自分用スニペット

gistfile1.txt

//------------ argparse
import argparse;

def check_bool(v):
    v = v.lower();
    if v == "true" or v == "1":
        return True;
    if v == "false" or v == "0":
        return False;
    raise Exception("true or false or 1 or 0 are expected.");
        

parser = argparse.ArgumentParser();
parser.add_argument("--infile",required= True) ;
parser.add_argument("--outdir",required= True) ;
parser.add_argument("--batch_size",required= True,type=int);
parser.add_argument("--checkk",required= True,type=check_bool);

args = parser.parse_args();
//----------------------------


//------ fasta 読み込み
import gzip;
def loadFasta(filename):
    if filename.endswith(".gz"):
        fin = gzip.open(filename,"rt");
    else:
        fin = open(filename,"r");
    ret = [];
    cdict = dict();
    cdict["seq"] = "";
    ret.append(cdict);
    
    for ll in fin:
        mat = re.search("[\s]*>",ll);
        if(not mat == None):
            cdict = dict();
            ret.append(cdict);
            nmat = re.search("[\s]*>[\s]*([^\s]+)",ll);
            if(not nmat == None):
                cdict["name"] = nmat.group(1);
                cdict["desc"] = "";
            dmat = re.search("[\s]*>[\s]*([^\s]+)[\s]+([^\s][^\r\n]*)",ll);
            if(not dmat == None):
                cdict["desc"] = dmat.group(2);
            cdict["seq"] = "";
        else:
            cdict["seq"] += re.sub("[\s]","",ll);
            
    if(len(ret[0]["seq"]) == 0):
        ret.pop(0);
    fin.close();
    return ret;
//----------------