a44421a79fb36cc2036fe116b97ea3bc9590cd0c
braney
  Fri Dec 2 09:34:39 2011 -0800
removed rcsid (#295)
diff --git src/hg/affyTransciptome/trackFromLifts.c src/hg/affyTransciptome/trackFromLifts.c
index 3b5398f..bf4d87b 100644
--- src/hg/affyTransciptome/trackFromLifts.c
+++ src/hg/affyTransciptome/trackFromLifts.c
@@ -1,86 +1,85 @@
 #include "common.h"
 #include "cheapcgi.h"
 
-static char const rcsid[] = "$Id: trackFromLifts.c,v 1.3 2003/05/06 07:22:13 kate Exp $";
 
 
 /* # script to automate the long process of creating affymetrix's  */
 /* # transcriptome track from their lift files. */
 
 void usage()
 {
     errAbort("trackFromLifts.pl - generate a track from the lift files provided by\n"
 	     "Simon Cawley at Affymetrix. Assumes that you are already in the directory.\n"
 	     "usage:\n\t"
 	     "trackFromLifts.pl <dbFreeze> <optional: directory containing sql files for tables.> <optional -noCleanup>\n");
 }
 
 int main(int argc, char *argv[])
 {
 char *freeze = NULL;
 char *sqlFileDir = "/projects/compbio/data/microarray/kapranov/maps/transcriptome/sci_21_22_paper/chr21_22/sql";
 char buff[2048];
 if(argc == 1)
     usage();
 
 freeze = cloneString(argv[1]);
 if(argc == 3)
     sqlFileDir = cloneString(argv[2]);
 
 warn("\nFreeze is %s", freeze);
 
 warn("\ngunzipping things, may take a while.");
 system("gunzip *.gz");
 
 warn("\nCatting files together.");
 if(system("catTriplets go") != 0) errAbort("Couldn't run catTriplets");
 
 warn("\nConverting to sample format (can take a while)");
 if(system("affyTransLiftedToSample 1000 *.s.*.tab") != 0)  errAbort("system call failed.\n");
 
 warn("\nAveraging experiments");
 if(system("avgTranscriptomeExps go -doAll suffix=tab.sample") != 0)  errAbort("system call failed.\n");
 
 warn("\nFinding Maximum vals");
 if(system("maxTranscriptomeExps max.s.1.tab.sample Transcriptome *.s.*.avg") != 0)  errAbort("system call failed.\n");
 //if(system("maxTranscriptomeExps max.b.1.tab.sample Transcriptome *.b.*.avg") != 0)  errAbort("system call failed.\n");
 //if(system("maxTranscriptomeExps max.c.1.tab.sample Transcriptome *.c.*.avg") != 0)  errAbort("system call failed.\n");
 
 warn("\nMerging averages");
 if(system("cat *.sample.avg | egrep \"chr21|chr22\" > all.chr2X.tab.samples") != 0)  errAbort("system call failed.\n");
 
 warn("\nMerging max vals into rest.");
 if(system("cat max.*.sample | egrep \"chr21|chr22\" >> all.chr2X.tab.samples") != 0)  errAbort("system call failed.\n");
 
 warn("\nCalculating zoom averages.");
 snprintf(buff, sizeof(buff), "averageZoomLevels 8 8 %s all.chr2X.tab.samples", freeze);
 if(system(buff) != 0)  errAbort("system call failed.\n");
 if(system("groupSamples 1000 all.chr2X.tab.samples.zoom_8 all.chr2X.tab.samples.zoom_8.group") != 0)  errAbort("system call failed.\n");
 if(system("groupSamples 1000 all.chr2X.tab.samples.zoom_1 all.chr2X.tab.samples.zoom_1.group") != 0)  errAbort("system call failed.\n");
 
 warn("\nScaling values between 1 and 1000 after multiplying by .3");
 if(system("scaleSampleFiles 1 1000 .3 all.chr2X.tab.samples") != 0)  errAbort("system call failed.\n");
 if(system("scaleSampleFiles 1 1000 1 all.chr2X.tab.samples.zoom*") != 0)  errAbort("system call failed.\n");
 
 warn("\nLoading into database");
 snprintf(buff, sizeof(buff), "hgLoadBed %s affyTranscriptome -sqlTable=%s/affyTranscriptome.sql all.chr2X.tab.samples.scale", freeze, sqlFileDir);
 if(system(buff) != 0) errAbort( "system call failed.\n");
 snprintf(buff, sizeof(buff), "hgLoadBed %s zoom1_affyTranscriptome -sqlTable=%s/zoom1_affyTranscriptome.sql all.chr2X.tab.samples.zoom_1.group.scale", freeze, sqlFileDir);
 if(system(buff) != 0) errAbort( "system call failed.\n");
 snprintf(buff, sizeof(buff), "hgLoadBed %s zoom2_affyTranscriptome -sqlTable=%s/zoom2_affyTranscriptome.sql all.chr2X.tab.samples.zoom_8.group.scale", freeze, sqlFileDir);
 if(system(buff) != 0) errAbort( "system call failed.\n");
 cgiSpoof(&argc, argv);
 if(!cgiBoolean("noCleanup"))
     {
     warn("\nCleaning up.");
     if(system("rm *sample* bed.tab") != 0) errAbort( "system call failed.\n");
     warn("\ngzipping up files. Will take a while...");
     if(system("gzip *.tab") != 0) errAbort("system call failed.\n");
     }
 else 
     {
     warn("\nSkipping cleanup");
     }
 warn ("Done.");
 return 0;
 }