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🐛 Fix Collapse bug #553

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merged 1 commit into from
Mar 1, 2024
Merged

🐛 Fix Collapse bug #553

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3 changes: 2 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -25,4 +25,5 @@ open_pbta_envs.txt
# Expression files in subset directories
analyses/molecular-subtyping*/*subset/*rsem-tpm*


# vs code
.vscode/
7 changes: 4 additions & 3 deletions analyses/collapse-rnaseq/cwl/scripts/liftover_collapse_rnaseq.py
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Expand Up @@ -64,11 +64,12 @@ def collapse_dups(dup_gene_sym_dict):
"""
Get highest mean for repeated gene symbols and output that row
"""
out_data = []
for gene_sym in dup_gene_sym_dict:
means = [mean(data) for data in dup_gene_sym_dict[gene_sym]]
top_idx = means.index(max(means))
out_data = "{}\t{}\n".format(gene_sym, '\t'.join(list(map(str, dup_gene_sym_dict[gene_sym][top_idx]))))
return out_data
out_data.append("{}\t{}".format(gene_sym, '\t'.join(list(map(str, dup_gene_sym_dict[gene_sym][top_idx])))))
return out_data


def main():
Expand Down Expand Up @@ -170,7 +171,7 @@ def main():
l += 1
print("Processing {} repeat gene symbols and choosing highest mean expression".format(dup_ct), file=sys.stderr)
out_data = collapse_dups(dup_gene_sym_dict)
out_collapse.write(out_data)
out_collapse.write("\n".join(out_data))
print("Done!", file=sys.stderr)


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2 changes: 1 addition & 1 deletion analyses/collapse-rnaseq/cwl/tools/convert_to_rds.cwl
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Expand Up @@ -6,7 +6,7 @@ doc: "Converts tsv table to rds"
requirements:
- class: ShellCommandRequirement
- class: DockerRequirement
dockerPull: 'rocker/tidyverse:3.5.3'
dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/annofuse:0.92.0'
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
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