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Commit 093b220c authored by Kieron Taylor's avatar Kieron Taylor :angry:
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Purge DAS documentation from repo

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docs/ensembl_das/Homo_sapiens.ini deleted 100644 → 0
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###############################################################################
#
# Name: Homo_sapiens.ini
#
# Description: Configuration file for Human ensembl
#
###############################################################################
#################
# GENERAL CONFIG
#################
[general]
# Database info: only specify values if different from those in DEFAULTS
# DATABASE_HOST =
# DATABASE_HOST_PORT =
# DATABASE_DBUSER =
# DATABASE_DBPASS =
# DATABASE_WRITE_USER =
# DATABASE_WRITE_PASS =
# Assembly info
ENSEMBL_PREFIX = ENS ; EnsEMBL gene id prefix
ENSEMBL_GOLDEN_PATH = NCBI34 ; Indentifier for the golden path type
ENSEMBL_CHROMOSOMES = [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y ]
# Search config
; list of features that are indexed ready for searching
ENSEMBL_SEARCH_IDXS = [ Disease Domain EST External Family Gene MRNA Marker Peptide Protein SNP SangerProject Sequence Unigene ]
# Display info
SPECIES_COMMON_NAME = Human
SPECIES_BIO_NAME = Homo sapiens
SPECIES_CODE = hs
ENSEMBL_PREDICTION_TEXT_CORE = Genes were annotated by the Ensembl automatic analysis pipeline using either a GeneWise model from a human/vertebrate protein, a set of aligned human cDNAs followed by GenomeWise for ORF prediction or from Genscan exons supported by protein, cDNA and EST evidence. GeneWise models are further combined with available aligned cDNAs to annotate UTRs.
ENSEMBL_PREDICTION_TEXT_PSEUDOGENE = Potential processed pseudogenes are detected from genewise predictions that have a single-exon with frameshifts, have their evidence spliced elsewhere in the genome and have no match in the syntenic genomic region in mouse.
ENSEMBL_PREDICTION_TEXT_ESTGENE = ESTs are mapped on the genome using a combination of Exonerate, Blast and Est_Genome, with a threshold of overall percentage identity of 90 and at least one exon having 97 or higher. The results are processed by merging the redundant ESTs and setting splice-sites to the most common ends, resulting in alternative spliced forms. This evidence is processed by Genomewise which finds the longest ORF, and assigns 5' and 3' UTRs.
ENSEMBL_PREDICTION_TEXT_VEGA = Finished genomic sequence is analysed on a clone by clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, GENEWISE). Gene structures are annotated on the basis of human interpretation of the combined supportive evidence generated during sequence analysis. In parallel, experimental methods are being applied to extend incomplete gene structures and discover new genes. The latter is initiated by comparative analysis of the finished sequence with vertebrate datasets such as the Riken mouse cDNAs, mouse whole-genome shotgun data and GenescopeTetraodon Ecores.
##################
# DATABASE CONFIG
# Change the values to the local names of these databases
##################
[databases]
DATABASE_DB = homo_sapiens_core_19_34b
DATABASE_VEGA = homo_sapiens_vega_19_34b
# The following are extra configuration parameters for the databases
# You can overide the default settings for specific databases. Just add a
# like this for each database you want to overide the settings for
#
# [ENSEMBL_FOO]
# USER = myothersqluser
# PASS =
# HOST = mydb_server.domain.org
# PORT = 3306
####################
# Help Database Config
####################
[ENSEMBL_WEBSITE]
# Accept defaults
####################
# Species-specific colours
####################
[ENSEMBL_COLOURS]
# Accept defaults
####################
# External Database ad Indexer Config
####################
[ENSEMBL_EXTERNAL_DATABASES]
# Accept defaults
[ENSEMBL_EXTERNAL_INDEXERS]
# Accept defaults
#############
# DAS CONFIG
#############
[ENSEMBL_GENE_DAS_SOURCES]
Demo = 1
[Demo]
dsn = demo
url = http://DasServerMachine:9000/das
type = swissprot
authority = http:/www.ensembl.org
on = [ protview geneview ]
[ENSEMBL_TRACK_DAS_SOURCES]
# None
[ENSEMBL_INTERNAL_DAS_SOURCES]
das_DEMO = 1
# To get an unlinked menu leave the linkURL field empty
# The following are the details of the DAS sources.
[das_DEMO]
dsn = demo
url = http://DasServerMachine:9000/das
label = demo data
caption = demo data
col = darkred
labelflag = U
strand = r
depth = 6
group = 1
on = 1
types = [ ]
####################
# Configure External Genome Browsers
####################
[EXTERNAL_GENOME_BROWSERS]
EGB_UCSC = UCSC browser
EGB_NCBI = NCBI browser
# EGB_TEST = Test external link
# KEY must be present in [ENSEMBL_EXTERNAL_URLS] section below which gives
# the URL.... for the click - the entry here just gives the text link
####################
# Configure External URLs
# These are mainly for (1) External Genome Browse {EGB_ }
# (2) DAS tracks {DAS_ }
####################
[ENSEMBL_EXTERNAL_URLS]
DAS_SNPSTATUS = http://hapmap.cshl.org/docs/snp_categories.html
DAS_ACEMBLY = http://www.ncbi.nlm.nih.gov/AceView/av.cgi?db=30&q=###ID###
DAS_HSGENEID = http://www1.imim.es/cgi-bin/das/das_genes_human.cgi?geneid=###ID###
DAS_HSTIGR = http://www.tigr.org/docs/tigr-scripts/nhgi_scripts/tc_report.pl?species=human;tc=###ID###
DAS_NCBIGSCAN = http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/GSfasta?label=###ID###
DAS_REFSEQ = http://www.ncbi.nlm.nih.gov/LocusLink/list.cgi?Q=###ID###
DAS_NCBITRANS = http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/hum_srch?chr=hum_chr.inf&query=###ID###&qchr=&advsrch=off
DAS_ONCOVIEW = http://www.sanger.ac.uk/perl/CGP/oncoview?&action=mutation&gene_name=###ID###
EGB_NCBI = http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?ORG=hum&CHR=###CHR###&BEG=###START###&END=###END###
EGB_UCSC = http://genome.cse.ucsc.edu/cgi-bin/hgTracks?position=chr###CHR###%3A###START###-###END###&Submit=Submit&db=hg16
DOTS = http://www.allgenes.org/allgenes/servlet?page=gene&id=###ID###
HVER121 = http://www.sanger.ac.uk/cgi-bin/microarrays/reporter_annotation?array_id=Hver1.2.1&reporter_id=###ID###
HVER131 = http://www.sanger.ac.uk/cgi-bin/microarrays/reporter_annotation?array_id=Hver1.3.1&reporter_id=###ID###
AFFY_HG_U133 = /homo_sapiens/fastaview?faid=DNA_affyU133AB_1834&id=###ID###
AFFY_HG_U95 = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834&id=###ID###
AFFY_HG_U133A = /homo_sapiens/fastaview?faid=DNA_affyU133AB_1834&id=###ID###
AFFY_HG_U133B = /homo_sapiens/fastaview?faid=DNA_affyU133AB_1834&id=###ID###
AFFY_HG_U133_ALL = /homo_sapiens/fastaview?faid=DNA_affyU133AB_1834&id=###ID###
AFFY_HG_U95AV2 = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834&id=###ID###
AFFY_HG_U95A = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834&id=###ID###
AFFY_HG_U95B = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834&id=###ID###
AFFY_HG_U95C = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834&id=###ID###
AFFY_HG_U95D = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834&id=###ID###
AFFY_HG_U95E = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834&id=###ID###
AFFY_HG_U95_ALL = /homo_sapiens/fastaview?faid=DNA_affyU95AE_1834&id=###ID###
####################
# Configure blast data sources.
# Used in blastview to generate database dropdown
####################
[ENSEMBL_BLAST_METHODS]
# Registers blast methods. Key values are the
# Bio::Tools::Run::Search classes used to run the search
# Accept defaults
[BLAST_DATASOURCES]
# Registers blast datasources. Key values are used as labels.
# Keys should be registered against methods in species.ini files
# Accept defaults
[BLASTN_DATASOURCES]
# Sequence databases to use with search method (BLASTN)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_human/data/fasta/
DATASOURCE_TYPE = dna
LATESTGP = Homo_sapiens.NCBI34.contig.fa
LATESTGP_MASKED = Homo_sapiens.NCBI34.contig_masked.fa
CDNA_ALL = Homo_sapiens.NCBI34b.cdna.fa
CDNA_KNOWN = Homo_sapiens.NCBI34b.cdna_known.fa
CDNA_NOVEL = Homo_sapiens.NCBI34b.cdna_novel.fa
CDNA_PSEUDO = Homo_sapiens.NCBI34b.cdna_pseudo.fa
[TBLASTX_DATASOURCES]
# Sequence databases to use with search method (TBLASTX)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_human/data/fasta/
DATASOURCE_TYPE = dna
LATESTGP = Homo_sapiens.NCBI34.contig.fa
LATESTGP_MASKED = Homo_sapiens.NCBI34.contig_masked.fa
CDNA_ALL = Homo_sapiens.NCBI34b.cdna.fa
CDNA_KNOWN = Homo_sapiens.NCBI34b.cdna_known.fa
CDNA_NOVEL = Homo_sapiens.NCBI34b.cdna_novel.fa
CDNA_PSEUDO = Homo_sapiens.NCBI34b.cdna_pseudo.fa
[TBLASTN_DATASOURCES]
# Sequence databases to use with search method (TBLASTN)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_human/data/fasta/
DATASOURCE_TYPE = peptide
LATESTGP = Homo_sapiens.NCBI34.contig.fa
LATESTGP_MASKED = Homo_sapiens.NCBI34.contig_masked.fa
CDNA_ALL = Homo_sapiens.NCBI34b.cdna.fa
CDNA_KNOWN = Homo_sapiens.NCBI34b.cdna_known.fa
CDNA_NOVEL = Homo_sapiens.NCBI34b.cdna_novel.fa
CDNA_PSEUDO = Homo_sapiens.NCBI34b.cdna_pseudo.fa
[BLASTP_DATASOURCES]
# Sequence databases to use with search method (BLASTP)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_human/data/fasta/
DATASOURCE_TYPE = peptide
PEP_ALL = Homo_sapiens.NCBI34b.pep.fa
PEP_KNOWN = Homo_sapiens.NCBI34b.pep_known.fa
PEP_NOVEL = Homo_sapiens.NCBI34b.pep_novel.fa
PEP_PREDICTION = Homo_sapiens.NCBI34b.pep_genscan.fa
[BLASTX_DATASOURCES]
# Sequence databases to use with search method (BLASTX)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_human/data/fasta/
DATASOURCE_TYPE = dna
PEP_ALL = Homo_sapiens.NCBI34b.pep.fa
PEP_KNOWN = Homo_sapiens.NCBI34b.pep_known.fa
PEP_NOVEL = Homo_sapiens.NCBI34b.pep_novel.fa
PEP_PREDICTION = Homo_sapiens.NCBI34b.pep_genscan.fa
[SSAHA_DATASOURCES]
# Sequence database server to use with search method (SSAHA)
# Format is HOST:PORT
# None
####################
# Configure the page header links
####################
[HEADER_LINKS]
IMAGE1_SRC = /gfx/header/human-header1.gif
IMAGE1_ALT = Ensembl Human
IMAGE1_URL = /Homo_sapiens
IMAGE1_WIDTH = 174
LINK3_TEXT = BlastSearch
LINK3_URL = /Multi/blastview?species=Homo_sapiens
LINK4_TEXT = MartSearch
LINK4_URL = /biomart/martview?species=Homo_sapiens
LINK5_TEXT = Export Data
LINK5_URL = /Homo_sapiens/exportview
####################
# Configure search example links
####################
[SEARCH_LINKS]
DEFAULT1_TEXT = AP000462
DEFAULT1_URL = contigview?clone=AP000462
DEFAULT2_TEXT = RH9632
DEFAULT2_URL = markerview?marker=RH9632
DEFAULT3_TEXT = cancer
DEFAULT3_URL = diseaseview?disease=cancer
CONTIGVIEW1_TEXT = AC067852
CONTIGVIEW1_URL = contigview?clone=AC067852
CONTIGVIEW2_TEXT = AP000869
CONTIGVIEW2_URL = contigview?clone=AP000462
GENEVIEW1_TEXT = ENSG00000139618
GENEVIEW1_URL = geneview?gene=ENSG00000139618
GENEVIEW2_TEXT = BRCA2
GENEVIEW2_URL = geneview?gene=BRCA2
DOMAINVIEW1_TEXT = IPR000504
DOMAINVIEW1_URL = domainview?domainentry=IPR000504
TRANSVIEW1_TEXT = ENST00000157775
TRANSVIEW1_URL = transview?transcript=ENST00000157775
PROTVIEW1_TEXT = ENSP00000267071
PROTVIEW1_URL = protview?peptide=ENSP00000267071
MAPVIEW1_TEXT = 12
MAPVIEW1_URL = mapview?chr=12
MAPVIEW2_TEXT = X
MAPVIEW2_URL = mapview?chr=X
MARKERVIEW1_TEXT = RH9632
MARKERVIEW1_URL = markerview?marker=RH9632
MARKERVIEW2_TEXT = D1S2806
MARKERVIEW2_URL = markerview?marker=D1S2806
SNPVIEW1_TEXT = 20410
SNPVIEW1_URL = snpview?snp=20410
DISEASEVIEW1_TEXT = cancer
DISEASEVIEW1_URL = diseaseview?disease=cancer
HAPLOVIEW1_TEXT = CHR22_A_10
HAPLOVIEW1_URL = haploview?haplotype=CHR22_A_10
HAPLOVIEW2_TEXT = CHR22_A_11
HAPLOVIEW2_URL = haploview?haplotype=CHR22_A_11
FAMILYVIEW1_TEXT = ENSF00000000117
FAMILYVIEW1_URL = familyview?family=ENSF00000000117
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[general]
prefork=5
maxclients=10
port=9000
[demo]
adaptor = demo
state = on
needed_arg = okay
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=head1 LICENSE
Copyright [1999-2016] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
package Bio::Das::ProServer::SourceAdaptor::demo;
use strict;
use vars qw(@ISA);
use Bio::Das::ProServer::SourceAdaptor;
@ISA = qw(Bio::Das::ProServer::SourceAdaptor);
my @id = qw(CLAT_HUMAN CLAT_HUMAN CLAT_HUMAN 10 AC073366 AC073366);
my @id2 = qw(CLAT_HUMAN CLAT_HUMAN not_same 10 AC073366 AC073366);
my @names = qw(PF00755 PF00755 CLAT_HUMAN 10 AC073366 AC073366);
my @starts = qw(30 100 50 50150000 1 );
my @ends = qw(748 550 650 50200000 900);
my @method =qw(description PFAM SCOP REPEAT BLAST ANOTH);
my @types = qw(typ1 typ2 typ3 typ4 typ5 typ6);
sub init {
my $self = shift;
$self->{'dsn'} = "demo";
$self->{'capabilities'} = {
'features' => '1.0',
};
}
sub length {
return 0;
}
sub build_features {
my ($self, $opts) = @_;
my $spid = $opts->{'segment'};
my $start = $opts->{'start'};
my $end = $opts->{'end'};
# print $self->config->{'needed_arg'}."\n";
#
#Create some dummy notes
#
my @notes=();
for(my $i=0; $i <= $#id; $i++){
$notes[$i] = "Demo annotation $i ??";
}
#create array of fearutes to return;
my @features = ();
for(my $i=0; $i <= $#id; $i++){
next if(($id[$i] ne $spid) ||
(defined($start) and ($ends[$i] < $start or $starts[$i] > $end)));
push @features, {
'id' => $id2[$i],
'type' => $types[$i], # needed for proteinview protein
# features names in graphical view
'feature'=> $names[$i],
'method' => $method[$i],
'start' => $starts[$i],
'end' => $ends[$i],
'note' => $notes[$i],
'link' => 'http://www.ensembl.org/Docs/enstour/',
'linktxt' => 'Tour',
};
}
return @features;
}
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