, 2018 · 0 comments
Closed
2 of 14 tasks

Possibly get rid of sqt dependency #85

marcelm opened this issue Nov 9, 2018 · 0 comments

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@marcelm
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marcelm commented Nov 9, 2018 •
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sqt pulls in some unnecessary dependencies (pysam, samtools, matplotlib instead of matplotlib-base). These are the functions or classes from sqt that IgDiscover uses at the moment:

  • sqt.align.consensus
  • sqt.align.edit_distance
  • sqt.align.hamming_distance
  • sqt.align.multialign
  • sqt.align.globalalign
  • sqt.dna.GENETIC_CODE
  • sqt.dna.nt_to_aa
  • sqt.dna.reverse_complement
  • sqt.FastaReader
  • sqt.HelpfulArgumentParser
  • sqt.SequenceReader
  • sqt.utils.available_cpu_count

These commands are used:

  • sqt readlenhisto
  • sqt fastxmod
@marcelm marcelm closed this as completed Nov 3, 2020
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