removed_subroutines.txt

#extra code that I've deleted from mytools/common, in case it needs to be re-inserted


def donothing():
        pass;



#
# -- BEGIN -- String methods
#

def get_454_fasta_id(s):
        """retrieve sequence ID from fasta files (qual file)"""

        # with descriptions
        try:
                return s[ 1 : s.index(" ")]

        # without descriptions
        except:
                return s.strip()[ 1 : ]



def trim_ref_gene_name(s):
        """
        return the first part of gene name by either "-" or "_"
        """
        ind = 0
        if s.find("_") > 0:                     # native gene
                ind = s.index("_")
                return s[ : ind]

        elif s.find("-") > 0:           # germline gene
                ind = s.index("-")
                return s[ind + 1 :]

def generate_random_string(string_len):
        all_letters, result = "0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ", []
        for i in range(string_len):
                result.append(random.choice(all_letters))
        return "".join(result)

def get_number_char(ind):
        all_chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
        return all_chars[ind - 1]
#
# -- END -- String methods
#


def sort_files_by_size(fs):
        """
        sort files based on size: from smaller to larger
        """
        z_files = []
        for f in fs:
                size = os.path.getsize(f)
                z_files.append((size, f))
        z_files = sorted(z_files)

        return [f for s, f in z_files]




def retrieve_name_body(s):
        """
        Remove folder and suffix
        """
        lind = s.rindex("/")
        rind = s.rindex(".")
        return s[lind + 1 : rind]

def folder_path2prj_name(s):
        ind = s.index("pt")
        s = s[ind :]
        return s[ : s.index("/")]