Modified add_manual_builds script so that it will include the build in parentheses after the name even if there are no chromosome lengths listed (previously would not because of line break after name); also added a couple of new manual builds

cron/add_manual_builds.py

@@ -21,12 +21,12 @@ def add_manual_builds(input_file, build_file, chr_dir):
     build_file_out = open(build_file,'a')
     for line in open(input_file):
         try:
-            fields = line.split("\t")
+            fields = line.replace("\n","").replace("\r","").split("\t")
             build = fields.pop(0)
             if build in existing_builds: continue # if build exists, leave alone
             name = fields.pop(0)
             try: # get chrom lens if included in file, otherwise still add build
-                chrs = fields.pop(0).replace("\n","").replace("\r","").split(",")
+                chrs = fields.pop(0).split(",")
             except:
                 chrs = []
             print>>build_file_out, build+"\t"+name+" ("+build+")"

tool-data/shared/ucsc/manual_builds.txt

@@ -698,3 +698,5 @@ Ptrichocarpa_156	Poplar (Populus trichocarpa)
 Hydra_JCVI	Hydra magnipapillata str. 105
 Araly1	Arabidopsis lyrata
 Zea_mays_B73_RefGen_v2	Maize (Zea mays)	chr1=301354135,chr2=237068928,chr3=232140222,chr4=241473566,chr5=217872898,chr6=169174371,chr7=176764813,chr8=175793772,chr9=156750718,chr10=150189513,chr11=7140224
+Homo_sapiens_AK1	Korean Man	chrM=16571,chr1=247249719,chr2=242951149,chr3=199501827,chr4=191273063,chr5=180857866,chr6=170899992,chr7=158821424,chr8=146274826,chr9=140273252,chr10=135374737,chr11=134452384,chr12=132349534,chr13=114142980,chr14=106368585,chr15=100338915,chr16=88827254,chr17=78774742,chr18=76117153,chr19=63811651,chr20=62435964,chr21=46944323,chr22=49691432,chrX=154913754,chrY=57772954
+Tcas_3.0	Red Flour Beetle (Tribolium castaneum)