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 0x4106722...
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 0x410...
Seq domain_hit_line = <Martel.Expression.Seq instance at 0x4...
Seq family_header = <Martel.Expression.Seq instance at 0x410...
Seq family_hit_line = <Martel.Expression.Seq instance at 0x4...
Seq files = <Martel.Expression.Seq instance at 0x4106764c>
HeaderFooter format = <Martel.Expression.HeaderFooter instance at 0x4...
Group header = <Martel.Expression.Group instance at 0x410675ac...
Seq match_symbols = <Martel.Expression.Seq instance at 0x410...
MaxRepeat model_name = <Martel.Expression.MaxRepeat instance at 0x...
Seq no_hit_line = <Martel.Expression.Seq instance at 0x41067...
Seq program_description = <Martel.Expression.Seq instance at...
Seq program_version = <Martel.Expression.Seq instance at 0x4...
Group record = <Martel.Expression.Group instance at 0x4107d04c...
Seq record_end = <Martel.Expression.Seq instance at 0x41078f...
Seq rf_line = <Martel.Expression.Seq instance at 0x41071c8c>
Seq sequence_info = <Martel.Expression.Seq instance at 0x410...
Alt symbol_forward = <Martel.Expression.Alt instance at 0x41...
Alt symbol_reverse = <Martel.Expression.Alt instance at 0x41...

Variable Details

alignment_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x4106c94c>                         

copyright

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x4106722c>                         

domain_align_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x41071c6c>                         

domain_align_middle

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x4107876c>                         

domain_align_top

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x4107864c>                         

domain_alignment

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x4107890c>                         

domain_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x41067dec>                         

domain_hit_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x4106cc8c>                         

family_header

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x41067bcc>                         

family_hit_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x41067f2c>                         

files

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x4106764c>                         

format

Type:
HeaderFooter
Value:
<Martel.Expression.HeaderFooter instance at 0x4107d08c>                

header

Type:
Group
Value:
<Martel.Expression.Group instance at 0x410675ac>                       

match_symbols

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x4106c1ac>                         

model_name

Type:
MaxRepeat
Value:
<Martel.Expression.MaxRepeat instance at 0x41067b2c>                   

no_hit_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x41067b6c>                         

program_description

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x41059ccc>                         

program_version

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x4106724c>                         

record

Type:
Group
Value:
<Martel.Expression.Group instance at 0x4107d04c>                       

record_end

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x41078f0c>                         

rf_line

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x41071c8c>                         

sequence_info

Type:
Seq
Value:
<Martel.Expression.Seq instance at 0x41067a4c>                         

symbol_forward

Type:
Alt
Value:
<Martel.Expression.Alt instance at 0x4106c08c>                         

symbol_reverse

Type:
Alt
Value:
<Martel.Expression.Alt instance at 0x4106c18c>                         

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