GlobPlot service, runner and result parser

[jabaws.git] / binaries / src / disembl / DisEMBL.py

diff --git a/binaries/src/disembl/DisEMBL.py b/binaries/src/disembl/DisEMBL.py
index d9618e2..7298e83 100644 (file)
--- a/binaries/src/disembl/DisEMBL.py
+++ b/binaries/src/disembl/DisEMBL.py
@@ -118,13 +118,8 @@ def reportSlicesTXT(slices, sequence):
             if i > 0:
                 sys.stdout.write(', ')
             sys.stdout.write( str(slices[i][0]+1) + '-' + str(slices[i][1]+1) )
-            s = s + upper(sequence[slices[i][0]:(slices[i][1]+1)])
-            if i < len(slices)-1:
-                s = s + lower(sequence[(slices[i][1]+1):(slices[i+1][0])])
-            elif slices[i][1] < len(sequence)-1:
-                s = s + lower(sequence[(slices[i][1]+1):(len(sequence))])
+           
     print ''
-    print s
 
 
 
@@ -144,7 +139,6 @@ def runDisEMBLpipeline():
     except:
         print '\nDisEMBL.py sequence_file \n'
         print 'A default run would be: ./DisEMBL.py fasta_file'
-        print 'Mode: "default"(nothing) or "scores" which will give scores per residue in TAB seperated format'
         raise SystemExit
     #db = sys.stdin
     parser = Fasta.RecordParser()
@@ -159,22 +153,17 @@ def runDisEMBLpipeline():
             REM465_smooth = SavitzkyGolay(smooth_frame,0,REM465_raw)
             COILS_smooth = SavitzkyGolay(smooth_frame,0,COILS_raw)
             HOTLOOPS_smooth = SavitzkyGolay(smooth_frame,0,HOTLOOPS_raw)
-            if mode == 'default':
-                sys.stdout.write('> '+cur_record.title+'_COILS ')
-                reportSlicesTXT( getSlices(COILS_smooth, fold_coils, join_frame, peak_frame, 0.43), sequence )
-                sys.stdout.write('> '+cur_record.title+'_REM465 ')
-                reportSlicesTXT( getSlices(REM465_smooth, fold_rem465, join_frame, peak_frame, 0.50), sequence )
-                sys.stdout.write('> '+cur_record.title+'_HOTLOOPS ')
-                reportSlicesTXT( getSlices(HOTLOOPS_smooth, fold_hotloops, join_frame, peak_frame, 0.086), sequence )
-                sys.stdout.write('\n')
-            elif mode == 'scores':
-                sys.stdout.write('> '+cur_record.title+'\n')
-                sys.stdout.write('# RESIDUE COILS REM465 HOTLOOPS\n')
-                for i in range(len(REM465_smooth)):
-                    sys.stdout.write(sequence[i]+'\t'+fpformat.fix(COILS_smooth[i],5)+'\t'+fpformat.fix(REM465_smooth[i],5)+'\t'+fpformat.fix(HOTLOOPS_smooth[i],5)+'\n')
-            else:
-                sys.stderr.write('Wrong mode given: '+mode+'\n')
-                raise SystemExit
+
+            sys.stdout.write('> '+cur_record.title+'\n')
+            sys.stdout.write('# COILS ')
+            reportSlicesTXT( getSlices(COILS_smooth, fold_coils, join_frame, peak_frame, 0.43), sequence )
+            sys.stdout.write('# REM465 ')
+            reportSlicesTXT( getSlices(REM465_smooth, fold_rem465, join_frame, peak_frame, 0.50), sequence )
+            sys.stdout.write('# HOTLOOPS ')
+            reportSlicesTXT( getSlices(HOTLOOPS_smooth, fold_hotloops, join_frame, peak_frame, 0.086), sequence )
+            sys.stdout.write('# RESIDUE COILS REM465 HOTLOOPS\n')
+            for i in range(len(REM465_smooth)):
+                sys.stdout.write(sequence[i]+'\t'+fpformat.fix(COILS_smooth[i],5)+'\t'+fpformat.fix(REM465_smooth[i],5)+'\t'+fpformat.fix(HOTLOOPS_smooth[i],5)+'\n')
         except AttributeError:
             break
     file.close()