Fix prepDE.py3 KeyError for transcripts missing from first sample#503
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Theob0t wants to merge 1 commit intogpertea:masterfrom
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Fix prepDE.py3 KeyError for transcripts missing from first sample#503Theob0t wants to merge 1 commit intogpertea:masterfrom
Theob0t wants to merge 1 commit intogpertea:masterfrom
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When StringTie -e is used with piped input (e.g. samtools view -q 255 | stringtie -), transcripts with zero passing-filter reads may be omitted from the output GTF. Since geneIDs is only populated from the first sample (loop 1 breaks after the first successful parse), transcripts that appear in later samples but not the first cause a KeyError at line 279. The current defaultdict(lambda: str) suppresses the crash but silently maps missing transcripts to the str type object, corrupting the gene count matrix. Fix: skip transcripts not present in geneIDs. These are transcripts with zero counts in the first sample — their transcript-level counts are still written correctly to the transcript count matrix from t_dict. Fixes gpertea#428, related to gpertea#337.
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Fixes #428, related to #337.
Problem
geneIDsis built from the first sample only (loop 1 breaks after first successful parse, line 176).t_dictaccumulates transcripts across all samples. When loop 2 iteratest_dictto build the gene count matrix, transcripts present in later samples but absent from sample 1 cause aKeyErrorat line 279.This triggers when some samples have zero coverage for transcripts present in other samples. Common with large diverse cohorts, especially when upstream filtering reduces read counts (e.g.
samtools view -q 255 | stringtie -e).The current
defaultdict(lambda: str)on master suppresses the crash but maps missing transcripts to thestrtype object as a key, silently corrupting the gene count matrix.Fix
Skip transcripts not in
geneIDs. Their per-sample counts are still written correctly to the transcript count matrix fromt_dict.Testing
334 RNA-seq samples via TEProf3 (
samtools view -q 255 | stringtie -e). Crashes without fix, both matrices generated successfully with fix.