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[Gmod-schema-cmts] schema/GMODTools/conf/bulkfiles drosmelgb.xml, 1.1, 1.2 filesets.xml, 1.10, 1.11 genbanksubmit.xml, 1.2, 1.3
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From: Don G. <don...@us...> - 2008-05-14 05:58:23
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Update of /cvsroot/gmod/schema/GMODTools/conf/bulkfiles In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv21431/conf/bulkfiles Modified Files: drosmelgb.xml filesets.xml genbanksubmit.xml Log Message: genbank submit update: works with NCBI tbl2asn now Index: filesets.xml =================================================================== RCS file: /cvsroot/gmod/schema/GMODTools/conf/bulkfiles/filesets.xml,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** filesets.xml 12 May 2008 04:50:44 -0000 1.10 --- filesets.xml 14 May 2008 05:58:22 -0000 1.11 *************** *** 210,213 **** --- 210,214 ---- id="genbanktbl" path="genbanksubmit/" + suffix="tbl" handler="GenbankSubmitWriter" title="Genbank genome submit table" Index: drosmelgb.xml =================================================================== RCS file: /cvsroot/gmod/schema/GMODTools/conf/bulkfiles/drosmelgb.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** drosmelgb.xml 13 May 2008 04:40:55 -0000 1.1 --- drosmelgb.xml 14 May 2008 05:58:22 -0000 1.2 *************** *** 30,34 **** <release_url>/genome/${species}/release-${release_id}.html</release_url> ! <org>drosmelgb</org> <species>Drosophila_melanogaster</species> --- 30,34 ---- <release_url>/genome/${species}/release-${release_id}.html</release_url> ! <org>dromel</org> <species>Drosophila_melanogaster</species> Index: genbanksubmit.xml =================================================================== RCS file: /cvsroot/gmod/schema/GMODTools/conf/bulkfiles/genbanksubmit.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** genbanksubmit.xml 13 May 2008 04:40:55 -0000 1.2 --- genbanksubmit.xml 14 May 2008 05:58:22 -0000 1.3 *************** *** 2,21 **** name="genbanksubmit" date="20080511" ! > <title>GenBank Submission table writer</title> ! <about> ! These are configurations for converting chado feature table dumps to ! Genbank submission table files. Most of these configs specify how to process and convert various features extracted from chado db. ! These are tied to methods in Bulkfiles::FeatureWriter.pm) See chadofeatconv.xml for similar methods. ! Valid options include ! ! recodekey id={one of feature keys} value=output-key ! ! </about> <!-- --- 2,26 ---- name="genbanksubmit" date="20080511" ! ! tbl2asn="${ARGOS_ROOT}/common/servers/blast/Bin/tbl2asn" ! tbl2asnopts="-t template.sbt -V vb -p ./ " > <title>GenBank Submission table writer</title> ! ! <about><![CDATA[ ! These are configurations for converting Chado genome features to ! Genbank submission table files. Most of these specify how to process and convert various features extracted from chado db. ! These are tied to methods in Bulkfiles::GenbankSubmitWriter/FeatureWriter See chadofeatconv.xml for similar methods. ! Refer to these specifications: ! http://www.ncbi.nlm.nih.gov/Genbank/eukaryotic_genome_submission.html ! http://www.ncbi.nlm.nih.gov/Genbank/eukaryotic_genome_submission_annotation.html ! http://www.ncbi.nlm.nih.gov/Genbank/tbl2asn2.html ! http://www.ncbi.nlm.nih.gov/Sequin/table.html ! http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html ! ]]></about> <!-- *************** *** 23,31 **** set of rewrite patterns and logic lives that gbsub also needs; should separate out good from old there into two files. - need some of these: mapattr_pattern**; maptype_pattern; mapname_pattern; ** feat_model --> - <include>chadofeatconv</include> --- 28,34 ---- *************** *** 35,54 **** <outformats>dummy</outformats> - <!-- genbank tags from internal tags - all ncRNA SO types become this - type ncRNA ; attr 'ncRNA_class snRNA' - --> <mapattr_key id="Dbxref">db_xref</mapattr_key> <mapattr_key id="Note">note</mapattr_key> - <mapattr_key id="synonym">gene_syn</mapattr_key> <mapattr_key id="cyto_range">cyt_map</mapattr_key> <mapattr_key id="map">cyt_map</mapattr_key> <mapattr_key id="eC_number">EC_number</mapattr_key> <!-- fix a GFFism --> ! ! ! <!-- Name is special case depending on feature type --> ! <mapattr_key id="Name">gene</mapattr_key> ! <!-- mapattr_key id="ID">locus_tag</mapattr_key --> ! <!-- ditto for ID : can become locus_tag; transcript_id ; protein_id ... --> <!-- see maptype_gff; all the type recodes here .. ncRNA ?? --- 38,91 ---- <outformats>dummy</outformats> <mapattr_key id="Dbxref">db_xref</mapattr_key> <mapattr_key id="Note">note</mapattr_key> <mapattr_key id="cyto_range">cyt_map</mapattr_key> <mapattr_key id="map">cyt_map</mapattr_key> + <mapattr_key id="species">organism</mapattr_key> <mapattr_key id="eC_number">EC_number</mapattr_key> <!-- fix a GFFism --> ! <!-- mapattr_key id="synonym" >gene_syn</mapattr_key --> ! ! <!-- ID, Name, others are special cases depending on feature type; ! see GenbankSubmitWriter::handleAttribOut() ! try this mapattr_feature ! --> ! <mapattr_key id="ID">db_xref</mapattr_key> ! <mapattr_key id="Name">name</mapattr_key> ! ! <mapattr_key_gene ! ID="locus_tag" ! Name="gene" ! synonym="gene_syn" ! locus_tag="old_locus_tag" ! gene="old_gene" ! /> ! <mapattr_key_mRNA match="RNA" ! ID="transcript_id" ! Parent="locus_tag" ! ParentName="gene" ! locus_tag="old_locus_tag" ! gene="old_gene" ! Name="product" ! transcript_id="old_transcript_id" ! product="old_product" ! /> ! <mapattr_key_CDS ! ID="protein_id" ! Parent="skip" ! ParentName="skip" ! GrandParent="locus_tag" ! GrandParentName="gene" ! locus_tag="old_locus_tag" ! gene="old_gene" ! Name="product" ! protein_id="old_protein_id" ! product="old_product" ! /> ! <mapattr_key_transposon ! ID="transposon" ! transposon="old_transposon" ! /> ! ! <!-- see maptype_gff; all the type recodes here .. ncRNA ?? *************** *** 128,132 **** </feat_model> - <!-- default structure for non-simple 'mRNA' types --> <!-- tRNA , rRNA are separate in Genbank ; equal to mRNA (snoRNA, scRNA, snRNA, miRNA, ncRNA, rRNA) --- 165,168 ---- *************** *** 166,168 **** --- 202,332 ---- + + <about id="submit_template_info"><![CDATA[ + ref: ncbi/doc/tbl2asn.txt + + SUBMISSION TEMPLATE FORMAT + + The submission template is an ASN.1 Submit-block that can be generated by + Sequin. A simple example is shown below. + + ]]></about> + + <doc id="submit_template" path="genbanksubmit/template.sbt"> + <!-- FIXME: configure this or expect customers to edit to taste ? --> + <![CDATA[ + + Submit-block ::= { + contact { + contact { + name + name { + last "Darwin" , + first "Charles" , + initials "C.R." , + suffix "" } , + affil + std { + affil "Oxbridge University" , + div "Evolutionary Biology Department" , + city "Camford" , + country "United Kingdom" , + street "1859 Tennis Court Lane" , + email "da...@be..." , + phone "01 44 171-007-1212" , + postal-code "OX1 2BH" } } } , + cit { + authors { + names + std { + { + name + name { + last "Darwin" , + first "Charles" , + initials "C.R." } } } , + affil + std { + affil "Oxbridge University" , + div "Evolutionary Biology Department" , + city "Camford" , + country "United Kingdom" , + street "1859 Tennis Court Lane" , + postal-code "OX1 2BH" } } , + date + std { + year 2003 , + month 2 , + day 28 } } , + subtype new } + ]]> + </doc> + + <about id="working notes"> + <![CDATA[ + working notes: + * add NCBI tbl2asn executable options as per blastfiles.xml + tbl2asn="${ARGOS_ROOT}/common/servers/blast/Bin/tbl2asn" + tbl2asnopts=" " + e.g. tbl2asn -t template.sbt -p path_to_files -a s -V v + + # this works .. with errors + $nb/tbl2asn -t template.sbt -V vb -p ./ + + GMODTools/data/genomes/Drosophila_melanogaster/drosmelgb_20080512/genbanktbl + + # outputs + 2415212 May 13 19:50 drosmelgb-all-drosmelgb4.gbf + 3910617 May 13 19:50 drosmelgb-all-drosmelgb4.sqn + 653387 May 13 19:50 drosmelgb-all-drosmelgb4.val == ERRORS list + + # inputs + 265366 May 13 19:48 drosmelgb-all-drosmelgb4.tbl + 1379004 May 13 19:31 drosmelgb-all-drosmelgb4.fsa == ../fasta/drosmelgb-all-chromosome-drosmelgb4.fasta + 296419 May 13 19:30 drosmelgb-all-drosmelgb4.pep == ../fasta/drosmelgb-all-translation-drosmelgb4.fasta + 1085 May 13 19:22 template.sbt + + # prot translations mostly bad: no start_codon= field *** only problem w/ genbank2chado ? + # ** need to always explicity write this field from CDS_span location? shouldn't this be + shouldn't need this; CDS locs should have start/stop + + perl -pi -e's/protein_id\tNP/old_protein_id\tNP/;' drosmelgb-all-drosmelgb4.tbl + perl -pi -e's/transcript_id\tNM_/old_transcript_id\tNM_/;' drosmelgb-all-drosmelgb4.tbl + + # all prots.pep missed : fix >IDs ?? + [NULL_Caption] Unable to find protein sequence CG17923.p01 + SeqID must match protein_id in the .tbl file + + + # ERRORS .val................ + + ERROR: valid [SEQ_DESCR.NoOrgFound] No organism name anywhere on this entire record. BIOSEQ: lcl|NC_004353: ra + w, dna len= 1351857 + >> change chromosome type to source type + + perl -pi -e's/1351857\tchromosome/1351857\tsource/;s/Drosophila_melanogaster/Drosophila melanogaster/;' drosmelgb-all-drosmelgb4.tbl + + WARNING: valid [SEQ_FEAT.IllegalDbXref] db_xref type GI is only created by the flatfile generator, + >> drop all db_xref == GI: + + perl -pi -e's/db_xref\tGI:/db_xref\told_GI:/;' drosmelgb-all-drosmelgb4.tbl + + ERROR: valid [SEQ_FEAT.SeqLocOrder] Location: Intervals out of order in SeqLoc [(lcl|NC_004353:c53751-53434, c + 53999-53817, c57083-56500, c61911-57142, c64403-63540)] FEATURE: CDS: plexin B CG17245-PA [(lcl|NC_004353:c537 + 51-53434, c53999-53817, c57083-56500, c61911-57142, c64403-63540)] [lcl|NC_004353: raw, dna len= 1351857] -> [ + lcl|plexB.p01] + >> this is probably revcomp error; put last first ... + + WARNING: valid [SEQ_FEAT.UnnecessaryGeneXref] Unnecessary gene cross-reference CG32005 FEATURE: CDS: CG32005-P + A [lcl|NC_004353:111840-113903] [lcl|NC_004353: raw, dna len= 1351857] -> [lcl|CG32005.p01] + >> + 111840 113903 CDS + protein_id CG32005.p01 + gene CG32005 <<< is this the problem? + product CG32005-PA + + + ]]> </about> + + </opt> |