itsxpress package

Submodules

• itsxpress.SeqSample module
  • Dedup
    • Dedup.matchdict
    • Dedup.uc_file
    • Dedup.rep_file
    • Dedup.seq_file
    • Dedup.fastq
    • Dedup.fastq2
    • Dedup.__init__()
    • Dedup._get_paired_seq_generator()
    • Dedup._get_trimmed_seq_generator()
    • Dedup.create_paired_trimmed_seqs()
    • Dedup.create_trimmed_seqs()
    • Dedup.parse()
  • ItsPosition
    • ItsPosition.domtable
    • ItsPosition.region
    • ItsPosition.ddict
    • ItsPosition.leftprefix
    • ItsPosition.rightprefix
    • ItsPosition.__init__()
    • ItsPosition._score()
    • ItsPosition.get_position()
    • ItsPosition.parse()
  • SeqSample
    • SeqSample.tempdir
    • SeqSample.fastq
    • SeqSample.uc_file
    • SeqSample.rep_file
    • SeqSample.dom_file
    • SeqSample.seq_file
    • SeqSample.r1
    • SeqSample.fastq2
    • SeqSample.__init__()
    • SeqSample._search()
    • SeqSample.cluster()
    • SeqSample.deduplicate()
    • SeqSample.orient_reads()
  • SeqSampleNotPaired
    • SeqSampleNotPaired.__init__()
  • SeqSamplePairedNotInterleaved
    • SeqSamplePairedNotInterleaved.__init__()
    • SeqSamplePairedNotInterleaved._merge_reads()
• itsxpress.definitions module
• itsxpress.main module
  • _check_fastqs()
  • _check_total_reads()
  • _is_paired()
  • _logger_setup()
  • create_runtime_hmm()
  • create_temp_directory()
  • main()
  • myparser()
  • read_file()
  • restricted_float()
• itsxpress.plugin_setup module
• itsxpress.q2_itsxpress module