Skip to content

Commit

Permalink
Add hmmer2-text related info in HmmerIO docs
Browse files Browse the repository at this point in the history
  • Loading branch information
@bow
bow committed Dec 9, 2012
1 parent 73e7ce3 commit 1ed793b
Showing 1 changed file with 18 additions and 17 deletions.
35 changes: 18 additions & 17 deletions Bio/SearchIO/HmmerIO/__init__.py
View file
Expand Up @@ -9,10 +9,10 @@
suite of programs implementing the profile hidden Markov models to find suite of programs implementing the profile hidden Markov models to find
homology across protein sequences. homology across protein sequences.
Bio.SearchIO.HmmerIO was tested on the following HMMER flavors and versions: Bio.SearchIO.HmmerIO was tested on the following HMMER versions and flavors:
- flavors: hmmscan, hmmsearch, phmmer - HMMER3 flavors: hmmscan, hmmsearch, phmmer
- version: 3.0 - HMMER2 flavors: hmmpfam, hmmsearch
More information on HMMER are available through these links: More information on HMMER are available through these links:
- Web page: http://hmmer.janelia.org/ - Web page: http://hmmer.janelia.org/
Expand Down Expand Up @@ -57,15 +57,16 @@
files written by a real HMMER program. files written by a real HMMER program.
hmmer3-text hmmer2-text and hmmer3-text
=========== ===========================
The parser for HMMER 3.0 plain text output can parse output files with alignment 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 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 are present, you can also parse files with variable alignment width (using the
'--notextw' or '--textw' flag). '--notextw' or '--textw' flag).
The following SearchIO objects attributes are provided: The following SearchIO objects attributes are provided. Rows marked with '*'
denotes attributes not available in the hmmer2-text format:
+-----------------+-------------------------+----------------------------------+ +-----------------+-------------------------+----------------------------------+
| Object | Attribute | Value | | Object | Attribute | Value |
Expand All @@ -78,19 +79,19 @@
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | program | HMMER flavor | | | program | HMMER flavor |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | seq_len | full length of query sequence | | | seq_len* | full length of query sequence |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | target | target search database | | | target | target search database |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | version | BLAST version | | | version | BLAST version |
+-----------------+-------------------------+----------------------------------+ +-----------------+-------------------------+----------------------------------+
| Hit | bias | hit-level bias | | Hit | bias* | hit-level bias |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | bitscore | hit-level score | | | bitscore | hit-level score |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | description | hit sequence description | | | description | hit sequence description |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | domain_exp_num | expected number of domains in | | | domain_exp_num* | expected number of domains in |
| | | the hit (exp column) | | | | the hit (exp column) |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | domain_obs_num | observed number of domains in | | | domain_obs_num | observed number of domains in |
Expand All @@ -100,32 +101,32 @@
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | id | hit sequence ID | | | id | hit sequence ID |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | is_included | boolean, whether the hit is in | | | is_included* | boolean, whether the hit is in |
| | | the inclusion threshold or not | | | | the inclusion threshold or not |
+-----------------+-------------------------+----------------------------------+ +-----------------+-------------------------+----------------------------------+
| HSP | acc_avg | expected accuracy per alignment | | HSP | acc_avg* | expected accuracy per alignment |
| | | residue (acc column) | | | | residue (acc column) |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | bias | hsp-level bias | | | bias* | hsp-level bias |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | bitscore | hsp-level score | | | bitscore | hsp-level score |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | domain_index | the domain index set by HMMER | | | domain_index | the domain index set by HMMER |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | env_end | end coordinate of the envelope | | | env_end* | end coordinate of the envelope |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | env_endtype | envelope end types (e.g. '[]', | | | env_endtype* | envelope end types (e.g. '[]', |
| | | '..', '[.', etc.) | | | | '..', '[.', etc.) |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | env_start | start coordinate of the envelope | | | env_start* | start coordinate of the envelope |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | evalue | hsp-level independent e-value | | | evalue | hsp-level independent e-value |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | evalue_cond | hsp-level conditional e-value | | | evalue_cond* | hsp-level conditional e-value |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | hit_endtype | hit sequence end types | | | hit_endtype | hit sequence end types |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
| | is_included | boolean, whether the hit of the | | | is_included* | boolean, whether the hit of the |
| | | hsp is in the inclusion | | | | hsp is in the inclusion |
| | | threshold | | | | threshold |
| +-------------------------+----------------------------------+ | +-------------------------+----------------------------------+
Expand Down

0 comments on commit 1ed793b

Please sign in to comment.