Appdoc:Aligncopy
From EMBOSS
Contents |
Function
Reads and writes 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 Reads and writes 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
| 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 | Alignment output file | <*>.aligncopy |
| 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 |
| -sformat1 -sformat_sequences | string | Input sequence format | Any string | |
| -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. 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 |
Input file format
aligncopy reads any normal sequence USAs.
Input 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 in 'simple' format.
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.
The Identity: value, if reported, is the percentage of identical matches between the two sequences over the reported aligned region (including any gaps in the length).
The Similarity: value, if reported, is the percentage of matches between the two sequences over the reported aligned region (including any gaps in the length).
See: AlignFormats for further information on alignment formats.
Output example
File: globins.aligncopy
########################################
# Program: aligncopy
# Rundate: Wed 15 Jul 2009 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.
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
See also
| aligncopypair | Reads and writes pairs from alignments |
| biosed | Replace or delete sequence sections |
| codcopy | Copy and reformat a codon usage table |
| cutseq | Removes a section from a sequence |
| degapseq | Removes non-alphabetic (e.g. gap) characters from sequences |
| descseq | Alter the name or description of a sequence |
| entret | Retrieves 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 | Reads and writes a feature table |
| featreport | Reads and writes a feature table |
| 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 | Masks all ambiguity characters in nucleotide sequences with N |
| maskambigprot | Masks 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 all 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 | Reads and writes (returns) one set of sequences from many |
| pasteseq | Insert one sequence into another |
| revseq | Reverse and complement a nucleotide sequence |
| seqret | Reads and writes (returns) sequences |
| seqretsetall | Reads and writes (returns) many sets of sequences |
| seqretsplit | Reads sequences and writes them to individual files |
| sizeseq | Sort sequences by size |
| skipredundant | Remove redundant sequences from an input set |
| skipseq | Reads and writes (returns) 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 | Removes 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 (@) 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
