Bio.expressions.hmmpfam

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 0x2aaaad7...`
`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 0x2aaaad7f4e1...`
`HeaderFooter`	`format` = `<Martel.Expression.HeaderFooter instance at 0x2...`
`Group`	`header` = `<Martel.Expression.Group instance at 0x2aaaad7f...`
`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 0x2aaaad80...`
`Seq`	`record_end` = `<Martel.Expression.Seq instance at 0x2aaaad...`
`Seq`	`rf_line` = `<Martel.Expression.Seq instance at 0x2aaaad7fb...`
`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 0x2aaaad7f9a70>

copyright

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7f4950>

domain_align_header

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7fbf38>

domain_align_middle

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7ff518>

domain_align_top

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7ff2d8>

domain_alignment

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad800290>

domain_header

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7f7368>

domain_hit_line

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7f9d40>

family_header

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7f5c68>

family_hit_line

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7f73b0>

files

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7f4e18>

format

Type:: HeaderFooter
Value:: <Martel.Expression.HeaderFooter instance at 0x2aaaad800758>

header

Type:: Group
Value:: <Martel.Expression.Group instance at 0x2aaaad7f5050>

match_symbols

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7f7908>

model_name

Type:: MaxRepeat
Value:: <Martel.Expression.MaxRepeat instance at 0x2aaaad7f5b00>

no_hit_line

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7f7098>

program_description

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7ed878>

program_version

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7f4830>

record

Type:: Group
Value:: <Martel.Expression.Group instance at 0x2aaaad8006c8>

record_end

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad800440>

rf_line

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7fbe18>

sequence_info

Type:: Seq
Value:: <Martel.Expression.Seq instance at 0x2aaaad7f59e0>

symbol_forward

Type:: Alt
Value:: <Martel.Expression.Alt instance at 0x2aaaad7f7758>

symbol_reverse

Type:: Alt
Value:: <Martel.Expression.Alt instance at 0x2aaaad7f78c0>

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