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<opt
name="dmelhetfeatconv"
date="20040821"
>
<title>Chado DB Feature info</title>
<about>
Use this one for D.melanogaster heterochromatin genome db.
These are configurations for converting chado feature table dumps to
standard feature/sequence files. Much of below specifies how to
process different features (tied to methods in ChadoFeatDump.pm
These configs should be data-set independent.
This works with, but is independent of SeqUtil2 configs.
</about>
<informat>feature_table</informat>
<outformats>fff</outformats>
<outformats>gff</outformats>
<outformats>fasta</outformats>
<!-- copied from db-release config files .. this is mostly common info,
but db-release config can override @featset, %featmap -->
<!-- moved featset/featmap tags to separate config file -->
<OLD_USAGE_rename_child_type>pseudogene|\w+RNA</OLD_USAGE_rename_child_type>
<mergematch></mergematch>
<noforwards_gff>1</noforwards_gff>
<!-- remapType: append this name pattern to type; works with maptype below -->
<name2type_pattern>[-_](repeatmasker|genscan|piecegenie|twinscan|genewise|trnascan)</name2type_pattern>
<!-- dont warn if these types have Parent oid not in data; e.g chromosome parent -->
<maptype_ignore_missingparent>^(match_part|match|gene|cytology|chromosome_band|oligo|BAC|protein_binding_site)</maptype_ignore_missingparent>
<!-- drop lengthy program.source from match name
match_sim4_na_EST_complete_dros RE37642.5prime-2L_wgs2cex-na_EST.complete.dros
also fix these ugly names repeating feature types;
match:sim4:na_STS.dros BACN11E12-T7-211000022278175-na_STS.dros-sim4
cuttype=1
match_part_blastx_aa_SPTR_dros
more cuttype names
-211000022278591-aa_SP.real.dros-blastx
match:blastx:aa_SPTR.dros ID|AAL57609|SPTR|AAL57609-211000022278591-aa_SPTR.dros-blastx
match:blastx:aa_TR.real.dros Q967T2-211000022278591-aa_TR.real.dros-blastx
match:blastx:aa_TR.real.dros Q94885-211000022279519-aa_TR.real.dros-blastx
match:blastx:aa_SPTR.dros ID|AAL90081|SPTR|AAL90081-linked_7-aa_SPTR.dros-blastx
match:blastx:aa_SPTR.dros ID|AAL48487|SPTR|AAL48487-AE003846R_extension-aa_SPTR.dros-blast
match:groupest:na_DGC.dros RH25653.3prime_revcomp-AABU01000160-na_DGC.dros-groupest
perl -pi.old \
-e's,\-AABU0\d+\S+dros\S+,,;'
-e's,\_extension\S+,,;' \
-e's,\-linked_\S+,,;' \
-e's,\-2110000\d+\S+,,;'
-->
<mapname_pattern name="1match" type="^match.*" cuttype="1" from="null" to="null"/>
<mapname_pattern name="2match" type="^match.*" from="\-?(2L|2R|3L|3R|4|X)[_\.].*$" to=""/>
<mapname_pattern name="3match" type="^match.*" from="\_extension\S+$" to=""/>
<mapname_pattern name="4match" type="^match.*" from="\-linked_\S+$" to=""/>
<mapname_pattern name="5match" type="^match.*" from="\-2110000\d+\S+$" to=""/>
<mapname_pattern name="6match" type="^match.*" from=";$" to=""/>
<mapname_pattern name="cex" from="_wgs3_centromere_extension" to="_wgs2cex"/>
<mapname_pattern name="dum" from="\-dummy\-" to=""/>
<mapname_pattern name="tep" type="transposable_element_pred"
from="JOSHTRANSPOSON\-" to=""/>
<!--
dmel r4 ugly match names: all the data appended ! see above cuttype=1
match:tblastxwrap_masked:na_baylorf1_scfchunk.dpse
Dpf1glom15-1-AE002603.4_22263978_22335911-na_baylorf1_scfchunk.d
-->
<maptype_pattern name="1match" from=":rui.chen" to=""/>
<maptype_pattern name="2match" from=":Brian.Bettencourt" to=""/>
<maptype_pattern name="3masked" from="_masked" to=""/>
<maptype_pattern name="null" typename="noname" from="null" to="null"/> -->
<!--
## SONG/so Revision: 1.45
## @is_a@oligo ; SO:0000696 ; SOFA:SOFA ; synonym:oligonucleotide
## 'so' is no longer valid
## old value: @is_a@so ; SO:1000000
## options are limited: located_sequence_feature, SO:0000110 ??
## in flybase, 'so' seems used for protein blast matches?
## segment not in this
## alt choices ...
# @is_a@assembly ; SO:0000353 ; SOFA:SOFA
# ** @is_a@golden_path ; SO:0000688 ; SOFA:SOFA <<
# ** @is_a@supercontig ; SO:0000148 ; SOFA:SOFA ; synonym:scaffold <<
# @is_a@tiling_path ; SO:0000472 ; SOFA:SOFA
# @is_a@virtual_sequence ; SO:0000499 ; SOFA:SOFA
# @is_a@chromosome ; SO:0000340
# @part_of@chromosome_arm ; SO:0000105
## aug04: add new analysis features (HDP,RNAiHDP,fgenesh,)
## these are like exons but parent feature lacks featureloc
## - need to join together by object_oid/parent_oid and compute parent feature (has name)
## SO type.subtype should be match.program
## SONG: match, match_part match_set nucleotide_match cross_genome_match cDNA_match EST_match
#? use '.' instead of '_' for part type? would that throw gnomap/gbrowse usage? probably
-->
<gene_is_complex>0</gene_is_complex>
<GModelParents>mRNA</GModelParents>
<GModelParts>protein,CDS,three_prime_UTR,five_prime_UTR</GModelParts>
<CDS_spanType>protein</CDS_spanType>
<CDS_exonType>exon</CDS_exonType>
<!-- rework above mess for gene models; handle pseudogene; ncRNAs ... -->
<feat_model id="mRNA">
<parts>exon</parts>
<parts>three_prime_UTR</parts>
<parts>five_prime_UTR</parts>
<submodels>protein</submodels> <!-- link to protein feat_model -->
</feat_model>
<feat_model id="protein"
typelabel="CDS"
parent="mRNA"
hasspan="1" makepartsfrom="exon"
>
<parts>CDS</parts>
</feat_model>
<!-- flybase chado has these with fmin == 1-origin, others are 0-origin; why?? -->
<origin_one
chromosome_arm="1"
chromosome_band="1"
chromosome="1"
golden_path="1"
NOTNOWintron="1"
transposable_element_insertion_site="1"
/>
<topsort
chromosome_arm="1"
chromosome="1"
golden_path="1"
/>
<segmentfeats
BAC="1"
chromosome_arm="1"
chromosome_band="1"
chromosome="1"
golden_path_region="1"
golden_path_fragment="1"
golden_path="1"
databank_scaffold="1"
scaffold="1"
segment="1"
source="1"
syntenic_region="1"
/>
<!--
## segment no longer valid SO; supercontig or golden_path are best
-->
<!-- simplefeat == segmentfeats + others -->
<simplefeat
BAC="1"
chromosome_arm="1"
chromosome_band="1"
chromosome="1"
golden_path_region="1"
golden_path_fragment="1"
golden_path="1"
databank_scaffold="1"
scaffold="1"
oligo="1" oligonucleotide="1"
point_mutation="1"
region="1"
repeat_region="1"
segment="1"
source="1"
transcription_start_site="1"
orthologous_region="1"
syntenic_region="1"
/>
<!-- skipaskid & segmentfeats ignored parent_oid ; dont try to
make dubious, maybe huge compound feature -->
<skipaskid
point_mutation="1"
region="1"
repeat_region="1"
pinsertion="1"
/>
<dropname
transcription_start_site="1"
mRNA_genscan="1"
match_genscan="1"
mRNA_piecegenie="1"
match_piecegenie="1"
tRNA_trnascan="1"
match_trnascan="1"
repeat_region="1"
match_blastn_na_dbEST_dpse="1"
match_blastz="1"
/>
<!-- nameisid include ones with only id => name ; similar to dropid -->
<nameisid
BAC="1"
chromosome_band="1"
oligo="1" oligonucleotide="1"
/>
<dropid
BAC="1"
cDNA_clone="1"
chromosome_band="1"
EST="1"
exon="1"
intron="1"
five_prime_UTR="1"
three_prime_UTR="1"
oligo="1" oligonucleotide="1"
processed_transcript="1"
repeat_region="1"
transcription_start_site="1"
transposable_element_pred="1"
/>
<dropfeat_fff
CDS_exon="1"
CDS="1"
exon="1"
intron="1"
remark="1"
OLD_USAGE_five_prime_UTR="1"
OLD_USAGE_three_prime_UTR="1"
/>
<dropfeat_gff
CDS_exon="1"
remark="1"
/>
<hasdups
three_prime_UTR="1"
intron="1"
five_prime_UTR="1"
exon="1"
match_repeat_runner_seg="1"
match_repeat_runner="1"
/>
<!-- hasdups match_repeat_runner="1"
? drop match_repeat_runner for match_repeat_runner_seg
match_repeat_runner="skip"
jan06: OLD_USAGE_:
changed CDS/CDS_exon mapping to GFFv3 usage: CDS == coding_exon not mRNA-like span
-->
<maptype
OLD_USAGE_protein="CDS"
OLD_USAGE_CDS="CDS_exon"
five_prime_untranslated_region="five_prime_UTR"
golden_path_region="scaffold"
oligonucleotide="oligo"
three_prime_untranslated_region="three_prime_UTR"
transposable_element_pred="transposable_element_pred"
mRNA_genewise="mRNA:genewise"
mRNA_twinscan="mRNA:twinscan"
mRNA_genscan="mRNA:genscan"
mRNA_piecegenie="mRNA:piecegenie"
gene_genewise="gene:genewise"
gene_twinscan="gene:twinscan"
gene_genscan="gene:genscan"
gene_piecegenie="gene:piecegenie"
mRNA_trnascan="tRNA:trnascan"
gene_trnascan="tRNA:trnascan"
match_tRNAscan_SE="tRNA:trnascan"
match_clonelocator_scaffoldBACs="BAC"
match_part_clonelocator_scaffoldBACs="skip"
match_bdgp_unknown_clonelocator_scaffoldBACs="BAC"
match_part_bdgp_unknown_clonelocator_scaffoldBACs="skip"
match_promoter="transcription_start_site"
match_locator_cytology="chromosome_band"
match_part_locator_cytology="skip"
match_aubrey_cytolocator_cytology="chromosome_band"
match_part_aubrey_cytolocator_cytology="skip"
match_JOSHTRANSPOSON_Sept="transposable_element_pred"
match_repeatmasker="repeat_region"
_repeatmasker="repeat_region"
match_repeat_runner_seg="repeat_region"
pinsertion="skip"
match_sim4_na_affy_oligo_dros="oligo"
match_dmel_r3_to_dmel_r4_migration_dmel_r3_affy_oligos="oligo"
match_sim4_na_users_i_dros="skip"
match_part_sim4_na_users_i_dros="skip"
match_sim4_aa_users_i_dros="skip"
match_part_sim4_aa_users_i_dros="skip"
match_part_repeat_runner="skip"
match_part_repeat_runner_seg="skip"
match_part_promoter="skip"
match_sim4_na_DGC_in_process_dros="match:sim4:na_DGC_dros"
match_sim4_na_HDP_RNAi_dmel="match:RNAiHDP"
match_sim4_na_HDP_mRNA_dmel="match:HDP"
match_sim4_na_gadfly_dros_RELEASE2="match:sim4:na_gadfly_dmel_r2"
match_sim4_na_transcript_dmel_RELEASE31="match:sim4:na_transcript_dmel_r31"
match_sim4_na_transcript_dmel_RELEASE32="match:sim4:na_transcript_dmel_r32"
match_tblastxwrap_na_baylorf1_scfchunk_dpse="match:tblastx:na_dpse"
match_tblastxwrap_na_scf_chunk_agambiae_fa="match:tblastx:na_agambiae"
match_part_sim4_na_DGC_in_process_dros="match_part:sim4:na_DGC_dros"
match_part_sim4_na_HDP_RNAi_dmel="match_part:RNAiHDP"
match_part_sim4_na_HDP_mRNA_dmel="match_part:HDP"
match_part_sim4_na_gadfly_dros_RELEASE2="match_part:sim4:na_gadfly_dmel_r2"
match_part_sim4_na_transcript_dmel_RELEASE31="match_part:sim4:na_transcript_dmel_r31"
match_part_sim4_na_transcript_dmel_RELEASE32="match_part:sim4:na_transcript_dmel_r32"
match_part_tblastxwrap_na_baylorf1_scfchunk_dpse="match_part:tblastx:na_dpse"
match_part_tblastxwrap_na_scf_chunk_agambiae_fa="match_part:tblastx:na_agambiae"
/>
<!--
so => "located_sequence_feature", ## leave in for now; no replacement for so ; SO:1000000
-->
<maptype_gff>
<transposable_element_pred>transposable_element:predicted</transposable_element_pred>
<tRNA_trnascan>tRNA:trnascan</tRNA_trnascan>
</maptype_gff>
</opt>
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