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aligncopypair |
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Function
Read and write pairs from alignmentsDescription
aligncopypair reads a set of aligned sequences and reports the alignment one pair at a time using any of the standard EMBOSS alignment formats.Usage
Here is a sample session with aligncopypair
% aligncopypair Read and write pairs from alignments Input (aligned) sequence set: globins.msf Output alignment [globins.aligncopypair]: |
Go to the input files for this example
Go to the output files for this example
Command line arguments
Read and write pairs from alignments
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-sequences] seqset File containing a sequence alignment.
[-outfile] align [*.aligncopypair] 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
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| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequences] (Parameter 1) |
seqset | File containing a sequence alignment. | Readable set of sequences | Required |
| [-outfile] (Parameter 2) |
align | Output alignment file name | (default -aformat simple) | <*>.aligncopypair |
| Additional (Optional) qualifiers | ||||
| -name | string | Name of the alignment | Any string | |
| -comment | string | Comment on the alignment | Any string | |
| -append | boolean | This allows you to append the name and comments you have given on to the end of the existing alignment header. | Boolean value Yes/No | No |
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-sequences" associated seqset qualifiers | ||||
| -sbegin1 -sbegin_sequences |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send1 -send_sequences |
integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_sequences |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_sequences |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_sequences |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_sequences |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_sequences |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_sequences |
boolean | Make upper case | Boolean value Yes/No | N |
| -scircular1 -scircular_sequences |
boolean | Sequence is circular | Boolean value Yes/No | N |
| -squick1 -squick_sequences |
boolean | Read id and sequence only | Boolean value Yes/No | N |
| -sformat1 -sformat_sequences |
string | Input sequence format | Any string | |
| -iquery1 -iquery_sequences |
string | Input query fields or ID list | Any string | |
| -ioffset1 -ioffset_sequences |
integer | Input start position offset | Any integer value | 0 |
| -sdbname1 -sdbname_sequences |
string | Database name | Any string | |
| -sid1 -sid_sequences |
string | Entryname | Any string | |
| -ufo1 -ufo_sequences |
string | UFO features | Any string | |
| -fformat1 -fformat_sequences |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequences |
string | Features file name | Any string | |
| "-outfile" associated align qualifiers | ||||
| -aformat2 -aformat_outfile |
string | Alignment format | Any string | simple |
| -aextension2 -aextension_outfile |
string | File name extension | Any string | |
| -adirectory2 -adirectory_outfile |
string | Output directory | Any string | |
| -aname2 -aname_outfile |
string | Base file name | Any string | |
| -awidth2 -awidth_outfile |
integer | Alignment width | Any integer value | 0 |
| -aaccshow2 -aaccshow_outfile |
boolean | Show accession number in the header | Boolean value Yes/No | N |
| -adesshow2 -adesshow_outfile |
boolean | Show description in the header | Boolean value Yes/No | N |
| -ausashow2 -ausashow_outfile |
boolean | Show the full USA in the alignment | Boolean value Yes/No | N |
| -aglobal2 -aglobal_outfile |
boolean | Show the full sequence in alignment | Boolean value Yes/No | N |
| 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
aligncopypair 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~~~
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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.aligncopypair
########################################
# Program: aligncopypair
# Rundate: Mon 15 Jul 2013 12:00:00
# Commandline: aligncopypair
# -sequences ../../data/globins.msf
# Align_format: simple
# Report_file: globins.aligncopypair
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: HBB_HUMAN
# 2: HBB_HORSE
# Matrix: EBLOSUM62
#
# Length: 164
# Identity: 122/164 (74.4%)
# Similarity: 146/164 (89.0%)
# Gaps: 18/164 (11.0%)
#
#
#=======================================
HBB_HUMAN 1 --------VHLTPEEKSAVTALWGKVN-VDEVGGEALGR-LLVVYPWTQR 40
|.|:.|||:||.|||.||| .:||||||||| ||||||||||
HBB_HORSE 1 --------VQLSGEEKAAVLALWDKVN-EEEVGGEALGR-LLVVYPWTQR 40
HBB_HUMAN 41 FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE 90
||:||||||.|.||||||||||||||||.:|.:|:.||||||||||.|||
HBB_HORSE 41 FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE 90
HBB_HUMAN 91 LHCDKLH--VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA 138
||||||| ||||||||||||||.|||.||||:|||.:||:|||||||||
HBB_HORSE 91 LHCDKLH--VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA 138
HBB_HUMAN 139 NALAHKYH------ 146
||||||||
HBB_HORSE 139 NALAHKYH------ 146
#=======================================
#
# Aligned_sequences: 2
# 1: HBB_HUMAN
# 2: HBA_HUMAN
# Matrix: EBLOSUM62
#
# Length: 164
# Identity: 48/164 (29.3%)
[Part of this file has been deleted for brevity]
MYG_PHYCA 1 -------VLSEGEWQLVLHVWAKVEAD-VAGHGQDILIR-LFKSHPETLE 41
.:..|.|..|...:..|.: ........... :.:..|...:
LGB2_LUPLU 1 --------GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD 42
MYG_PHYCA 42 KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ 91
.|...|......:...........|..|....||..:..........|..
LGB2_LUPLU 43 LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN 92
MYG_PHYCA 92 SHATKHK--IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR 139
..:.... :...:...:.|||:..:.......:..:...|...|.:...
LGB2_LUPLU 93 LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA 142
MYG_PHYCA 140 KDIAAKYKELGYQG 153
..|..:..:..
LGB2_LUPLU 143 IVIKKEMNDAA--- 153
#=======================================
#
# Aligned_sequences: 2
# 1: GLB5_PETMA
# 2: LGB2_LUPLU
# Matrix: EBLOSUM62
#
# Length: 164
# Identity: 17/164 (10.4%)
# Similarity: 149/164 (90.9%)
# Gaps: 23/164 (14.0%)
#
#
#=======================================
GLB5_PETMA 1 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE 50
..|:.::...::|:|....:..........:......|||::
LGB2_LUPLU 1 --------GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD 42
GLB5_PETMA 51 FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD 100
.|...||.:...|..............:.........:.........|::
LGB2_LUPLU 43 LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN 92
GLB5_PETMA 101 LSGKHAK--SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA 148
|...|.. .........|.........|.......|...:........|
LGB2_LUPLU 93 LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA 142
GLB5_PETMA 149 Y------------- 149
.
LGB2_LUPLU 143 IVIKKEMNDAA--- 153
#---------------------------------------
#---------------------------------------
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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 |
|---|---|
| aligncopy | Read and write 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 IsonEuropean 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.