From dd95f51bbd4913b1ad1c1587b2a108e02eee8a48 Mon Sep 17 00:00:00 2001 From: ml6 <> Date: Mon, 19 Mar 2007 12:47:38 +0000 Subject: [PATCH] added loutre attribs --- misc-scripts/attribute_types/attrib_type.txt | 45 ++++++++++++-------- 1 file changed, 28 insertions(+), 17 deletions(-) diff --git a/misc-scripts/attribute_types/attrib_type.txt b/misc-scripts/attribute_types/attrib_type.txt index 3039ecdde0..2080ccdeda 100644 --- a/misc-scripts/attribute_types/attrib_type.txt +++ b/misc-scripts/attribute_types/attrib_type.txt @@ -1,7 +1,7 @@ # this file is intended to hold all valid attrib_type # table entries for all ensembl databases that we release # -# If you use the provided upload script, commentlines and +# If you use the provided upload script, commentlines and # emptry lines should be automatically removed, all # other lines should contain tab delimited database entries # for the attrib_type table @@ -44,9 +44,9 @@ # Snps on a seq_region. See above. 10 SNPCount SNP Count Total Number of SNPs -# another seq_region attribute. When a seq_region should be used with a +# another seq_region attribute. When a seq_region should be used with a # different codon table this attrbutes value should contain its number. -# This is a bioperl codon table, find out from there which number to use +# This is a bioperl codon table, find out from there which number to use # for your seq_region # Useful for Mitochondrium and Bacteria with non standard codon tables 11 codon_table Codon Table Alternate codon table @@ -60,25 +60,25 @@ 13 bacend bacend -# Contains the htg phase for clones. +# Contains the htg phase for clones. 14 htg htg High Throughput phase attribute 15 miRNA Micro RNA Coordinates of the mature miRNA # A sequence region that you consider not part of the reference genome should # be tagged as non_ref in seq_region_attrib. Chromosome 6 haplotypes in human -# are exmaples of that. +# are exmaples of that. 16 non_ref Non Reference Non Reference Sequence Region 17 sanger_project Sanger Project name -18 clone_name Clone name +18 clone_name Clone name -19 fish FISH location +19 fish FISH location -21 org Sequencing centre +21 org Sequencing centre -22 method Method +22 method Method 23 superctg Super contig id @@ -86,13 +86,13 @@ 25 inner_end Min end value -26 state Current state of clone +26 state Current state of clone 27 organisation Organisation sequencing clone -28 seq_len Accession length +28 seq_len Accession length -29 fp_size FP size +29 fp_size FP size 30 BACend_flag BAC end flags @@ -135,7 +135,7 @@ 56 KnownPTCount processed_transcript_KNOWN Number of Known Processed Transcripts 57 ccds CCDS CCDS identifier -# make first amino acid methionine +# make first amino acid methionine 58 initial_met Initial methionine Set first amino acid to methionine # label frameshifts modelled as short (1,2,4,5 bp) introns @@ -184,8 +184,8 @@ 94 alt_org Alt org # anacode attribs added by ml6 29/11/06 - seen in yeast but not others -95 intl_clone_name International Clone Name -96 embl_version EMBL Version +95 intl_clone_name International Clone Name +96 embl_version EMBL Version 97 chr Chromosome Name Chromosome Name Contained in the Assembly 98 equiv_asm Equivalent EnsEMBL assembly For full chromosomes made from NCBI AGPs 99 GeneNo_ncRNA ncRNA Gene Count Number of ncRNA Genes @@ -197,9 +197,9 @@ 109 HitSimilarity hit similarity percentage id to parent transcripts 110 HitCoverage hit coverage coverage of parent transcripts 111 PropNonGap proportion non gap proportion non gap -112 NumStops number of stops +112 NumStops number of stops 113 GapExons gap exons number of gap exons -114 SourceTran source transcript source transcript +114 SourceTran source transcript source transcript 115 EndNotFound end not found end not found 116 StartNotFound start not found start not found @@ -209,3 +209,14 @@ 118 ensembl_name Ensembl name Name of equivalent Ensembl chromosome 119 NoAnnotation NoAnnotation Clones without manual annotation 120 hap_contig Haplotype contig Contig present on a haplotype + +# loutre attribs added by ml6 +121 annotated Clone Annotation Status +122 keyword Clone Keyword +123 hidden_remark Hidden Remark +124 mRNA_start_NF mRNA start not found +125 mRNA_end_NF mRNA end not found +126 cds_start_NF cds start not not +127 cds_end_NF cds end not found +128 write_access Write access for Sequence Set 1 for writable , 0 for read-only +129 hidden Hidden Sequence Set -- GitLab