Bio.SearchIO.InfernalIO package

Submodules

• Bio.SearchIO.InfernalIO.infernal_tab module
  • InfernalTabParser
    • InfernalTabParser.__init__()
    • InfernalTabParser.__iter__()
  • InfernalTabIndexer
    • InfernalTabIndexer.__init__()
    • InfernalTabIndexer.__iter__()
    • InfernalTabIndexer.get_raw()
    • InfernalTabIndexer.__abstractmethods__
    • InfernalTabIndexer.__annotations__
• Bio.SearchIO.InfernalIO.infernal_text module
  • InfernalTextParser
    • InfernalTextParser.__init__()
    • InfernalTextParser.__iter__()
    • InfernalTextParser.__annotations__
  • InfernalTextIndexer
    • InfernalTextIndexer.__init__()
    • InfernalTextIndexer.__iter__()
    • InfernalTextIndexer.get_raw()
    • InfernalTextIndexer.__abstractmethods__
    • InfernalTextIndexer.__annotations__

Module contents

Bio.SearchIO support for Infernal output formats.

This module adds support for parsing Infernal outputs. Infernal is a suite of programs for searching DNA sequence databases for RNA structure and sequence similarities using covariance models (CMs).

Bio.SearchIO.InfernalIO was tested on the following Infernal versions and flavors:

• Infernal (1.0.0+): cmscan and cmsearch

More information on HMMER are available through these links:

• Web page: http://eddylab.org/infernal/

• User guide: http://eddylab.org/infernal/Userguide.pdf

Supported formats

Bio.SearchIO.InfernalIO supports the following Infernal output formats:

• Plain text - ‘infernal-text’ - parsing, indexing

• Tabular - ‘infernal-tab’ - parsing, indexing

For all output formats, Infernal uses ‘mdl’ for ‘query’ and ‘seq’ for ‘hit’. InfernalIO is aware of this different naming scheme, and will use ‘query’ and ‘hit’ to fit SearchIO’s object model.

Infernal sometime reports ‘local ends’ (i.e., a large insertion or deletion in the optimal alignment), which are expresented by a number in brackets in the alignment (ex. AUUAC*[88]*GUAGU). In InfernalIO, these local alignment are split into fragments of the same HSP.

infernal-text

The Infernal plain text parser supports output files with alignment blocks (default) or without (with the ‘-noali’ flag). If the alignment blocks are present, it can parse files with variable alignment width (using the ‘-notextw’ or ‘-textw’ flag). Both CM or HMM searches (with the ‘–hmmonly’ flag) output are supported. The parser only supports non-verbose output formats.

The following SearchIO objects attributes are provided.

Object	Attribute	Value
QueryResult	accession	query accession
	description	query sequence description
	id	query sequence ID
	program	Infernal flavor
	seq_len	full length of query sequence
	target	target search database
	version	Infernal version
Hit	description	hit sequence description
	id	hit sequence ID
HSP	evalue	hsp evalue
	bias	hsp bias
	bitscore	hsp score
	gc	gc fraction
	is_included	boolean, whether the hit of the hsp is in the inclusion threshold
	query_start	query start position
	query_end	query end position
	query_endtype	query sequence end types (e.g., ‘[]’, ‘..’, ‘[.’, ‘.]’, etc.)
	hit_start	hit start position
	hit_end	hit end position
	hit_endtype	hit sequence end types
	acc_avg	expected accuracy per alignment residue (acc column)
	model	type of model used (cm or hmm)
	truncated	indicate if the hit is truncated (5’, 3’ or both) or not
HSPFragment	aln_annotation	alignment similarity string and other annotations (PP, CS, similarity and NC (except for –hmmonly))
	aln_span	length of alignment fragment
	hit	hit sequence
	hit_start	local alignment sequence start coordinate (seq from)
	hit_end	local alignment sequence end coordinate (seq to)
	hit_strand	hit sequence strand
	query	query sequence
	query_start	local model alignment start coordinate (mdl from)
	query_end	local model alignment end coordinate (mdl to)

infernal-tab

The Infernal plain text parser supports the standard cmsearch tabular output and cmscan tabular output files formats 1, 2 and 3 (inferred automatically from the header).

Rows marked with ‘*’ denotes attributes not available in the default format.

Object	Attribute	Value
QueryResult	accession	query accession
	id	query sequence ID
	clan*	Rfam clan
	seq_len*	query sequence length
Hit	description	hit sequence description
	id	hit sequence ID
	accession	hit accession
	seq_len*	hit sequence length
HSP	evalue	hsp evalue
	bias	hsp bias
	bitscore	hsp score
	gc	gc fraction
	is_included	boolean, whether the hit of the hsp is in the inclusion threshold
	model	type of model used (cm or hmm)
	truncated	indicate if the hit is truncated (5’, 3’ or both) or not
	pipeline_pass	pipeline pass at which the hit was identified
	olp*	overlap status of this hit (‘*’, ‘^’, ‘$’ or ‘=’)
	anyidx*	index of the best scoring overlapping hit (or none if there are no overlap)
	afrct1*	fraction of this hit that overlap with anyidx hit (or none if there are no overlap)
	afrct2*	fraction of anyidx hit with this hit (or none if there are no overlap)
	winidx*	index of the best scoring hit that overlaps with this hit that is marked as ‘^’ (or none if there are no overlap)
	wfrct1*	fraction of this hit that overlap with winidx hit (or none if there are no overlap)
	wfrct2*	fraction of winidx hit with this hit (or none if there are no overlap)
HSPFragment (also via HSP)	hit_start	local alignment sequence start coordinate (seq from)
	hit_end	local alignment sequence end coordinate (seq to)
	hit_strand	hit sequence strand
	query_start	local model alignment start coordinate (mdl from)
	query_end	local model alignment end coordinate (mdl to)