assemblyget

 

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Function

Get assembly of sequence reads

Description

Searches for a sequence assembly and returns the data in one of the EBOSS assembly formats.

Usage

Here is a sample session with assemblyget 


% assemblyget bam::samspec1.4example.bam -oformat sam -auto

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

Command line arguments 

Get assembly of sequence reads
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-assembly]          assembly   (no help text) assembly value
  [-outassembly]       outassembly (no help text) outassembly value

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-assembly" associated qualifiers
   -cbegin1            integer    Start of the contig/consensus sequences
   -cend1              integer    End of the contig/consensus sequences
   -iformat1           string     Input assembly format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -idbname1           string     User-provided database name

   "-outassembly" associated qualifiers
   -odirectory2        string     Output directory
   -oformat2           string     Assembly output format

   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
[-assembly]
(Parameter 1)		 assembly (no help text) assembly value Assembly of sequence reads  
[-outassembly]
(Parameter 2)		 outassembly (no help text) outassembly value Assembly of sequence reads  
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-assembly" associated assembly qualifiers
-cbegin1
-cbegin_assembly		 integer Start of the contig/consensus sequences Any integer value 0
-cend1
-cend_assembly		 integer End of the contig/consensus sequences Any integer value 0
-iformat1
-iformat_assembly		 string Input assembly format Any string  
-iquery1
-iquery_assembly		 string Input query fields or ID list Any string  
-ioffset1
-ioffset_assembly		 integer Input start position offset Any integer value 0
-idbname1
-idbname_assembly		 string User-provided database name Any string  
"-outassembly" associated outassembly qualifiers
-odirectory2
-odirectory_outassembly		 string Output directory Any string  
-oformat2
-oformat_outassembly		 string Assembly output format 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

assemblyget reads a sequence assembly.

The input is a standard EMBOSS assembly query.

The major assembly sources are files in SAM and BAM format.

Input files for usage example

File: samspec1.4example.bam

This file contains non-printing characters and so cannot be displayed here.

Output file format

assemblyget writes a sequence assembly.

The output is a standard EMBOSS assembly query.

The major assembly formats are files in SAM and BAM format.

Output files for usage example

File: 4example.sam

@HD	VN:1.3	SO:coordinate
@PG	ID:assemblyget	VN:6.6.0.0	CL:[-assembly] bam::../../data/samspec1.4example.bam -oformat sam -auto
@SQ	SN:ref	LN:45
r001	163	ref	7	30	8M2I4M1D3M	=	37	39	TTAGATAAAGGATACTG	*
r002	0	ref	9	30	3S6M1P1I4M	*	0	0	AAAAGATAAGGATA	*
r003	0	ref	9	30	5H6M	*	0	0	AGCTAA	*	NM:i:1
r004	0	ref	16	30	6M14N5M	*	0	0	ATAGCTTCAGC	*
r003	16	ref	29	30	6H5M	*	0	0	TAGGC	*	NM:i:0
r001	83	ref	37	30	9M	=	7	-39	CAGCGCCAT	*

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
infoassembly Display information about assemblies

Author(s)

Mahmut Uludag
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

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

Comments

None