Bio.SearchIO.HmmerIO package
Submodules
- Bio.SearchIO.HmmerIO.hmmer2_text module
Hmmer2TextParserHmmer2TextParser.__init__()Hmmer2TextParser.__iter__()Hmmer2TextParser.read_next()Hmmer2TextParser.push_back()Hmmer2TextParser.parse_key_value()Hmmer2TextParser.parse_preamble()Hmmer2TextParser.parse_qresult()Hmmer2TextParser.parse_hits()Hmmer2TextParser.parse_hsps()Hmmer2TextParser.parse_hsp_alignments()
Hmmer2TextIndexer
- 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.org
User guide: http://eddylab.org/software/hmmer/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 |