080080a547e9d89adf4393c2a349544443c35962,rnaseq/src/aggregate_rnaseqc_metrics.py,,,#,6

Before Change

assert len(args.annotation_tsvs)==len(annotation_headers)

path_s = pd.read_csv(args.input_files_tsv, sep="\t", index_col=0, header=None, names=["sample_id","metrics_path"])["metrics_path"]
metrics_df = pd.concat([pd.read_csv(i, sep="\t") for i in path_s], axis=0)
metrics_df.index = metrics_df["Sample"]

// add optional annotations as additional columns
for h,tsv in zip(annotation_headers, args.annotation_tsvs):

After Change

df = pd.read_csv(path_s.iloc[0], sep="\t", header=None)
if df.shape[0]==2:  // RNA-SeQC v1.1.9
    dfs = [pd.read_csv(i, sep="\t") for i in path_s]
elif df.shape[1]==2:  // RNA-SeQC v2
    dfs = [pd.read_csv(i, sep="\t", header=None, index_col=0).T for i in path_s]
else:
    raise ValueError("Unrecognized input format (shape {}).".format(df.shape))
metrics_df = pd.concat(dfs, axis=0)
metrics_df.index = metrics_df["Sample"]

// add optional annotations as additional columns

Instances