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Incorporate lists of fingerprint data rather than summaries. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6044 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
droazen 2011-06-22 22:54:23 +00:00
parent 9a00d81d57
commit f7fa373643
1 changed files with 12 additions and 11 deletions
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23
python/generate_per_sample_metrics.py
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@ -64,7 +64,7 @@ sample_summary_metrics_types = [ (HsMetrics,'hybrid_selection_metrics'),
(InsertSizeMetrics, 'insert_size_metrics'),
(DbSnpMatchMetrics, 'dbsnp_matches') ]
header = ['sample','SUM_OF_FINGERPRINT_LODS','HAPLOTYPES_CONFIDENTLY_MATCHING.MIN','HAPLOTYPES_CONFIDENTLY_MATCHING.MAX','HAPLOTYPES_CONFIDENTLY_MATCHING.MEDIAN']
header = ['sample','FINGERPRINT_LODS','HAPLOTYPES_CONFIDENTLY_MATCHING']
for metric_type in sample_summary_metrics_types:
header.extend(get_sample_summary_metrics_fields(metric_type[0]))
print string.join(header,'\t')
@ -88,18 +88,19 @@ for sample_id,filename in samples.items():
fingerprinting_summary_metrics = get_all_metrics('%s.%s' % (basepath,'fingerprinting_summary_metrics'))
if fingerprinting_summary_metrics != None:
haplotypes_confidently_matching = [metric.HAPLOTYPES_CONFIDENTLY_MATCHING for metric in fingerprinting_summary_metrics]
sum_of_fingerprint_lods = str(sum([metric.LOD_EXPECTED_SAMPLE for metric in fingerprinting_summary_metrics]))
min_haplotypes_confidently_matching = str(min(haplotypes_confidently_matching))
max_haplotypes_confidently_matching = str(max(haplotypes_confidently_matching))
median_haplotypes_confidently_matching = str(median(haplotypes_confidently_matching))
haplotypes_confidently_matching = [str(metric.HAPLOTYPES_CONFIDENTLY_MATCHING) for metric in fingerprinting_summary_metrics]
fingerprint_lods = [str(metric.LOD_EXPECTED_SAMPLE) for metric in fingerprinting_summary_metrics]
# min_haplotypes_confidently_matching = str(min(haplotypes_confidently_matching))
# max_haplotypes_confidently_matching = str(max(haplotypes_confidently_matching))
# median_haplotypes_confidently_matching = str(median(haplotypes_confidently_matching))
else:
sum_of_fingerprint_lods = 'NA'
min_haplotypes_confidently_matching = 'NA'
max_haplotypes_confidently_matching = 'NA'
median_haplotypes_confidently_matching = 'NA'
haplotypes_confidently_matching = []
fingerprint_lods = []
# min_haplotypes_confidently_matching = 'NA'
# max_haplotypes_confidently_matching = 'NA'
# median_haplotypes_confidently_matching = 'NA'
data = [sample_id,sum_of_fingerprint_lods,min_haplotypes_confidently_matching,max_haplotypes_confidently_matching,median_haplotypes_confidently_matching]
data = [sample_id,'c('+string.join(fingerprint_lods,',')+')','c('+string.join(haplotypes_confidently_matching,',')+')']
for metrics_type,metrics_extension in sample_summary_metrics_types:
metrics = get_sample_summary_metrics('%s.%s' % (basepath,metrics_extension))