EMBOSS: oalistat

oalistat

Wiki

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Function

Statistics for multiple alignment files

Description

EMBASSY HMMER is a port of the original hmmer v2.2.1 applications written by Sean Eddy.

Algorithm

Please read the Userguide.pdf distributed with the original HMMER and included in the EMBASSY HMMER distribution under the DOCS directory.

Usage

Here is a sample session with oalistat

% oalistat ../ohmmalign-keep/globins630.ali Statistics for multiple alignment files HMMER alistat program output file [globins630.oalistat]:

Go to the input files for this example
Go to the output files for this example

Command line arguments

Statistics for multiple alignment files
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            infile     HMMER alistat program input file
  [-outfile]           outfile    [*.oalistat] HMMER alistat program output
                                  file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -additional         boolean    [N] Show additional information
   -fast               boolean    [N] Use sampling method

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default

Standard (Mandatory) qualifiers

[-infile]
(Parameter 1) infile HMMER alistat program input file Input file Required

[-outfile]
(Parameter 2) outfile HMMER alistat program output file Output file <*>.oalistat

Additional (Optional) qualifiers

(none)

Advanced (Unprompted) qualifiers

-additional boolean Show additional information Boolean value Yes/No No

-fast boolean Use sampling method Boolean value Yes/No No

Associated qualifiers

"-outfile" associated outfile qualifiers

-odirectory2
-odirectory_outfile string Output directory Any string

General qualifiers

-auto boolean Turn off prompts Boolean value Yes/No N

-stdout boolean Write first file to standard output Boolean value Yes/No N

-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N

-options boolean Prompt for standard and additional values Boolean value Yes/No N

-debug boolean Write debug output to program.dbg Boolean value Yes/No N

-verbose boolean Report some/full command line options Boolean value Yes/No Y

-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N

-warning boolean Report warnings Boolean value Yes/No Y

-error boolean Report errors Boolean value Yes/No Y

-fatal boolean Report fatal errors Boolean value Yes/No Y

-die boolean Report dying program messages Boolean value Yes/No Y

-version boolean Report version number and exit Boolean value Yes/No N

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-infile] (Parameter 1)	infile	HMMER alistat program input file	Input file	Required
[-outfile] (Parameter 2)	outfile	HMMER alistat program output file	Output file	<>*.oalistat
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-additional	boolean	Show additional information	Boolean value Yes/No	No
-fast	boolean	Use sampling method	Boolean value Yes/No	No
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile	string	Output directory	Any string
General qualifiers
-auto	boolean	Turn off prompts	Boolean value Yes/No	N
-stdout	boolean	Write first file to standard output	Boolean value Yes/No	N
-filter	boolean	Read first file from standard input, write first file to standard output	Boolean value Yes/No	N
-options	boolean	Prompt for standard and additional values	Boolean value Yes/No	N
-debug	boolean	Write debug output to program.dbg	Boolean value Yes/No	N
-verbose	boolean	Report some/full command line options	Boolean value Yes/No	Y
-help	boolean	Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose	Boolean value Yes/No	N
-warning	boolean	Report warnings	Boolean value Yes/No	Y
-error	boolean	Report errors	Boolean value Yes/No	Y
-fatal	boolean	Report fatal errors	Boolean value Yes/No	Y
-die	boolean	Report dying program messages	Boolean value Yes/No	Y
-version	boolean	Report version number and exit	Boolean value Yes/No	N

Input file format

oalistat reads any normal sequence USAs.

Input files for usage example

File: ../ohmmalign-keep/globins630.ali

#=AU HMMER 2.1.1
#=SQ BAHG_VITSP 1.0000 BAHG_VITSP - 0..0::0 -
#=SQ GLB1_ANABR 1.0000 GLB1_ANABR - 0..0::0 -
#=SQ GLB1_ARTSX 1.0000 GLB1_ARTSX - 0..0::0 -
#=SQ GLB1_CALSO 1.0000 GLB1_CALSO - 0..0::0 -
#=SQ GLB1_CHITH 1.0000 GLB1_CHITH - 0..0::0 -
#=SQ GLB1_GLYDI 1.0000 GLB1_GLYDI - 0..0::0 -
#=SQ GLB1_LUMTE 1.0000 GLB1_LUMTE - 0..0::0 -
#=SQ GLB1_MORMR 1.0000 GLB1_MORMR - 0..0::0 -
#=SQ GLB1_PARCH 1.0000 GLB1_PARCH - 0..0::0 -
#=SQ GLB1_PETMA 1.0000 GLB1_PETMA - 0..0::0 -
#=SQ GLB1_PHESE 1.0000 GLB1_PHESE - 0..0::0 -
#=SQ GLB1_SCAIN 1.0000 GLB1_SCAIN - 0..0::0 -
#=SQ GLB1_TYLHE 1.0000 GLB1_TYLHE - 0..0::0 -
#=SQ GLB2_ANATR 1.0000 GLB2_ANATR - 0..0::0 -
#=SQ GLB2_CALSO 1.0000 GLB2_CALSO - 0..0::0 -
#=SQ GLB2_CHITH 1.0000 GLB2_CHITH - 0..0::0 -
#=SQ GLB2_LUMTE 1.0000 GLB2_LUMTE - 0..0::0 -
#=SQ GLB2_MORMR 1.0000 GLB2_MORMR - 0..0::0 -
#=SQ GLB2_TYLHE 1.0000 GLB2_TYLHE - 0..0::0 -
#=SQ GLB3_CHITH 1.0000 GLB3_CHITH - 0..0::0 -
#=SQ GLB3_CHITP 1.0000 GLB3_CHITP - 0..0::0 -
#=SQ GLB3_LAMSP 1.0000 GLB3_LAMSP - 0..0::0 -
#=SQ GLB3_MORMR 1.0000 GLB3_MORMR - 0..0::0 -
#=SQ GLB3_MYXGL 1.0000 GLB3_MYXGL - 0..0::0 -
#=SQ GLB3_PETMA 1.0000 GLB3_PETMA - 0..0::0 -
#=SQ GLB3_TYLHE 1.0000 GLB3_TYLHE - 0..0::0 -
#=SQ GLB4_CHITH 1.0000 GLB4_CHITH - 0..0::0 -
#=SQ GLB4_GLYDI 1.0000 GLB4_GLYDI - 0..0::0 -
#=SQ GLB4_LUMTE 1.0000 GLB4_LUMTE - 0..0::0 -
#=SQ GLB4_TYLHE 1.0000 GLB4_TYLHE - 0..0::0 -
#=SQ GLB5_PETMA 1.0000 GLB5_PETMA - 0..0::0 -
#=SQ GLB6_CHITH 1.0000 GLB6_CHITH - 0..0::0 -
#=SQ GLB7_ARTSX 1.0000 GLB7_ARTSX - 0..0::0 -
#=SQ GLB7_CHITH 1.0000 GLB7_CHITH - 0..0::0 -
#=SQ GLB8_CHITH 1.0000 GLB8_CHITH - 0..0::0 -
#=SQ GLB9_CHITH 1.0000 GLB9_CHITH - 0..0::0 -
#=SQ GLBA_ANATR 1.0000 GLBA_ANATR - 0..0::0 -
#=SQ GLBA_SCAIN 1.0000 GLBA_SCAIN - 0..0::0 -
#=SQ GLBB_ANATR 1.0000 GLBB_ANATR - 0..0::0 -
#=SQ GLBB_SCAIN 1.0000 GLBB_SCAIN - 0..0::0 -
#=SQ GLBC_CAUAR 1.0000 GLBC_CAUAR - 0..0::0 -
#=SQ GLBC_CHITH 1.0000 GLBC_CHITH - 0..0::0 -
#=SQ GLBD_CAUAR 1.0000 GLBD_CAUAR - 0..0::0 -
#=SQ GLBD_CHITH 1.0000 GLBD_CHITH - 0..0::0 -
#=SQ GLBE_CHITH 1.0000 GLBE_CHITH - 0..0::0 -
#=SQ GLBF_CHITH 1.0000 GLBF_CHITH - 0..0::0 -
#=SQ GLBH_CHITH 1.0000 GLBH_CHITH - 0..0::0 -
#=SQ GLBI_CHITP 1.0000 GLBI_CHITP - 0..0::0 -
#=SQ GLBM_ANATR 1.0000 GLBM_ANATR - 0..0::0 -


  [Part of this file has been deleted for brevity]

MYG_GALJA   ................................................
MYG_GLOME   ................................................
MYG_GORBE   ................................................
MYG_GRAGE   ................................................
MYG_HALGR   ................................................
MYG_HETPO   ................................................
MYG_HORSE   ................................................
MYG_HUMAN   ................................................
MYG_HYLAG   ................................................
MYG_INIGE   ................................................
MYG_KOGSI   ................................................
MYG_LAGLA   ................................................
MYG_LAGMA   ................................................
MYG_LEPMU   ................................................
MYG_LOXAF   ................................................
MYG_LUTLU   ................................................
MYG_LYCPI   ................................................
MYG_MACFA   ................................................
MYG_MACRU   ................................................
MYG_MEGNO   ................................................
MYG_MELME   ................................................
MYG_MESCA   ................................................
MYG_MOUSE   ................................................
MYG_MUSAN   ................................................
MYG_NYCCO   ................................................
MYG_OCHPR   ................................................
MYG_ORCOR   ................................................
MYG_ORNAN   ................................................
MYG_ORYAF   ................................................
MYG_PANTR   ................................................
MYG_PAPAN   ................................................
MYG_PERPO   ................................................
MYG_PHOPH   ................................................
MYG_PHYCA   ................................................
MYG_PIG     ................................................
MYG_PONPY   ................................................
MYG_PROGU   ................................................
MYG_RABIT   ................................................
MYG_ROUAE   ................................................
MYG_SAISC   ................................................
MYG_SHEEP   ................................................
MYG_SPAEH   ................................................
MYG_TACAC   ................................................
MYG_THUAL   ................................................
MYG_TUPGL   ................................................
MYG_TURTR   ................................................
MYG_VARVA   ................................................
MYG_VULCH   ................................................
MYG_ZALCA   ................................................
MYG_ZIPCA   ................................................

Output file format

oalistat outputs a graph to the specified graphics device. outputs a report format file. The default format is ...

Output files for usage example

File: globins630.oalistat

alistat 1.5m, Sept 1997

Format:              SELEX alignment
Number of sequences: 630
Total # residues:    91425
Smallest:            121
Largest:             162
Average length:      145.1
Alignment length:    398
Average identity:    39%
Most related pair:   99%
Most unrelated pair: 0%
Most distant seq:    11%

Data files

None

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Program name	Description
domainalign	Generate alignments (DAF file) for nodes in a DCF file
domainrep	Reorder DCF file to identify representative structures
matcher	Waterman-Eggert local alignment of two sequences
seqalign	Extend alignments (DAF file) with sequences (DHF file)
seqmatchall	All-against-all word comparison of a sequence set
supermatcher	Calculate approximate local pair-wise alignments of larger sequences
water	Smith-Waterman local alignment of sequences
wordfinder	Match large sequences against one or more other sequences
wordmatch	Find regions of identity (exact matches) of two sequences

Author(s)

This program is an EMBOSS conversion of a program written by Sean Eddy as part of his HMMER package.

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

File: ../ohmmalign-keep/globins630.ali

Output file format

Output files for usage example

File: globins630.oalistat

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments