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Add hmmer2-text related info in HmmerIO docs

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1 parent 73e7ce3 commit 1ed793b51cb123399dc51e1a6625fb9df6e4c72f @bow bow committed Dec 9, 2012
Showing with 18 additions and 17 deletions.
  1. +18 −17 Bio/SearchIO/HmmerIO/__init__.py
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35 Bio/SearchIO/HmmerIO/__init__.py
@@ -9,10 +9,10 @@
suite of programs implementing the profile hidden Markov models to find
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
- - version: 3.0
+ - HMMER3 flavors: hmmscan, hmmsearch, phmmer
+ - HMMER2 flavors: hmmpfam, hmmsearch
More information on HMMER are available through these links:
- Web page: http://hmmer.janelia.org/
@@ -57,15 +57,16 @@
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
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:
+The following SearchIO objects attributes are provided. Rows marked with '*'
+denotes attributes not available in the hmmer2-text format:
+-----------------+-------------------------+----------------------------------+
| Object | Attribute | Value |
@@ -78,19 +79,19 @@
| +-------------------------+----------------------------------+
| | program | HMMER flavor |
| +-------------------------+----------------------------------+
-| | seq_len | full length of query sequence |
+| | seq_len* | full length of query sequence |
| +-------------------------+----------------------------------+
| | target | target search database |
| +-------------------------+----------------------------------+
| | version | BLAST version |
+-----------------+-------------------------+----------------------------------+
-| Hit | bias | hit-level bias |
+| Hit | bias* | hit-level bias |
| +-------------------------+----------------------------------+
| | bitscore | hit-level score |
| +-------------------------+----------------------------------+
| | description | hit sequence description |
| +-------------------------+----------------------------------+
-| | domain_exp_num | expected number of domains in |
+| | domain_exp_num* | expected number of domains in |
| | | the hit (exp column) |
| +-------------------------+----------------------------------+
| | domain_obs_num | observed number of domains in |
@@ -100,32 +101,32 @@
| +-------------------------+----------------------------------+
| | 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 |
+-----------------+-------------------------+----------------------------------+
-| HSP | acc_avg | expected accuracy per alignment |
+| HSP | acc_avg* | expected accuracy per alignment |
| | | residue (acc column) |
| +-------------------------+----------------------------------+
-| | bias | hsp-level bias |
+| | bias* | hsp-level bias |
| +-------------------------+----------------------------------+
| | bitscore | hsp-level score |
| +-------------------------+----------------------------------+
| | 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.) |
| +-------------------------+----------------------------------+
-| | env_start | start coordinate of the envelope |
+| | env_start* | start coordinate of the envelope |
| +-------------------------+----------------------------------+
| | 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 |
| +-------------------------+----------------------------------+
-| | is_included | boolean, whether the hit of the |
+| | is_included* | boolean, whether the hit of the |
| | | hsp is in the inclusion |
| | | threshold |
| +-------------------------+----------------------------------+

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