src/hg/archaeStuff/scripts/make-browser-2.0 1.43
1.43 2009/08/02 05:07:15 pchan
add igenics and blastx tracks
Index: src/hg/archaeStuff/scripts/make-browser-2.0
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/archaeStuff/scripts/make-browser-2.0,v
retrieving revision 1.42
retrieving revision 1.43
diff -b -B -U 4 -r1.42 -r1.43
--- src/hg/archaeStuff/scripts/make-browser-2.0 29 Jun 2009 04:30:35 -0000 1.42
+++ src/hg/archaeStuff/scripts/make-browser-2.0 2 Aug 2009 05:07:15 -0000 1.43
@@ -71,16 +71,16 @@
# Program option variables
our ($opt_getseqs, $opt_joinassembly, $opt_initdb, $opt_hidedb, $opt_droptable, $opt_initblat, $opt_gc, $opt_repeats, $opt_iselements,
- $opt_desc, $opt_info, $opt_pfam, $opt_scanpfam, $opt_swissprot, $opt_pfamdesc,
+ $opt_desc, $opt_info, $opt_pfam, $opt_scanpfam, $opt_swissprot, $opt_pfamdesc, $opt_igenics,
$opt_syncg,$opt_synct,$opt_syncd, $opt_syncc, $opt_syncdw, $opt_loaddump, $opt_allorg,$opt_snapshot,
$opt_genes, $opt_gbhits, $opt_genepred, $opt_cogs, $opt_kegg, $opt_gbrnas, $opt_trnas, $opt_snornas,$opt_auth,
$opt_rfam, $opt_tigr, $opt_jgi, $opt_easy, $opt_startblat, $opt_killblat, $opt_blatscript, $opt_selfz, $opt_multiz, $opt_ultracons,
$opt_plfold, $opt_pldensity, $opt_custwig, $opt_wiki, $opt_wikibme, $opt_promsd, $opt_term, $opt_stringdb,
$opt_arkops, $opt_tigrops, $opt_commit, $opt_perm, $opt_tracksup, $opt_altdb, $opt_primers,
$opt_precomp, $opt_blastp, $opt_force, $opt_delete,$opt_web, $opt_public, $opt_all,
- $opt_makeblastdb, $opt_pubmultiz, $opt_cdd, $opt_blastpall, $opt_mblastx, $opt_mblastxall, $opt_aligntracks);
+ $opt_makeblastdb, $opt_pubmultiz, $opt_cdd, $opt_blastpall, $opt_blastx, $opt_blastxall, $opt_mblastx, $opt_mblastxall, $opt_aligntracks);
# By default, we are not looking for any particular organism to start our work
@@ -161,8 +161,9 @@
if ($opt_gc || $opt_all) { &Load_GC_track(\%global_vars); }
if ($opt_repeats || $opt_all) { &Load_simple_repeats_track(\%global_vars); }
if ($opt_iselements || $opt_all) { &Load_is_elements_track(\%global_vars); }
if ($opt_genes || $opt_all) { &Load_cds_gene_track(\%global_vars); }
+ if ($opt_igenics || $opt_all) { &Load_igenics(\%global_vars); }
if ($opt_gbhits || $opt_all) { &Load_Genbank_hits(\%global_vars); }
if ($opt_term || $opt_all) { &Load_terminator_tracks(\%global_vars); }
if ($opt_desc || $opt_all) { &Load_desc_page(\%global_vars); }
if ($opt_cogs || $opt_all) { &Load_COG_info(\%global_vars); }
@@ -196,8 +197,10 @@
if ($opt_aligntracks) { &Load_align_genes_track(\%global_vars); }
if ($opt_cdd) { &Load_Conserved_Domains(\%global_vars) }
if ($opt_blastp) { &Load_BlastP_track(\%global_vars,"incremental"); }
if ($opt_blastpall) { &Load_BlastP_track(\%global_vars,"full-rescan"); }
+ if ($opt_blastx) { &Load_igenics(\%global_vars); &Load_BlastX_track(\%global_vars,"incremental"); }
+ if ($opt_blastxall) { &Load_igenics(\%global_vars); &Load_BlastX_track(\%global_vars,"full-rescan"); }
if ($opt_mblastx) { &Load_mBlastX_track(\%global_vars,"incremental"); }
if ($opt_mblastxall) { &Load_mBlastX_track(\%global_vars,"full-rescan"); }
if ($opt_commit || $opt_all) { &CVS_commit(\%global_vars); }
if ($opt_tracksup || $opt_all) { &Update_tracks(\%global_vars); }
@@ -383,15 +386,15 @@
Getopt::Long::GetOptions("getseqs","joinassembly", "initdb","hidedb","droptable=s","initblat","gc","gbhits",
"repeats","iselements", "desc","info",
"pfam","scanpfam",
- "genes","genepred","cogs","kegg","gbrnas","trnas","snornas","delete=s",
+ "genes","genepred","cogs","kegg","gbrnas","trnas","snornas","delete=s", "igenics",
"syncg","synct","syncd","syncc","syncdw","loaddump", "swissprot=s", "pfamdesc",
"rfam","tigr","jgi","easy","startblat","killblat","blatscript","selfz","multiz", "ultracons",
"stringdb",
"plfold","pldensity","custwig=s","wiki", "wikibme","promsd","term","arkops","tigrops","auth=s",
"commit","perm","tracksup","altdb=s","primers","precomp=s","snapshot=s",
- "blastp","blastpall","mblastx","mblastxall","force","web=s","public","all","allorg","makeblastdb", "pubmultiz", "cdd", "aligntracks");
+ "blastp","blastpall","blastx","blastxall","mblastx","mblastxall","force","web=s","public","all","allorg","makeblastdb", "pubmultiz", "cdd", "aligntracks");
if ($#ARGV < 0)
{
die "\nUsage: make-browser [-options] <Org-ident>\n\n",
@@ -440,8 +443,9 @@
" --all : Create/Load/Run all tasks (does not set --force)\n",
" --gc : Run G/C percent track\n",
" --repeats : Run simple repeats\n",
" --genes : Load primary gene track (i.e. Genbank Refseq or other)\n",
+ " --igenics : Load intergenic regions between CDS\n",
" --gbhits : Map sequenced genes & cDNAs in Genbank to genome\n",
" --promsd : Load precomputed promotor & Shine-Dalgarno tracks, if present\n",
" --precomp=<trackname> : Load specified precomputed track (ex. insertionRegions, or 'all'), if present\n",
" --term : Load terminator poly-T track\n",
@@ -457,8 +461,10 @@
" --jgi : Load JGI genes track\n",
" --easy : Load Krogh lab's EasyGene track\n",
" --blastp : Run blastp on all unscanned species' proteins\n",
" --blastpall : Run blastp on ALL species' proteins (slow!)\n",
+ " --blastx : Run blastx on all unscanned species' proteins for intergenic regions between proteins\n",
+ " --blastxall : Run blastx on All species' proteins for intergenic regions between proteins\n",
" --mblastx : Run blastx on all unscanned species' proteins for metagenomes with concatenated scaffolds\n",
" --mblastxall : Run blastx on All species' proteins for metagenomes with concatenated scaffolds\n",
" --primers : Load available primer tracks\n",
" --arkops : Load operon info from Arkin microbesonline database\n",