Package Bio :: Package expressions :: Module hmmpfam
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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 0x2aaaae6...
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 0x2aa...
Seq domain_hit_line = <Martel.Expression.Seq instance at 0x2...
Seq family_header = <Martel.Expression.Seq instance at 0x2aa...
Seq family_hit_line = <Martel.Expression.Seq instance at 0x2...
Seq files = <Martel.Expression.Seq instance at 0x2aaaae6a6bd...
HeaderFooter format = <Martel.Expression.HeaderFooter instance at 0x2...
Group header = <Martel.Expression.Group instance at 0x2aaaae6a...
Seq match_symbols = <Martel.Expression.Seq instance at 0x2aa...
MaxRepeat model_name = <Martel.Expression.MaxRepeat instance at 0x...
Seq no_hit_line = <Martel.Expression.Seq instance at 0x2aaaa...
Seq program_description = <Martel.Expression.Seq instance at...
Seq program_version = <Martel.Expression.Seq instance at 0x2...
Group record = <Martel.Expression.Group instance at 0x2aaaae6b...
Seq record_end = <Martel.Expression.Seq instance at 0x2aaaae...
Seq rf_line = <Martel.Expression.Seq instance at 0x2aaaae6ae...
Seq sequence_info = <Martel.Expression.Seq instance at 0x2aa...
Alt symbol_forward = <Martel.Expression.Alt instance at 0x2a...
Alt symbol_reverse = <Martel.Expression.Alt instance at 0x2a...

Variable Details

alignment_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6ac5a8>                     

copyright

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6a6488>                     

domain_align_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6aea70>                     

domain_align_middle

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6b0050>                     

domain_align_top

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6afdd0>                     

domain_alignment

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6b0368>                     

domain_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6ab050>                     

domain_hit_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6ac878>                     

family_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6aa7a0>                     

family_hit_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6aaea8>                     

files

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6a6bd8>                     

format

Type:
HeaderFooter
Value:
<Martel.Expression.HeaderFooter instance at 0x2aaaae6b2290>            

header

Type:
Group
Value:
<Martel.Expression.Group instance at 0x2aaaae6a6b48>                   

match_symbols

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6ab440>                     

model_name

Type:
MaxRepeat
Value:
<Martel.Expression.MaxRepeat instance at 0x2aaaae6aa638>               

no_hit_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6aab90>                     

program_description

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6a2368>                     

program_version

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6a6368>                     

record

Type:
Group
Value:
<Martel.Expression.Group instance at 0x2aaaae6b2200>                   

record_end

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6b0f38>                     

rf_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6ae950>                     

sequence_info

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x2aaaae6aa518>                     

symbol_forward

Type:
Alt
Value:
<Martel.Expression.Alt instance at 0x2aaaae6ab290>                     

symbol_reverse

Type:
Alt
Value:
<Martel.Expression.Alt instance at 0x2aaaae6ab3f8>                     

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