defuse: tool-data/defuse.loc.sample annotate

annotate tool-data/defuse.loc.sample @ 4:679a5c7b1294 draft

deFuse version 0.5.0 - Use tool_dependencies.xml

author	Jim Johnson <jj@umn.edu>
date	Fri, 04 Jan 2013 13:29:03 -0600
parents	4245c2b047de
children

rev	line source
4 679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml Jim Johnson <jj@umn.edu> parents: 2 diff changeset	1 ## Configurstion info for prepared data references for DeFuse
1 36306d8086fa Remove defuse dir Jim Johnson <jj@umn.edu> parents: diff changeset	2 ## http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2
36306d8086fa Remove defuse dir Jim Johnson <jj@umn.edu> parents: diff changeset	3 ## 3 columns separated by the TAB character
36306d8086fa Remove defuse dir Jim Johnson <jj@umn.edu> parents: diff changeset	4 ## The 3rd column has dictionary values that will be substituted in the config file for defuse
36306d8086fa Remove defuse dir Jim Johnson <jj@umn.edu> parents: diff changeset	5 ## It should likely contain keys: dataset_directory gene_models genome_fasta repeats_filename est_fasta est_alignments unigene_fasta
4 679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml Jim Johnson <jj@umn.edu> parents: 2 diff changeset	6 ## If this is not a Homo_sapiens reference also need keys: gene_id_pattern transcript_id_pattern chromosomes
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml Jim Johnson <jj@umn.edu> parents: 2 diff changeset	7
1 36306d8086fa Remove defuse dir Jim Johnson <jj@umn.edu> parents: diff changeset	8 #db_key name {'config_key':'config_value'}
4 679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml Jim Johnson <jj@umn.edu> parents: 2 diff changeset	9 #hg19 GRCh37(hg19) {'gene_id_pattern':'ENSG\d+', 'transcript_id_pattern':'ENST\d+', 'dataset_directory':'/data/genomes/Hsapiens/hg19/defuse', 'gene_models':'$(dataset_directory)/Homo_sapiens.GRCh37.62.gtf', 'genome_fasta':'$(dataset_directory)/Homo_sapiens.GRCh37.62.dna.chromosome.fa', 'repeats_filename':'$(dataset_directory)/rmsk.txt', 'est_fasta':'$(dataset_directory)/est.fa', 'est_alignments':'$(dataset_directory)/intronEst.txt', 'unigene_fasta':'$(dataset_directory)/Hs.seq.uniq', '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,MT', 'mt_chromosome':'MT', 'gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding', 'ig_gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene', 'rrna_gene_sources':'Mt_rRNA,rRNA,rRNA_pseudogene'}
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml Jim Johnson <jj@umn.edu> parents: 2 diff changeset	10 #mm9 NCBIM37(mm9) {'gene_id_pattern':'ENSMUSG\d+', 'transcript_id_pattern':'ENSMUST\d+', 'dataset_directory':'/data/genomes/Mmusculus/mm9/defuse', 'gene_models':'$(dataset_directory)/Mus_musculus.NCBIM37.63.gtf', 'genome_fasta':'$(dataset_directory)/Mus_musculus.NCBIM37.63.dna.chromosome.fa', 'repeats_filename':'$(dataset_directory)/rmsk.txt', 'est_fasta':'$(dataset_directory)/est.fa', 'est_alignments':'$(dataset_directory)/intronEst.txt', 'unigene_fasta':'$(dataset_directory)/Mm.seq.uniq', 'chromosomes':'1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT', 'mt_chromosome':'MT', 'gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding', 'ig_gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene', 'rrna_gene_sources':'Mt_rRNA,rRNA,rRNA_pseudogene'}
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml Jim Johnson <jj@umn.edu> parents: 2 diff changeset	11 #mm8 NCBIM36(mm8) {'gene_id_pattern':'ENSMUSG\d+', 'transcript_id_pattern':'ENSMUST\d+', 'dataset_directory':'/data/genomes/Mmusculus/mm9/defuse', 'gene_models':'$(dataset_directory)/Mus_musculus.NCBIM36.46.gtf', 'genome_fasta':'$(dataset_directory)/Mus_musculus.NCBIM36.46.dna.chromosome.fa', 'repeats_filename':'$(dataset_directory)/rmsk.txt', 'est_fasta':'$(dataset_directory)/est.fa', 'est_alignments':'$(dataset_directory)/intronEst.txt', 'unigene_fasta':'$(dataset_directory)/Mm.seq.uniq', 'mt_chromosome':'MT', 'gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding', 'ig_gene_sources':'IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene', 'rrna_gene_sources':'Mt_rRNA,rRNA,rRNA_pseudogene'}