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 0xb70454e...
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 0xb70...
Seq domain_hit_line = <Martel.Expression.Seq instance at 0xb...
Seq family_header = <Martel.Expression.Seq instance at 0xb70...
Seq family_hit_line = <Martel.Expression.Seq instance at 0xb...
Seq files = <Martel.Expression.Seq instance at 0xb704590c>
HeaderFooter format = <Martel.Expression.HeaderFooter instance at 0xb...
Group header = <Martel.Expression.Group instance at 0xb704586c...
Seq match_symbols = <Martel.Expression.Seq instance at 0xb70...
MaxRepeat model_name = <Martel.Expression.MaxRepeat instance at 0x...
Seq no_hit_line = <Martel.Expression.Seq instance at 0xb7045...
Seq program_description = <Martel.Expression.Seq instance at...
Seq program_version = <Martel.Expression.Seq instance at 0xb...
Group record = <Martel.Expression.Group instance at 0xb6fdc30c...
Seq record_end = <Martel.Expression.Seq instance at 0xb6fdc1...
Seq rf_line = <Martel.Expression.Seq instance at 0xb6fd1f4c>
Seq sequence_info = <Martel.Expression.Seq instance at 0xb70...
Alt symbol_forward = <Martel.Expression.Alt instance at 0xb7...
Alt symbol_reverse = <Martel.Expression.Alt instance at 0xb7...

Variable Details

alignment_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb704cc0c>                         

copyright

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb70454ec>                         

domain_align_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6fd1f2c>                         

domain_align_middle

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6fbda2c>                         

domain_align_top

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6fbd90c>                         

domain_alignment

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6fdc14c>                         

domain_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb704c0cc>                         

domain_hit_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb704cf4c>                         

family_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb7045e8c>                         

family_hit_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb704c20c>                         

files

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb704590c>                         

format

Type:
HeaderFooter
Value:
<Martel.Expression.HeaderFooter instance at 0xb6fdc34c>                

header

Type:
Group
Value:
<Martel.Expression.Group instance at 0xb704586c>                       

match_symbols

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb704c46c>                         

model_name

Type:
MaxRepeat
Value:
<Martel.Expression.MaxRepeat instance at 0xb7045dec>                   

no_hit_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb7045e2c>                         

program_description

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb703afac>                         

program_version

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb704550c>                         

record

Type:
Group
Value:
<Martel.Expression.Group instance at 0xb6fdc30c>                       

record_end

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6fdc1ec>                         

rf_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb6fd1f4c>                         

sequence_info

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0xb7045d0c>                         

symbol_forward

Type:
Alt
Value:
<Martel.Expression.Alt instance at 0xb704c3cc>                         

symbol_reverse

Type:
Alt
Value:
<Martel.Expression.Alt instance at 0xb704c44c>                         

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