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rule all:
input:
"graph_plus.gfa"
rule compact_paths:
input:
"phased_alleles_read_set_id_1.txt"
output:
temp("compacted_facts_int.txt")
shell:
"python3 /Users/ppeterlo/projets/phasing_disco/create_graph_fact/k3000/K3000.py {input} > {output}"
rule GFA_construction:
input:
"compacted_facts_int.txt"
output:
temp("compacted_facts.gfa")
shell:
"python3 /Users/ppeterlo/projets/phasing_disco/create_graph_fact/k3000/K3000_facts_to_gfa.py {input} > {output}"
rule enhance_graph:
input:
"phased_alleles_read_set_id_1.txt",
"compacted_facts.gfa"
output:
temp("graph.gfa")
shell:
"python3 /Users/ppeterlo/projets/phasing_disco/create_graph_fact/k3000/enhance_gfa.py compacted_facts.gfa {input} > {output}"
rule detect_snp_succesion:
input:
"graph.gfa",
"discoRad_k_31_c_3_D_0_P_5_m_5_coherent_raw.fa"
# "discoRes_k_31_c_2_D_0_P_3_b_2_coherent.fa"
output:
"graph_plus.gfa"
shell:
"python3 /Users/ppeterlo/projets/phasing_disco/create_graph_fact/k3000/find_unitig_connected_pairs_of_facts.py {input} > {output}"
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