Python biom_taxonomy_formatter Beispiele

Beispiel #1

Datei: otu_significance.py Projekt: rob-knight/qiime

def _add_metadata(bt, md_key, lines):
    """Add metadata to formatted correlation output lines."""
    taxonomy_md = biom_taxonomy_formatter(bt, md_key)
    if taxonomy_md is not None:
        for i in range(len(lines)-1): #one more line than OTU
            lines[i+1]=lines[i+1]+'\t'+taxonomy_md[i] #skip header line in lines
        return lines
    else: # remove md_header from the first line
        nls = ['\t'.join(lines[0].split('\t')[:-1])] + lines[1:]
        return nls

Beispiel #2

Datei: otu_significance.py Projekt: rob-knight/qiime

def _add_metadata(bt, md_key, lines):
    """Add metadata to formatted correlation output lines."""
    taxonomy_md = biom_taxonomy_formatter(bt, md_key)
    if taxonomy_md is not None:
        for i in range(len(lines) - 1):  #one more line than OTU
            lines[i + 1] = lines[i + 1] + '\t' + taxonomy_md[
                i]  #skip header line in lines
        return lines
    else:  # remove md_header from the first line
        nls = ['\t'.join(lines[0].split('\t')[:-1])] + lines[1:]
        return nls