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


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