Bio.SearchIO.HmmerIO package

Submodules

• Bio.SearchIO.HmmerIO.hmmer2_text module
• Bio.SearchIO.HmmerIO.hmmer3_domtab module
• Bio.SearchIO.HmmerIO.hmmer3_tab module
• Bio.SearchIO.HmmerIO.hmmer3_text module

Module contents

Bio.SearchIO support for HMMER output formats.

This module adds support for parsing HMMER outputs. HMMER is a suite of programs implementing the profile hidden Markov models to find similarity across protein sequences.

Bio.SearchIO.HmmerIO was tested on the following HMMER versions and flavors:

• HMMER3 flavors: hmmscan, hmmsearch, phmmer

• HMMER2 flavors: hmmpfam, hmmsearch

More information on HMMER are available through these links:

• Web page: http://hmmer.janelia.org/

• User guide: ftp://selab.janelia.org/pub/software/hmmer3/3.0/Userguide.pdf

Supported formats

Bio.SearchIO.HmmerIO supports the following HMMER output formats:

• Plain text, v3.0 - ‘hmmer3-text’ - parsing, indexing

• Table, v3.0 - ‘hmmer3-tab’ - parsing, indexing, writing

• Domain table, v3.0 - ‘hmmer3-domtab’* - parsing, indexing, writing

• Plain text, v2.x - ‘hmmer2-text’ - parsing, indexing

• For the domain table output, due to the way HMMER outputs the sequence coordinates, you have to specify what HMMER flavor produced the output as the file format. So instead of using ‘hmmer3-domtab’, you have to use either ‘hmmscan3-domtab’, ‘hmmsearch3-domtab’, or ‘phmmer3-domtab’ as the file format name.

Note that for all output formats, HMMER uses its own convention of input and output coordinates. It does not use the term ‘hit’ or ‘query’, instead it uses ‘hmm’ or ‘ali’. For example, ‘hmmfrom’ is the start coordinate of the HMM sequence while ‘alifrom’ is the start coordinate of the protein sequence.

HmmerIO is aware of this different naming scheme and will adjust them accordingly to fit SearchIO’s object model. If HmmerIO sees that the output file to parse was written by hmmsearch or phmmer, all ‘hmm’ coordinates will be the hit coordinates and ‘ali’ coordinates will be the query coordinates. Conversely, if the HMMER flavor is hmmscan, ‘hmm’ will be query and ‘ali’ will be hit.

This is why the ‘hmmer3-domtab’ format has to be specified with the source HMMER flavor. The parsers need to know which is the hit and which is the query. ‘hmmer3-text’ has its source program information present in the file, while ‘hmmer3-tab’ does not output any coordinates. That’s why both of these formats do not need direct flavor specification like ‘hmmer3-domtab’.

Also note that when using the domain table format writers, it will use HMMER’s naming convention (‘hmm’ and ‘ali’) so the files you write will be similar to files written by a real HMMER program.

hmmer2-text and hmmer3-text

The parser for HMMER 3.0 plain text output can parse output files with alignment blocks (default) or without (with the ‘–noali’ flag). If the alignment blocks are present, you can also parse files with variable alignment width (using the ‘–notextw’ or ‘–textw’ flag).

The following SearchIO objects attributes are provided. Rows marked with ‘*’ denotes attributes not available in the hmmer2-text format:

Object	Attribute	Value
QueryResult	accession	accession (if present)
	description	query sequence description
	id	query sequence ID
	program	HMMER flavor
	seq_len*	full length of query sequence
	target	target search database
	version	BLAST version
Hit	bias*	hit-level bias
	bitscore	hit-level score
	description	hit sequence description
	domain_exp_num*	expected number of domains in the hit (exp column)
	domain_obs_num	observed number of domains in the hit (N column)
	evalue	hit-level e-value
	id	hit sequence ID
	is_included*	boolean, whether the hit is in the inclusion threshold or not
HSP	acc_avg*	expected accuracy per alignment residue (acc column)
	bias*	hsp-level bias
	bitscore	hsp-level score
	domain_index	the domain index set by HMMER
	env_end*	end coordinate of the envelope
	env_endtype*	envelope end types (e.g. ‘[]’, ‘..’, ‘[.’, etc.)
	env_start*	start coordinate of the envelope
	evalue	hsp-level independent e-value
	evalue_cond*	hsp-level conditional e-value
	hit_endtype	hit sequence end types
	is_included*	boolean, whether the hit of the hsp is in the inclusion threshold
	query_endtype	query sequence end types
HSPFragment (also via HSP)	aln_annotation	alignment similarity string and other annotations (e.g. PP, CS)
	aln_span	length of alignment fragment
	hit	hit sequence
	hit_end	hit sequence end coordinate, may be ‘hmmto’ or ‘alito’ depending on the HMMER flavor
	hit_start	hit sequence start coordinate, may be ‘hmmfrom’ or ‘alifrom’ depending on the HMMER flavor
	hit_strand	hit sequence strand
	query	query sequence
	query_end	query sequence end coordinate, may be ‘hmmto’ or ‘alito’ depending on the HMMER flavor
	query_start	query sequence start coordinate, may be ‘hmmfrom’ or ‘alifrom’ depending on the HMMER flavor
	query_strand	query sequence strand

hmmer3-tab

The following SearchIO objects attributes are provided:

Object	Attribute	Column / Value
QueryResult	accession	query accession (if present)
	description	query sequence description
	id	query name
Hit	accession	hit accession
	bias	hit-level bias
	bitscore	hit-level score
	description	hit sequence description
	cluster_num	clu column
	domain_exp_num	exp column
	domain_included_num	inc column
	domain_obs_num	dom column
	domain_reported_num	rep column
	env_num	env column
	evalue	hit-level evalue
	id	target name
	overlap_num	ov column
	region_num	reg column
HSP	bias	bias of the best domain
	bitscore	bitscore of the best domain
	evalue	evalue of the best domain

hmmer3-domtab

To parse domain table files, you must use the HMMER flavor that produced the file. So instead of using ‘hmmer3-domtab’, use either ‘hmmsearch3-domtab’, ‘hmmscan3-domtab’, or ‘phmmer3-domtab’.

The following SearchIO objects attributes are provided:

Object	Attribute	Value
QueryResult	accession	accession
	description	query sequence description
	id	query sequence ID
	seq_len	full length of query sequence
Hit	accession	accession
	bias	hit-level bias
	bitscore	hit-level score
	description	hit sequence description
	evalue	hit-level e-value
	id	hit sequence ID
	seq_len	length of hit sequence or HMM
HSP	acc_avg	expected accuracy per alignment residue (acc column)
	bias	hsp-level bias
	bitscore	hsp-level score
	domain_index	the domain index set by HMMER
	env_end	end coordinate of the envelope
	env_start	start coordinate of the envelope
	evalue	hsp-level independent e-value
	evalue_cond	hsp-level conditional e-value
HSPFragment (also via HSP)	hit_end	hit sequence end coordinate, may be ‘hmmto’ or ‘alito’ depending on the HMMER flavor
	hit_start	hit sequence start coordinate, may be ‘hmmfrom’ or ‘alifrom’ depending on the HMMER flavor
	hit_strand	hit sequence strand
	query_end	query sequence end coordinate, may be ‘hmmto’ or ‘alito’ depending on the HMMER flavor
	query_start	query sequence start coordinate, may be ‘hmmfrom’ or ‘alifrom’ depending on the HMMER flavor
	query_strand	query sequence strand