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assemblyget
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
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
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 ATAGCTTC
AGC *
r003 16 ref 29 30 6H5M * 0 0 TAGGC
* NM:i:0
r001 83 ref 37 30 9M = 7 -39 CAGCGCCA
T *
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 (c) 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
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