alignparse package

alignparse

Submodules

• ccs
• Summaries
  • Summaries.summaries
  • Summaries.ccs_stats()
  • Summaries.has_stat()
  • Summaries.has_zmw_stats()
  • Summaries.plot_ccs_stats()
  • Summaries.plot_zmw_stats()
  • Summaries.zmw_stats()
• Summary
  • Summary.name
  • Summary.fastqfile
  • Summary.reportfile
  • Summary.zmw_stats
  • Summary.passes
  • Summary.accuracy
  • Summary.length
• get_ccs_stats()
• report_to_stats()
• consensus
• Mutations
  • Mutations.deletions
  • Mutations.insertions
  • Mutations.substitutions
• add_mut_info_cols()
• empirical_accuracy()
• process_mut_str()
• simple_mutconsensus()
• constants
• CBPALETTE
• cs_tag
• Alignment
  • Alignment.query_name
  • Alignment.target_name
  • Alignment.cs
  • Alignment.query_clip5
  • Alignment.query_clip3
  • Alignment.target_clip5
  • Alignment.target_lastpos
  • Alignment.orientation
  • Alignment.extract_cs()
  • Alignment.get_accuracy()
• cs_introns_to_deletions()
• cs_op_len_target()
• cs_op_type()
• cs_to_mutation_str()
• cs_to_nt_mutation_count()
• cs_to_op_mutation_count()
• cs_to_sequence()
• split_cs()
• minimap2
• Mapper
  • Mapper.options
  • Mapper.prog
  • Mapper.version
  • Mapper.retain_tags
  • Mapper.map_to_sam()
• OPTIONS_CODON_DMS
• OPTIONS_VIRUS_W_DEL
• targets
• Feature
  • Feature.name
  • Feature.seq
  • Feature.start
  • Feature.end
  • Feature.length
• Target
  • Target.seq
  • Target.name
  • Target.length
  • Target.features
  • Target.feature_names
  • Target.get_feature()
  • Target.get_name()
  • Target.has_feature()
  • Target.image()
• Targets
  • Targets.targets
  • Targets.target_names
  • Targets.target_seqs
  • Targets.align()
  • Targets.align_and_parse()
  • Targets.feature_parse_specs()
  • Targets.features_to_parse()
  • Targets.get_target()
  • Targets.parse_alignment()
  • Targets.plot()
  • Targets.write_fasta()
• utils
• InFrameDeletionsToSubs
  • InFrameDeletionsToSubs.geneseq
  • InFrameDeletionsToSubs.dels_to_subs()
  • InFrameDeletionsToSubs.shiftable()
• MutationRenumber
  • MutationRenumber.old_to_new_site
  • MutationRenumber.old_to_wt
  • MutationRenumber.renumber_muts()
• merge_dels()
• qvals_to_accuracy()
• sort_mutations()