                                  aligncopy



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Function

   Read and write alignments

Description

   aligncopy reads a set of aligned sequences and reports the alignment
   using any of the standard EMBOSS alignment formats that can report on
   the size of the input alignment. An input of two aligned sequences will
   allow any of the pairwise formats to be used. Other input sizes will
   reject any pairwise alignment format. Use aligncopypair to print these
   alignments one pair at a time.

Usage

   Here is a sample session with aligncopy


% aligncopy
Read and write alignments
Input (aligned) sequence set: globins.msf
Output alignment [globins.aligncopy]:


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

Command line arguments

Read and write alignments
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequences]         seqset     File containing a sequence alignment.
  [-outfile]           align      [*.aligncopy] Output alignment file name
                                  (default -aformat simple)

   Additional (Optional) qualifiers:
   -name               string     Name of the alignment (Any string)
   -comment            string     Comment on the alignment (Any string)
   -append             boolean    [N] This allows you to append the name and
                                  comments you have given on to the end of the
                                  existing alignment header.

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

   "-sequences" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -aformat2           string     Alignment format
   -aextension2        string     File name extension
   -adirectory2        string     Output directory
   -aname2             string     Base file name
   -awidth2            integer    Alignment width
   -aaccshow2          boolean    Show accession number in the header
   -adesshow2          boolean    Show description in the header
   -ausashow2          boolean    Show the full USA in the alignment
   -aglobal2           boolean    Show the full sequence in alignment

   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

   aligncopy reads aligned nucleotide or protein sequences.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  Input files for usage example

  File: globins.msf

!!AA_MULTIPLE_ALIGNMENT 1.0

  ../data/globins.msf MSF:  164 Type: P 25/06/01 CompCheck: 4278 ..

  Name: HBB_HUMAN Len: 164  Check: 6914 Weight: 0.61
  Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.65
  Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.65
  Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.83
  Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 1.00
  Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.91
  Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.43

//

           1                                               50
HBB_HUMAN  ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR
HBB_HORSE  ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR
HBA_HUMAN  ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS
HBA_HORSE  ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG
MYG_PHYCA  ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE
GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE
LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD

           51                                             100
HBB_HUMAN  FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE
HBB_HORSE  FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE
HBA_HUMAN  FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
HBA_HORSE  FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD
MYG_PHYCA  KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ
GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD
LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN

           101                                            150
HBB_HUMAN  LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA
HBB_HORSE  LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA
HBA_HUMAN  LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS
HBA_HORSE  LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS
MYG_PHYCA  SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR
GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA
LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA

           151        164
HBB_HUMAN  NALAHKYH~~~~~~
HBB_HORSE  NALAHKYH~~~~~~
HBA_HUMAN  TVLTSKYR~~~~~~
HBA_HORSE  TVLTSKYR~~~~~~
MYG_PHYCA  KDIAAKYKELGYQG
GLB5_PETMA Y~~~~~~~~~~~~~
LGB2_LUPLU IVIKKEMNDAA~~~


Output file format

   The output is a standard EMBOSS alignment file.

   The results can be output in one of several styles by using the
   command-line qualifier -aformat xxx, where 'xxx' is replaced by the
   name of the required format. Some of the alignment formats can cope
   with an unlimited number of sequences, while others are only for pairs
   of sequences.

   The available multiple alignment format names are: multiple, simple,
   fasta, msf, clustal, mega, meganon, nexus,, nexusnon, phylip,
   phylipnon, selex, treecon, tcoffee, debug, srs.

   The available pairwise alignment format names are: pair, markx0,
   markx1, markx2, markx3, markx10, match, sam, bam, score, srspair

   See: http://emboss.sf.net/docs/themes/AlignFormats.html for further
   information on alignment formats.

  Output files for usage example

  File: globins.aligncopy

########################################
# Program: aligncopy
# Rundate: Mon 15 Jul 2013 12:00:00
# Commandline: aligncopy
#    -sequences ../../data/globins.msf
# Align_format: simple
# Report_file: globins.aligncopy
########################################

#=======================================
#
# Aligned_sequences: 7
# 1: HBB_HUMAN
# 2: HBB_HORSE
# 3: HBA_HUMAN
# 4: HBA_HORSE
# 5: MYG_PHYCA
# 6: GLB5_PETMA
# 7: LGB2_LUPLU
# Matrix: EBLOSUM62
#
# Length: 164
# Identity:       1/164 ( 0.6%)
# Similarity:    93/164 (56.7%)
# Gaps:          31/164 (18.9%)
#
#
#=======================================

HBB_HUMAN          1 --------VHLTPEEKSAVTALWGKVN-VDEVGGEALGR-LLVVYPWTQR     40
HBB_HORSE          1 --------VQLSGEEKAAVLALWDKVN-EEEVGGEALGR-LLVVYPWTQR     40
HBA_HUMAN          1 --------------VLSPADKTNVKAA-WGKVGAHAGEYGAEALERMFLS     35
HBA_HORSE          1 --------------VLSAADKTNVKAA-WSKVGGHAGEYGAEALERMFLG     35
MYG_PHYCA          1 -------VLSEGEWQLVLHVWAKVEAD-VAGHGQDILIR-LFKSHPETLE     41
GLB5_PETMA         1 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE     50
LGB2_LUPLU         1 --------GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD     42
                               ::  : : :.: : : :   :::: ::   :  : :  :

HBB_HUMAN         41 FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE     90
HBB_HORSE         41 FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE     90
HBA_HUMAN         36 FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD     85
HBA_HORSE         36 FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD     85
MYG_PHYCA         42 KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ     91
GLB5_PETMA        51 FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD    100
LGB2_LUPLU        43 LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN     92
                     :: ::  ::  : : :: ::: :::::: :: : : ::::::   : |::

HBB_HUMAN         91 LHCDKLH--VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA    138
HBB_HORSE         91 LHCDKLH--VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA    138
HBA_HUMAN         86 LHAHKLR--VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS    133
HBA_HORSE         86 LHAHKLR--VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS    133
MYG_PHYCA         92 SHATKHK--IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR    139
GLB5_PETMA       101 LSGKHAK--SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA    148
LGB2_LUPLU        93 LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA    142
                     ::: :::  ::: ::::: : :: ::: :   :::::: ::: : :: ::

HBB_HUMAN        139 NALAHKYH------    146
HBB_HORSE        139 NALAHKYH------    146
HBA_HUMAN        134 TVLTSKYR------    141
HBA_HORSE        134 TVLTSKYR------    141
MYG_PHYCA        140 KDIAAKYKELGYQG    153
GLB5_PETMA       149 Y-------------    149
LGB2_LUPLU       143 IVIKKEMNDAA---    153
                       :  ::


#---------------------------------------
#---------------------------------------

Data files

   For protein sequences EBLOSUM62 is used for the substitution matrix.
   For nucleotide sequence, EDNAFULL is used.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat


   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata". Files
   for all EMBOSS runs can be put in the user's home directory, or again
   in a subdirectory called ".embossdata".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

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
   aligncopypair    Read and write pairs from alignments
   biosed           Replace or delete sequence sections
   codcopy          Copy and reformat a codon usage table
   cutseq           Remove a section from a sequence
   degapseq         Remove non-alphabetic (e.g. gap) characters from sequences
   descseq          Alter the name or description of a sequence
   entret           Retrieve sequence entries from flatfile databases and files
   extractalign     Extract regions from a sequence alignment
   extractfeat      Extract features from sequence(s)
   extractseq       Extract regions from a sequence
   featcopy         Read and write a feature table
   featmerge        Merge two overlapping feature tables
   featreport       Read and write a feature table
   feattext         Return a feature table original text
   listor           Write a list file of the logical OR of two sets of sequences
   makenucseq       Create random nucleotide sequences
   makeprotseq      Create random protein sequences
   maskambignuc     Mask all ambiguity characters in nucleotide sequences with
                    N
   maskambigprot    Mask all ambiguity characters in protein sequences with X
   maskfeat         Write a sequence with masked features
   maskseq          Write a sequence with masked regions
   newseq           Create a sequence file from a typed-in sequence
   nohtml           Remove mark-up (e.g. HTML tags) from an ASCII text file
   noreturn         Remove carriage return from ASCII files
   nospace          Remove whitespace from an ASCII text file
   notab            Replace tabs with spaces in an ASCII text file
   notseq           Write to file a subset of an input stream of sequences
   nthseq           Write to file a single sequence from an input stream of
                    sequences
   nthseqset        Read and write (return) one set of sequences from many
   pasteseq         Insert one sequence into another
   revseq           Reverse and complement a nucleotide sequence
   seqcount         Read and count sequences
   seqret           Read and write (return) sequences
   seqretsetall     Read and write (return) many sets of sequences
   seqretsplit      Read sequences and write them to individual files
   sizeseq          Sort sequences by size
   skipredundant    Remove redundant sequences from an input set
   skipseq          Read and write (return) sequences, skipping first few
   splitsource      Split sequence(s) into original source sequences
   splitter         Split sequence(s) into smaller sequences
   trimest          Remove poly-A tails from nucleotide sequences
   trimseq          Remove unwanted characters from start and end of sequence(s)
   trimspace        Remove extra whitespace from an ASCII text file
   union            Concatenate multiple sequences into a single sequence
   vectorstrip      Remove vectors from the ends of nucleotide sequence(s)
   yank             Add a sequence reference (a full USA) to a list file

Author(s)

   Jon Ison
   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
