Modified script that adds manual builds to add build even if chrom length details not present; added a few new manual builds

cron/add_manual_builds.py

@@ -25,12 +25,16 @@ def add_manual_builds(input_file, build_file, chr_dir):
             build = fields.pop(0)
             if build in existing_builds: continue # if build exists, leave alone
             name = fields.pop(0)
-            chrs = fields.pop(0).replace("\n","").replace("\r","").split(",")
+            try: # get chrom lens if included in file, otherwise still add build
+                chrs = fields.pop(0).replace("\n","").replace("\r","").split(",")
+            except:
+                chrs = []
             print>>build_file_out, build+"\t"+name+" ("+build+")"
-            chr_len_out=open( os.path.join(chr_dir,build+".len"),'w')
-            for chr in chrs:
-                print>>chr_len_out, chr.replace("=","\t")
-            chr_len_out.close()
+            if chrs: # create len file if provided chrom lens
+                chr_len_out=open( os.path.join(chr_dir,build+".len"),'w')
+                for chr in chrs:
+                    print>>chr_len_out, chr.replace("=","\t")
+                chr_len_out.close()
         except:
             continue
     build_file_out.close()
@@ -42,4 +46,4 @@ if __name__ == "__main__":
     input_file = sys.argv[1]
     build_file = sys.argv[2]
     chr_dir = sys.argv[3]
-    add_manual_builds(input_file,build_file,chr_dir)
+    add_manual_builds(input_file,build_file,chr_dir)

tool-data/shared/ucsc/manual_builds.txt

@@ -690,5 +690,9 @@ Schizosaccharomyces_pombe_1.1	Fission Yeast (S. pombe)	chrII=4539804,chrIII=2452
 Xanthomonas_oryzae_PXO99A	Xanthomonas oryzae pv. oryzae PXO99A	chr=5240075
 eschColi_EC4115	Escherichia coli EC4115	chr=5572075,plasmid_pO157=94644,plasmid_pEC4115=37452
 eschColi_TW14359	Escherichia coli TW14359	chr=5528136,plasmid_pO157=94601
-pUC18	pUC18 Plasmid
+pUC18	pUC18 Plasmid	plasmid=2686
 nomLeu1	Gibbon	chr1=245538060,chr10=135320619,chr10_random=51011,chr11=134551115,chr12=132397767,chr12_random=336702,chr13=114140689,chr14=106383727,chr15=100373758,chr15_random=814500,chr16=88836341,chr16_random=121782,chr17=78641643,chr17_random=2617017,chr18=76124575,chr19=63791437,chr19_random=297341,chr1_random=3502083,chr2=242756806,chr20=62432189,chr21=47019833,chr22=49520868,chr22_random=31530,chr2_random=335351,chr3=199337376,chr3_random=950829,chr4=191633586,chr4_random=923474,chr5=180612635,chr5_random=150620,chr6=170839170,chr6_random=1837487,chr7=158619002,chr7_random=805938,chr8=146283503,chr8_random=649034,chr9=138402467,chr9_random=1315712,chrUn=217400297,chrX=154793867,chrX_random=1690203,chrY=57470892
+Saccharomcyes_cerevisiae_S288C_SGD2010	S. cerevisae str. S288C	chr1=230218,chr2=813184,chr3=316620,chr4=1531933,chr5=576874,chr6=270161,chr7=1090940,chr8=562643,chr9=439888,chr10=745751,chr11=666816,chr12=1078177,chr13=924431,chr14=784333,chr15=1091291,chr16=948066,chrM=85779
+Spur_v2.6	Purple Sea Urchin (Strongylocentrotus purpuratus) v2.6
+Ptrichocarpa_156	Poplar (Populus trichocarpa)
+Hydra_JCVI	Hydra magnipapillata str. 105