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[Gmod-schema-cmts] schema/GMODTools/lib/Bio/GMOD/Bulkfiles BulkWriter.pm, 1.6, 1.7 FeatureWriter.pm, 1.11, 1.12 TableWriter.pm, 1.3, 1.4
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From: Don G. <don...@us...> - 2007-10-17 01:01:36
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Update of /cvsroot/gmod/schema/GMODTools/lib/Bio/GMOD/Bulkfiles In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv14197/lib/Bio/GMOD/Bulkfiles Modified Files: BulkWriter.pm FeatureWriter.pm TableWriter.pm Log Message: bulkfiles 1.1 added go_association file output; bug and config fixes Index: TableWriter.pm =================================================================== RCS file: /cvsroot/gmod/schema/GMODTools/lib/Bio/GMOD/Bulkfiles/TableWriter.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** TableWriter.pm 15 Oct 2007 16:19:29 -0000 1.3 --- TableWriter.pm 17 Oct 2007 01:01:32 -0000 1.4 *************** *** 114,117 **** --- 114,120 ---- ## my $seqsql = handler()->getSeqSql($fdump->{config},$fdump->{ENV}); + # 0710: no_csomesplit : no perchr files, only makeall + my $no_csomesplit= $self->handler_config->{no_csomesplit} || 0; # FIXME: 0710 + print STDERR "TableWriter::makeFiles\n" if $DEBUG; # debug my $fileset = $args{infiles}; *************** *** 130,138 **** my $chrlist=""; $chromosomes= $self->handler->getChromosomes(); # want all, not subset ?? ! foreach my $chr (@$chromosomes) { $chrlist .= "'$chr', "; } $ENV{'chromosomes'}= $chrlist; $self->readFFF($fileset); # collate feature info ## chromosome_summary ; do this before in Bulkfiles with others? ## this file is named in chadosql entry - fixme --- 133,148 ---- my $chrlist=""; $chromosomes= $self->handler->getChromosomes(); # want all, not subset ?? ! if($no_csomesplit) { ! $chrlist= "'sum', "; #?? only this, or none? ! } else { ! foreach my $chr (@$chromosomes) { $chrlist .= "'$chr', "; } ! } $ENV{'chromosomes'}= $chrlist; + + ## FIXME: need option here or elsewhere for other input, e.g. SQL query, GFF, ... $self->readFFF($fileset); # collate feature info + ## chromosome_summary ; do this before in Bulkfiles with others? ## this file is named in chadosql entry - fixme *************** *** 161,167 **** my $fset= $self->handler->getFilesetInfo($trg); unless($fset) { warn "TableWriter: No handler for target=$trg\n"; next; } - # $fset->{path}; - # $fset->{config}; << look for docs to write - # $fset->{handler}; << see handler()->getWriter($fset->{handler}) $self->writeTargetDocs($trg,$fset); } --- 171,174 ---- *************** *** 228,234 **** } - } sub readFFF { --- 235,241 ---- } } + sub readFFF { *************** *** 284,288 **** my $tconfig= $self->handler->callReadConfig( $configfile); ! ## need some fix to writeDocs for doc->path at top level or not-releasedir my $docs = $tconfig->{doc}; --- 291,296 ---- my $tconfig= $self->handler->callReadConfig( $configfile); ! ! ## should have ## need some fix to writeDocs for doc->path at top level or not-releasedir my $docs = $tconfig->{doc}; *************** *** 339,347 **** my $fh= new FileHandle(">$sumfile"); my $title = $self->config->{title}; ! my $date = $self->{reldate}; ! # $date= $self->handler()->config->{relfull} || $self->handler()->{date}; ! # $date= $ENV{date} || $self->handler()->{date}; - ##my $org = $self->{config}->{species} || $self->{config}->{org}; my $org= $self->{org} || $self->handler()->{config}->{org}; print $fh "# Genome feature summary of $org from $title [$date]\n"; --- 347,352 ---- my $fh= new FileHandle(">$sumfile"); my $title = $self->config->{title}; ! my $date = $self->{reldate}; # || $self->handler()->{date}; my $org= $self->{org} || $self->handler()->{config}->{org}; print $fh "# Genome feature summary of $org from $title [$date]\n"; *************** *** 440,475 **** - # =item openInput( $fileset ) - # - # handle input files - # - # =cut - # - # sub openInput - # { - # my $self= shift; - # my( $fileset )= @_; # do per-csome/name - # my @files= (); - # my $inh= undef; - # return undef unless(ref $fileset); - # - # my $intype = $self->config->{informat} || 'fff'; #? maybe array - # my $featset= $self->config->{featset} || []; - # - # print STDERR "openInput: type=$intype \n" if $DEBUG; - # - # foreach my $fs (@$fileset) { - # my $fp= $fs->{path}; - # my $name= $fs->{name}; - # my $type= $fs->{type}; # want also/instead featset type here ? gene,mrna,cds,... - # next unless( $fs->{type} =~ /$intype/); # could it be 'dna/fasta', 'amino/fasta' ? - # unless(-e $fp) { warn "missing intype file $fp"; next; } - # - # push(@files, $fp); - # } - # - # return @files; - # } - --- 445,448 ---- *************** *** 489,494 **** - - sub maxrange { my $self= shift; --- 462,465 ---- Index: BulkWriter.pm =================================================================== RCS file: /cvsroot/gmod/schema/GMODTools/lib/Bio/GMOD/Bulkfiles/BulkWriter.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** BulkWriter.pm 15 Oct 2007 16:19:29 -0000 1.6 --- BulkWriter.pm 17 Oct 2007 01:01:31 -0000 1.7 *************** *** 128,132 **** my $self = shift; unless($self->{outputpath}) { ! my $outputpath= $self->handler()->getReleaseSubdir( $self->getconfig('path') || $self->BULK_TYPE); $self->{outputpath} = $outputpath; } --- 128,133 ---- my $self = shift; unless($self->{outputpath}) { ! my $outputpath= $self->handler()->getReleaseSubdir( ! $self->getconfig('path') || $self->BULK_TYPE); $self->{outputpath} = $outputpath; } *************** *** 319,328 **** my %args= @_; print STDERR "makeFiles\n" if $DEBUG; # debug ! my $fileset = $args{infiles}; my $status= 0; ! unless(ref $fileset) { warn "makeFiles: needs infiles => \@filesets "; return; } ! # my @seqfiles= $self->openInput( $fileset ); # my $res= $self->processBlastInput( \@seqfiles); if ($self->config->{makeall} && $status > 0) { --- 320,343 ---- my %args= @_; print STDERR "makeFiles\n" if $DEBUG; # debug ! my $status= 0; ! my $name = $args{name} || $self->{bulktype}; ! my $filesetinfo = $args{filesetinfo}; # hash of <fileset xxxx=yyy> configs ! my $infiles = $args{infiles}; # array ref of file specs ! unless(ref $filesetinfo or ref $infiles) { ! warn "makeFiles $name: needs infiles => \@infiles "; return; ! } ! # my @seqfiles= $self->openInput( $infiles ); # my $res= $self->processBlastInput( \@seqfiles); + + ## no input files here, input from sql query; should be new module, SQLWriter ?? + my $dumpfiles= undef; + if( $filesetinfo->{input} eq "sql_query" ) { + #?? $filesetinfo->{ENV}= \%ENV; # dang, need this for ${variable} replacement in sql? + $dumpfiles = $self->handler->dumpFeatures($filesetinfo, undef, "colnames"); + $status= scalar(@$dumpfiles); # + print STDERR "$name: sql_query status = $status\n" if $DEBUG; + } if ($self->config->{makeall} && $status > 0) { *************** *** 335,338 **** --- 350,354 ---- } + sub makeall { Index: FeatureWriter.pm =================================================================== RCS file: /cvsroot/gmod/schema/GMODTools/lib/Bio/GMOD/Bulkfiles/FeatureWriter.pm,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** FeatureWriter.pm 15 Oct 2007 16:58:36 -0000 1.11 --- FeatureWriter.pm 17 Oct 2007 01:01:31 -0000 1.12 *************** *** 264,267 **** --- 264,269 ---- my @saveformats= @outformats; + ## this may be a mistake: config formats are what we need to make(?) + ## args{formats} are what caller/customer wants as result if ($args{formats}) { my $formats= $args{formats}; |