createBarcodeDictionary.py

#!/usr/bin/env python
import pickle

bLen=snakemake.params[0]
d={}
print(bLen)
with open(snakemake.input[0],'r') as txt:
    for line in txt:
        counts=int(line.strip().split()[1])
        ln=line.strip().split()[0]
        r=ln[bLen:].strip()
        if r in d:
            if ln[:bLen] in d[r]:
                d[r][ln[:bLen]]+=counts
            else:
                d[r][ln[:bLen]]=counts
        else:
            d[r]={ln[:bLen]:counts}

i=1
sd={}
with open(snakemake.output[1],'w') as f:
    for key in d:
        sd[i]=d[key]
        f.write('>'+str(i)+'\n')
        f.write(key+'\n')
        i+=1

with open(snakemake.output[0],'wb') as f:
    pickle.dump(sd,f,pickle.HIGHEST_PROTOCOL)