Merge branch 'master' of https://github.com/hillerlab/CESAR2.0

README.md

@@ -85,9 +85,10 @@ chmod +x jobList
 
 # Convert results into genePred format (excluding 0-bp exons due to complete deletions)
 for species in `echo $querySpecies | sed 's/,/ /g'`; do 
-  echo "bed2GenePred.pl $species $outputDir /dev/stdout | awk '{if ($4 != $5) print $0}' > $resultsDir/$species.gp"
+  echo "bed2GenePred.pl $species $outputDir /dev/stdout | awk '{if (\$4 != \$5) print \$0}' > $resultsDir/$species.gp"
 done > jobListGenePred
 chmod +x jobListGenePred
+mkdir $resultsDir
 ./jobListGenePred
 # This will take ~15 minutes
 
@@ -158,9 +159,10 @@ or run it in parallel by using a compute cluster.
 After each realignment job succeeded, collect the results as a single genePred file for each query species by running: 
 ```
 for species in `echo $querySpecies | sed 's/,/ /g'`; do 
-  echo "bed2GenePred.pl $species $outputDir /dev/stdout | awk '{if ($4 != $5) print $0}' > $resultsDir/$species.gp"
+  echo "bed2GenePred.pl $species $outputDir /dev/stdout | awk '{if (\$4 != \$5) print \$0}' > $resultsDir/$species.gp"
 done > jobListGenePred
 chmod +x jobListGenePred
+mkdir $resultsDir
 ./jobListGenePred
 ```
 

tools/bed2GenePred.pl

@@ -25,10 +25,10 @@
 my %accListHash = my %hashFromFile = ();
 ## Collect all exons of that species and convert it to a 2 dimensional hash, the first dimension is the accession, the second is just a number, the value is the line.
 my $call = "find $dir -type f -path '*/${species}/*' -exec cat {} \\;";
-print "executing  '$call'  ...\n";
+print STDERR "executing  '$call'  ...\n";
 my @results = `$call`;
 die "ERROR: $call failed\n" if ($? != 0 || ${^CHILD_ERROR_NATIVE} != 0);
-print "gives ", $#results+1, " exons\n";
+print STDERR "gives ", $#results+1, " exons\n";
 for (my $i = 0; $i<=$#results; $i++) {
 	my $line = $results[$i];	
 	$line =~s/\s+$//;
@@ -167,7 +167,7 @@
 }
 close FO;
 `rm $tmpBed $tmpBedFile $tmpFileB2L`;
-print "Results for $species are in $genePred\n";
+print STDERR "Results for $species are in $genePred\n";
 
 ### Sub-routines