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<HTML>
<HEAD>
<TITLE>
EMBOSS: embossdata
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
embossdata
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Finds or fetches data files read by EMBOSS programs
<H2>
Description
</H2>
This is a utility to indicate which directories can hold EMBOSS
data files and what the names of these files are.
<p>
The names of EMBOSS data files all start with the character 'E', by
convention, to distinguish them somewhat from any other files,
especially files in your home directory.
<p>
EMBOSS data files are read in by assorted EMBOSS programs, for
example the files holding the various genetic codes to translate from
nucleic acid codons to amino acids are held in files called "EGC.0",
"EGC.1", "EGC.2", etc. These files normally are kept in a standard data
directory under the EMBOSS package installation position:
".../emboss/emboss/data/". When EMBOSS programs require a data file,
they search for it, in order, through the following set of
directories:
<ul>
<li> The current directory
<li> '.embossdata' in the current directory
<li> Your home directory
<li> '.embossdata' in your home directory
<li> The EMBOSS standard data directory
</ul>
<p>
If a data file is placed in the current directory, EMBOSS
programs will use it in preference to the file of the same name in the
EMBOSS standard data directory. Thus if you wish to modify a
data file to change the behaviour of an EMBOSS program, you
should obtain it from the EMBOSS standard data directory, edit it, and
place it in one of the other directories, such as the current directory
or your home directory.
<p>
The program embossdata is a utility to enable you to check on
the location of the directories which could hold data files, to display
the names of data files in those directories and to make local copies
of the data files from the EMBOSS standard data directory in
order for you to modify them.
<H2>
Usage
</H2>
<b>Here is a sample session with embossdata</b>
<p>
Display the directories searched for EMBOSS data files:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>embossdata </b>
Finds or fetches data files read by EMBOSS programs
Data file name: <b></b>
# The following directories can contain EMBOSS data files.
# They are searched in the following order until the file is found.
# If the directory does not exist, then this is noted below.
# '.' is the UNIX name for your current working directory.
. Exists
.embossdata Does not exist
/homes/pmr Exists
/homes/pmr/.embossdata Does not exist
/homes/pmr/local/share/EMBOSS/data/ Exists
</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 2</b>
<p>
Display the names of data files in all of the possible data directories: This is run on a small test system and so the results will probably be different when you run this.
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>embossdata -showall </b>
Finds or fetches data files read by EMBOSS programs
Data file name: <b></b>
DIRECTORY: /homes/pmr/local/share/EMBOSS/data/
EGC.10
EGC.11
EGC.12
EGC.13
EGC.14
EGC.15
EGC.16
EGC.21
EGC.22
EGC.23
EPAM10
EPAM20
EPAM30
EPAM40
EPAM50
EPAM60
EPAM70
EPAM80
EPAM90
edialignmat
Eenergy.dat
EDNAMAT
Etags.swiss
Matrices.proteinstructure
Emass.dat
Etags.gffprotein
EGC.txt
Ehth87.dat
Eaa_hydropathy.dat
Enakai.dat
EGC.0
EGC.1
EGC.2
EGC.3
EGC.4
EGC.5
EGC.6
EGC.9
Eangles_tri.dat
Epprofile
Efreqs.dat
Emwfilter.dat
ENUC.4.2
ENUC.4.4
Etags.embl
Etags.gff3
tp400_trans
Etags.gff
Etags.pir
EPAM100
EPAM110
EPAM120
EPAM130
EPAM140
EPAM150
EPAM160
EPAM170
EPAM180
EPAM190
EPAM200
EPAM210
EPAM220
EPAM230
EPAM240
EPAM250
EPAM260
EPAM270
EPAM280
EPAM290
EPAM300
EPAM310
EPAM320
EPAM330
EPAM340
EPAM350
EPAM360
EPAM370
EPAM380
EPAM390
EPAM400
EPAM410
EPAM420
EPAM430
EPAM440
EPAM450
EPAM460
EPAM470
EPAM480
EPAM490
EPAM500
Ehet.dat
Evdw.dat
Edna.melt
Eaa_properties.dat
Eamino.dat~
EBLOSUMN
Eangles.dat
tfinsect
tffungi
Etcode.dat
tfother
tfplant
Ehth.dat
Etags.emboss
tp400_dna
Ebases.iub
Efeatures.gff
Efeatures.pir
Etags.protein
Eaa_acc_surface.dat
Epepcoil.dat
Ememe.dat
Efeatures.gffprotein
Eprior1.plib
Efeatures.embl
Efeatures.gff3
EBLOSUM30
EBLOSUM35
EBLOSUM40
EBLOSUM45
EBLOSUM50
EBLOSUM55
EBLOSUM60
EBLOSUM62
EBLOSUM65
EBLOSUM70
EBLOSUM75
EBLOSUM80
EBLOSUM85
EBLOSUM90
EDNAFULL
Emassmod.dat
Efeatures.emboss
Matrices.nucleotide
Epk.dat
tfvertebrate
Efeatures.protein
Erna.melt
Eamino.dat
EBLOSUM62-12
Eantigenic.dat
Efeatures.swiss
Eembl.ior
tp400_prot
Eprior30.plib
Esig.euk
Esig.pro
EGC.index
Ewhite-wimley.dat
Matrices.protein
embossre.equ
Edayhoff.freq
DIRECTORY: /homes/pmr/local/share/EMBOSS/data/REBASE
dummyfile
embossre.enz
embossre.equ
embossre.ref
embossre.sup
DIRECTORY: /homes/pmr/local/share/EMBOSS/data/AAINDEX
dummyfile
kytj820101
chop780101
chop780201
chop780202
chop780203
chop780204
chop780205
chop780206
chop780207
chop780208
chop780209
chop780210
chop780211
chop780212
chop780213
chop780214
chop780215
chop780216
DIRECTORY: /homes/pmr/local/share/EMBOSS/data/CODONS
EAedes_aegypti.cut
Ecyapa.cut
Eerwct.cut
Ehuman.cut
Eratsp.cut
Esta.cut
Ecaeel.cut
EAedes_atropalpus.cut
Estaau.cut
Edrome_high.cut
Echmp.cut
Eyerpe.cut
Ecrisp.cut
Efish.cut
Esty.cut
Ehalsa.cut
Emyctu.cut
Esus.cut
Echnt.cut
Edicdi.cut
Echos.cut
EAmblyomma_americanum.cut
Encr.cut
Epolyomaa2.cut
EAphrodite_aculeata.cut
Ebommo.cut
Eysc_h.cut
Eschpo_high.cut
Etob.cut
Eneu.cut
Etom.cut
Ephix174.cut
Emedsa.cut
Eanidmit.cut
Emsa.cut
Engo.cut
Emse.cut
Epethy.cut
Esynsp.cut
Emta.cut
Etrb.cut
Eani_h.cut
Etheth.cut
Echicken.cut
Emtu.cut
Emva.cut
Ebpphx.cut
Eschpo_cai.cut
Emus.cut
Eacc.cut
Eorysa.cut
Eham.cut
Ebraja.cut
Eshpsp.cut
Emanse.cut
Emaize_chl.cut
Edro_h.cut
Echzm.cut
Echzmrubp.cut
Emze.cut
Evibch.cut
Epombecai.cut
EAstacus_astacus.cut
Ebrana.cut
Erhoca.cut
Eemeni_high.cut
Evco.cut
Ehha.cut
Eanasp.cut
Ebacme.cut
Esyhsp.cut
Erabit.cut
Eneigo.cut
Ecanal.cut
Ehin.cut
Elyces.cut
Eklepn.cut
Ebrare.cut
Eyscmt.cut
Epseae.cut
Eemeni_mit.cut
Ehma.cut
Eani.cut
Ecanfa.cut
Emixlg.cut
Ecaucr.cut
Epae.cut
Ephavu.cut
Ebovin.cut
Ehorvu.cut
Ebacst.cut
Ebacsu.cut
Echlre.cut
Epea.cut
Edrome.cut
Esheep.cut
Erabsp.cut
Epfa.cut
Esalsa.cut
Easn.cut
Ebacsu_high.cut
Eecoli_high.cut
Eath.cut
Epet.cut
Ebja.cut
Emacfa.cut
EAcanthocheilonema_viteae.cut
Esalsp.cut
Eyeast_cai.cut
Eatu.cut
Echltr.cut
Eoncmy.cut
Eavi.cut
Ecac.cut
Eemeni.cut
Esalty.cut
Ehum.cut
Eprovu.cut
Epig.cut
Esoybn.cut
Ecal.cut
Ephv.cut
Ephy.cut
Ebme.cut
Erhosh.cut
Ebna.cut
Ewht.cut
Ebly.cut
Ebmo.cut
Ef1.cut
Emetth.cut
EAnadara_trapezia.cut
Ebovsp.cut
Eccr.cut
Erhile.cut
Eplafa.cut
Erhime.cut
Ebov.cut
Ecel.cut
Eoncsp.cut
Epsepu.cut
Estrco.cut
Echi.cut
Epot.cut
Echk.cut
Epsesm.cut
Etetsp.cut
Eklula.cut
Etetth.cut
Ebsu_h.cut
Ebst.cut
Ebsu.cut
Emaize.cut
Eppu.cut
Exel.cut
Emouse.cut
Eagrtu.cut
Epse.cut
Eserma.cut
Eazovi.cut
Epsy.cut
Ewheat.cut
Eyeast.cut
Eacica.cut
Erab.cut
Eddi.cut
EAedes_albopictus.cut
Espo_h.cut
Epvu.cut
Etobac.cut
Erat.cut
Erca.cut
Eaidlav.cut
Ezebrafish.cut
Ecpx.cut
Ecre.cut
Cut.index
Estrmu.cut
Efmdvpolyp.cut
Etobcp.cut
Eyeastcai.cut
Estrpn.cut
Eyen.cut
Ectr.cut
Estrpu.cut
Emzecp.cut
Exenopus.cut
Edrosophila.cut
Eeco_h.cut
Eorysa_chl.cut
Erhm.cut
Eric.cut
Ekla.cut
Earath.cut
Eeca.cut
Echick.cut
EAedes.cut
Eeco.cut
Erle.cut
Edog.cut
Emam_h.cut
Eyeast_high.cut
Erme.cut
Esau.cut
Esoltu.cut
Emammal_high.cut
Esco.cut
Ekpn.cut
Edro.cut
Eadenovirus5.cut
Exenla.cut
Eadenovirus7.cut
Etobac_chl.cut
Elacdl.cut
Esgi.cut
EDictyostelium_discoideum.cut
Erabbit.cut
Eddi_h.cut
Eshp.cut
Ersp.cut
Eysc.cut
Ella.cut
Ecrigr.cut
Emac.cut
Emarpo_chl.cut
Eecoli.cut
Edicdi_high.cut
Eysp.cut
Esv40.cut
Eyeren.cut
Edayhoff.cut
Etrybr.cut
Ehaein.cut
Etrycr.cut
Esli.cut
Esynco.cut
Esma.cut
Eslm.cut
Eschma.cut
Esmi.cut
Esyncy.cut
Ezma.cut
Etbr.cut
Esmu.cut
Etcr.cut
Ehalma.cut
Eneucr.cut
Echisp.cut
Espi.cut
Emussp.cut
Ecloab.cut
Epombe.cut
Espiol.cut
Esoy.cut
Espn.cut
Espo.cut
Eter.cut
Eyeast_mit.cut
Eschpo.cut
Espu.cut
</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 3</b>
<p>
Make a copy of an EMBOSS data file in the current directory:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>embossdata -fetch Epepcoil.dat </b>
Finds or fetches data files read by EMBOSS programs
File '/homes/pmr/local/share/EMBOSS/data/Epepcoil.dat' has been copied successfully.
</pre></td></tr></table><p>
<p>
<a href="#output.3">Go to the output files for this example</a><p><p>
<p>
<b>Example 4</b>
<p>
Display the directories which contain a particular EMBOSS data file:
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>embossdata EPAM60 </b>
Finds or fetches data files read by EMBOSS programs
# The following directories can contain EMBOSS data files.
# They are searched in the following order until the file is found.
# If the directory does not exist, then this is noted below.
# '.' is the UNIX name for your current working directory.
File ./EPAM60 Does not exist
File .embossdata/EPAM60 Does not exist
File /homes/pmr/EPAM60 Does not exist
File /homes/pmr/.embossdata/EPAM60 Does not exist
File /homes/pmr/local/share/EMBOSS/data/EPAM60 Exists
</pre></td></tr></table><p>
<p>
<p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Standard (Mandatory) qualifiers:
[-filename] string This specifies the name of the file that
should be fetched into the current directory
or searched for in all of the directories
that EMBOSS programs search when looking for
a data file. The name of the file is not
altered when it is fetched. (Any string is
accepted)
Additional (Optional) qualifiers (* if not always prompted):
-showall toggle Show all potential EMBOSS data files
* -fetch boolean Fetch a data file
-outfile outfile [stdout] This specifies the name of the file
that the results of a search for a file in
the various data directories is written to.
By default these results are written to the
screen (stdout).
Advanced (Unprompted) qualifiers:
-reject selection [3, 5, 6] This specifies the names of the
sub-directories of the EMBOSS data directory
that should be ignored when displaying data
directories.
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write 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. 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
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-filename]<br>(Parameter 1)</td>
<td>This specifies the name of the file that should be fetched into the current directory or searched for in all of the directories that EMBOSS programs search when looking for a data file. The name of the file is not altered when it is fetched.</td>
<td>Any string is accepted</td>
<td><i>An empty string is accepted</i></td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-showall</td>
<td>Show all potential EMBOSS data files</td>
<td>Toggle value Yes/No</td>
<td>No</td>
</tr>
<tr>
<td>-fetch</td>
<td>Fetch a data file</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr>
<td>-outfile</td>
<td>This specifies the name of the file that the results of a search for a file in the various data directories is written to. By default these results are written to the screen (stdout).</td>
<td>Output file</td>
<td>stdout</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-reject</td>
<td>This specifies the names of the sub-directories of the EMBOSS data directory that should be ignored when displaying data directories.</td>
<td>Choose from selection list of values</td>
<td>3, 5, 6</td>
</tr>
</table>
<H2>
Input file format
</H2>
None.
<p>
<H2>
Output file format
</H2>
All output is to stdout by default.
<p>
<a name="output.3"></a>
<h3>Output files for usage example 3</h3>
<p><h3>File: Epepcoil.dat</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
# Input data for PEPCOIL
# from Lupas A, van Dyke M & Stock J; Science 252:1162-4 (1991)
#
# Freq in Relative occurrence at heptad position
# R GenBank a b c d e f g
L 9.33 3.167 0.297 0.398 3.902 0.585 0.501 0.483
I 5.35 2.597 0.098 0.345 0.894 0.514 0.471 0.431
V 6.42 1.665 0.403 0.386 0.949 0.211 0.342 0.360
M 2.34 2.240 0.370 0.480 1.409 0.541 0.772 0.663
F 3.88 0.531 0.076 0.403 0.662 0.189 0.106 0.013
Y 3.16 1.417 0.090 0.122 1.659 0.190 0.130 0.155
G 7.10 0.045 0.275 0.578 0.216 0.211 0.426 0.156
A 7.59 1.297 1.551 1.084 2.612 0.377 1.248 0.877
K 5.72 1.375 2.639 1.763 0.191 1.815 1.961 2.795
R 5.39 0.659 1.163 1.210 0.031 1.358 1.937 1.798
H 2.25 0.347 0.275 0.679 0.395 0.294 0.579 0.213
E 6.10 0.262 3.496 3.108 0.998 5.685 2.494 3.048
D 5.03 0.030 2.352 2.268 0.237 0.663 1.620 1.448
Q 4.27 0.179 2.114 1.778 0.631 2.550 1.578 2.526
N 4.25 0.835 1.475 1.534 0.039 1.722 2.456 2.280
S 7.28 0.382 0.583 1.052 0.419 0.525 0.916 0.628
T 5.97 0.169 0.702 0.955 0.654 0.791 0.843 0.647
C 1.86 0.824 0.022 0.308 0.152 0.180 0.156 0.044
W 1.41 0.240 0.0 0.0 0.456 0.019 0.0 0.0
P 5.28 0.0 0.008 0.0 0.013 0.0 0.0 0.0
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
No data files are read by this program.
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
When copying a file, this program will report if the file has
been copied successfully, e.g.:
<pre>
"'Epepcoil.dat' has been copied successfully."
</pre>
<H2>
Exit status
</H2>
It always exits with status 0
<H2>
Known bugs
</H2>
None noted.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="embossversion.html">embossversion</a></td>
<td>Writes the current EMBOSS version number</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
<H2>
History
</H2>
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
It should be possible to format the output for html.
</BODY>
</HTML>