zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

fix typo. Check explicitly that fingerprint files exist. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2821 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-02-10 21:29:54 +00:00
parent d16a1b5645
commit 60f05379a7
1 changed files with 6 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
python/getBamFilesFromSpreadsheet.py
View File

@ -36,7 +36,7 @@ else:
fpref = "human_b36"
outputFile = projectName+"_bam_files.txt"
OUTPUT_HEADER = ["sample_id","recalbrated_bam_file","individual_id","fingerprint_file","reference_file","dbsnp_file","interval_list","max_reads_at_locus","min_confidence","min_mapping_quality","min_base_quality"]
OUTPUT_HEADER = ["sample_id","recalibrated_bam_file","individual_id","fingerprint_file","reference_file","dbsnp_file","interval_list","max_reads_at_locus","min_confidence","min_mapping_quality","min_base_quality"]
if ( spreadsheetPath.find("/") > -1 ):
newSpreadsheet = spreadsheetPath.rsplit("/",1)[1].rsplit(".",1)[0]+"_proper_format.tsv"
@ -72,5 +72,9 @@ for line in project_info.readlines():
versioningDirectory = bamfile_base+spline[project_index]+"/"+spline[sample_index]+"/"
version = getNewestVersion(versioningDirectory)
bamfile = versioningDirectory+version+"/"+spline[sample_index]+".bam"
fingerprint_file = fingerprint_base+spline[project_index]+"/"+fpref+"/"+spline[sample_index]+".fingerprint.geli"
fingerprint_path = fingerprint_base+spline[project_index]+"/"+fpref+"/"
if ( spline[sample_index]+".fingerprint.geli" in os.listdir(fingerprint_path) ):
fingerprint_file = fingerprint_path+spline[sample_index]+".fingerprint.geli"
else:
fingerprint_file = ""
outputFile.write(projectName+"_"+spline[sample_index]+"\t"+bamfile+"\t"+groupName+"\t"+fingerprint_file+"\t"+reference+"\t"+dbsnp+"\t"+intervals+"\t"+max_reads+"\t"+min_conf+"\t"+min_map_q+"\t"+min_base_q+"\n")