scripts/preprocessing/relabel_seed.py
def stockhom_to_pfam_format(stk_msa, dest_dir=None):
    """
    Converts a stockholm MSA to the Pfam format

    stk_msa: A valid MSA in strockholm format
    dest_dir: The destination directory where the new MSA
    will be generated

    return: The output MSA in Pfam format, None otherwise
    """
    filename = os.path.basename(stk_msa).partition('.')[0]
    output_pfam_msa = os.path.join(dest_dir, filename + ".pfam")

    cmd = "esl-reformat pfam %s > %s" % (stk_msa, output_pfam_msa)

    subprocess.call(cmd, shell=True)

    if not os.path.exists(output_pfam_msa):
        return None

    return output_pfam_msa

    Converts a stockholm MSA to the Pfam format

    stk_msa: A valid MSA in strockholm format
    dest_dir: The destination directory where the new MSA
    will be generated

    return: The output MSA in Pfam format, None otherwise
    
Converts a stockholm MSA to the Pfam format
stk_msa: A valid MSA in strockholm format
dest_dir: The destination directory where the new MSA
will be generated

The output MSA in Pfam format, None otherwise
Converts a stockholm MSA to the Pfam format stk_msa : A valid MSA in strockholm format dest_dir : The destination directory where the new MSA will be generated The output MSA in Pfam format None otherwise
def stockhom_to_pfam_format(stk_msa, dest_dir=None):
    filename = os.path.basename(stk_msa).partition('.')[0]
    output_pfam_msa = os.path.join(dest_dir, filename + ".pfam")
    cmd = "esl-reformat pfam %s > %s" % (stk_msa, output_pfam_msa)
    subprocess.call(cmd, shell=True)
    if not os.path.exists(output_pfam_msa):
        return None
    return output_pfam_msa
def stockhom_to_pfam_format ( stk_msa , dest_dir = None ) : filename = os . path . basename ( stk_msa ) . partition ( '.' ) [ 0 ] output_pfam_msa = os . path . join ( dest_dir , filename + ".pfam" ) cmd = "esl-reformat pfam %s > %s" % ( stk_msa , output_pfam_msa ) subprocess . call ( cmd , shell = True ) if not os . path . exists ( output_pfam_msa ) : return None return output_pfam_msa
Converts a stockholm MSA to the Pfam format
stk_msa: A valid MSA in strockholm format
dest_dir: The destination directory where the new MSA
will be generated
Converts a stockholm MSA to the Pfam format stk_msa : A valid MSA in strockholm format dest_dir : The destination directory where the new MSA will be generated
"""
    Converts a stockholm MSA to the Pfam format

    stk_msa: A valid MSA in strockholm format
    dest_dir: The destination directory where the new MSA
    will be generated

    return: The output MSA in Pfam format, None otherwise
    """
stk_msa
dest_dir