Package Bio :: Package expressions :: Module hmmpfam
[show private | hide private]
[frames | no frames]

Module Bio.expressions.hmmpfam

Martel expression for the hmmpfam database search program in hmmer.

This has been tested with version 2.2g. I should also make it work with 2.1.1 output.

XXX This isn't completely finished and doesn't do everything quite right. The main two problems being that it isn't well tested for a wide variety of outputs and that the family line is not parsed into it's respective parts (see multitude of comments on this below).
Variable Summary
Seq alignment_header = <Martel.Expression.Seq instance at 0x...
Seq copyright = <Martel.Expression.Seq instance at 0xb6f572e...
Seq domain_align_header = <Martel.Expression.Seq instance at...
Seq domain_align_middle = <Martel.Expression.Seq instance at...
Seq domain_align_top = <Martel.Expression.Seq instance at 0x...
Seq domain_alignment = <Martel.Expression.Seq instance at 0x...
Seq domain_header = <Martel.Expression.Seq instance at 0xb6f...
Seq domain_hit_line = <Martel.Expression.Seq instance at 0xb...
Seq family_header = <Martel.Expression.Seq instance at 0xb6f...
Seq family_hit_line = <Martel.Expression.Seq instance at 0xb...
Seq files = <Martel.Expression.Seq instance at 0xb6f5770c>
HeaderFooter format = <Martel.Expression.HeaderFooter instance at 0xb...
Group header = <Martel.Expression.Group instance at 0xb6f5766c...
Seq match_symbols = <Martel.Expression.Seq instance at 0xb6f...
MaxRepeat model_name = <Martel.Expression.MaxRepeat instance at 0x...
Seq no_hit_line = <Martel.Expression.Seq instance at 0xb6f57...
Seq program_description = <Martel.Expression.Seq instance at...
Seq program_version = <Martel.Expression.Seq instance at 0xb...
Group record = <Martel.Expression.Group instance at 0xb6f6d10c...
Seq record_end = <Martel.Expression.Seq instance at 0xb6f68f...
Seq rf_line = <Martel.Expression.Seq instance at 0xb6f61d4c>
Seq sequence_info = <Martel.Expression.Seq instance at 0xb6f...
Alt symbol_forward = <Martel.Expression.Alt instance at 0xb6...
Alt symbol_reverse = <Martel.Expression.Alt instance at 0xb6...

Variable Details

alignment_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f5ca0c>                         

copyright

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f572ec>                         

domain_align_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f61d2c>                         

domain_align_middle

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f6882c>                         

domain_align_top

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f6870c>                         

domain_alignment

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f689cc>                         

domain_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f5c06c>                         

domain_hit_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f5cd4c>                         

family_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f57c8c>                         

family_hit_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f57fec>                         

files

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f5770c>                         

format

Type:
HeaderFooter
Value:
<Martel.Expression.HeaderFooter instance at 0xb6f6d14c>                

header

Type:
Group
Value:
<Martel.Expression.Group instance at 0xb6f5766c>                       

match_symbols

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f5c26c>                         

model_name

Type:
MaxRepeat
Value:
<Martel.Expression.MaxRepeat instance at 0xb6f57bec>                   

no_hit_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f57c2c>                         

program_description

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f4cdec>                         

program_version

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f5730c>                         

record

Type:
Group
Value:
<Martel.Expression.Group instance at 0xb6f6d10c>                       

record_end

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f68fcc>                         

rf_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f61d4c>                         

sequence_info

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6f57b0c>                         

symbol_forward

Type:
Alt
Value:
<Martel.Expression.Alt instance at 0xb6f5c1cc>                         

symbol_reverse

Type:
Alt
Value:
<Martel.Expression.Alt instance at 0xb6f5c24c>                         

Generated by Epydoc 2.1 on Thu Aug 10 20:01:07 2006 http://epydoc.sf.net