From b5ee9ee8c7d20d70bbe2df9d303173d26ac075be Mon Sep 17 00:00:00 2001 From: Kelly Vincent Date: Thu, 10 Mar 2011 13:28:33 -0500 Subject: [PATCH] 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 | 16 ++++++++++------ tool-data/shared/ucsc/manual_builds.txt | 6 +++++- 2 files changed, 15 insertions(+), 7 deletions(-) diff --git a/cron/add_manual_builds.py b/cron/add_manual_builds.py index 6370381e7b2..c8b71428a83 100644 --- a/cron/add_manual_builds.py +++ b/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) \ No newline at end of file + add_manual_builds(input_file,build_file,chr_dir) diff --git a/tool-data/shared/ucsc/manual_builds.txt b/tool-data/shared/ucsc/manual_builds.txt index 3757ebd421f..b36d41ec40c 100644 --- a/tool-data/shared/ucsc/manual_builds.txt +++ b/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