quark.snake

import os

currdir=os.getcwd()
mince=os.path.abspath("./Mince-Binaries-0.6.1/mince_linux")
quark=os.path.abspath("./build/src/quark")
decoder=os.path.abspath("./build/src/decoder")


#index related parameters

#common
output_path=config["out"]


rule make_index:
    run:
        if(not os.path.isdir(output_path)):
            shell("mkdir -p {}".format(output_path))
        shell("{} index -t {} -o {} -k {}".format(quark,config['fasta'],output_path,config['kmer']))


rule encode:
    run:
        if(not os.path.isdir(output_path)):
            shell("mkdir -p {}".format(output_path))
        if(config['lib'] == "paired"):
            mate_1=config['m1']
            mate_2=config['m2']
            if(config['quality'] == "1"):
                print("We are in the quality branch")
                shell("{} quant -i {} -l IU -1 <(gunzip -c {}) -2 <(gunzip -c {}) -p {} -o {} --quality".format(quark,config['index'],mate_1,mate_2,config['p'],output_path))
            else:
                print("We are not in the quality branch")
                shell("{} quant -i {} -l IU -1 <(gunzip -c {}) -2 <(gunzip -c {}) -p {} -o {}".format(quark,config['index'],mate_1,mate_2,config['p'],output_path))
            os.chdir(os.path.join(output_path,'aux'))
            print (os.getcwd())
            shell("{} -e -l IU -1 unmapped_1.fastq -2 unmapped_2.fastq -p {} -o m_".format(mince,config['p']))
            os.chdir(currdir)
            shell("cp {}/aux/*.lz {}/".format(output_path,output_path))
            #shell("rm -r {}/aux".format(output_path))
            shell("rm -r {}/logs".format(output_path))
            shell("rm {}/cmd_info.json".format(output_path))
        else:
            mate=config['r']
            if(config['quality'] == "1"):
                shell("{} quant -i {} -l U -r <(gunzip -c {}) -p {} -o {} --quality".format(quark,config['index'],mate,config['p'],output_path))
            else:
                shell("{} quant -i {} -l U -r <(gunzip -c {}) -p {} -o {} ".format(quark,config['index'],mate,config['p'],output_path))
            os.chdir(os.path.join(output_path,'aux'))
            shell("{} -e -l U -r unmapped.fastq -p {} -o m_".format(mince,config['p']))
            os.chdir(currdir)
            shell("cp {}/aux/*.lz {}/".format(output_path,output_path))
            shell("rm -r {}/aux".format(output_path))
            shell("rm -r {}/logs".format(output_path))
            shell("rm {}/cmd_info.json".format(output_path))

rule decode:
    run:
        input_path=config['in']
        output_path=config['out']
        if(not os.path.isdir(output_path)):
            shell("mkdir -p {}".format(output_path))
        shell("plzip -k -d {}/islands.txt.lz".format(input_path))
        os.chdir(input_path)
        shell("{} -d -i m_ -o um_".format(mince))
        os.chdir(currdir)
        if(config['lib'] == "paired"):
            if(config['quality'] == "1"):
                shell("plzip -k -d {}/quality_1.quark.lz".format(input_path))
                shell("plzip -k -d {}/quality_2.quark.lz".format(input_path))
                shell("{} {} {} P Q".format(decoder, input_path, output_path))
            else:
                shell("{} {} {} P N".format(decoder, input_path, output_path))
        else:
            if(config['quality'] == "1"):
                shell("plzip -k -d {}/quality.quark.lz".format(input_path))
                shell("{} {} {} S Q".format(decoder, input_path, output_path))
            else:
                shell("{} {} {} S N".format(decoder, input_path, output_path))
        shell("rm {}/um_*".format(input_path))
        shell("rm {}/islands.txt".format(input_path))