Commit fd4f4a4d by MARIJON Pierre

generate some different gfa with or not containment internal match

parent 3731ead1
......@@ -16,7 +16,8 @@ canu_paf = os.path.join(in_path, "canu_paf")
canu_gfa = canu_paf + ".gfa"
canu_paf_gfa_rename = canu_paf + "_rename.gfa"
canu_gfa_rename = canu_bog + "_rename.gfa"
canu_paf_gfa_containment_rename = canu_paf + "_rename.containment.gfa"
canu_paf_gfa_containment_rename = canu_paf + ".containment.gfa"
canu_paf_gfa_containment_internal_rename = canu_paf + ".containment.internal.gfa"
canu_contig_report = os.path.join(in_path, "contig_report")
......
......@@ -77,7 +77,7 @@ rule search_path:
canu2realname = canu_bog_readname,
read2contig = canu_read2tig,
contig2color = canu_contig_on_canu_paf + '.legend.csv',
canu_paf = canu_paf_gfa_containment_rename
canu_paf = canu_paf_gfa_containment_internal_rename
output:
result = "{prefix}_{name}_extremity_result.csv"
threads: 99
......
......@@ -37,8 +37,8 @@ rule search_path:
canu2realname = canu_bog_readname,
read2contig = canu_read2tig,
contig2color = canu_contig_on_minimap_paf + '.legend.csv',
canu_paf = canu_paf_gfa_rename,
minimap_paf = minimap_gfa_containment
canu_paf = canu_paf_gfa_containment_internal_rename,
minimap_paf = minimap_gfa_containment_internal
output:
result = "{prefix}_{name}_extremity_result.csv"
threads: 99
......
......@@ -2,6 +2,7 @@
minimap_paf = os.path.splitext(os.path.abspath(config["minimap_path"]))[0]
minimap_gfa_rename = minimap_paf + "_rename.gfa"
minimap_gfa_containment = minimap_paf + ".containment.gfa"
minimap_gfa_containment_internal = minimap_paf + ".containment.internal.gfa"
minimap_search_path_out = os.path.join(out_path, "find_path")
minimap_search_path_prefix = os.path.join(canu_search_path_out, "path_minimap")
......@@ -8,7 +8,7 @@ rule paf2gfa:
gfa="{filename}.gfa"
shell:
config['paf2gfa']['bin'] + " {input.paf} {output.gfa} --remove-all-containement"
config['paf2gfa']['bin'] + " {input.paf} {output.gfa} --remove-all-containement --remove-all-internal"
rule paf2gfa_containment:
input:
......@@ -20,6 +20,16 @@ rule paf2gfa_containment:
shell:
config['paf2gfa']['bin'] + " {input.paf} {output.gfa}"
rule paf2gfa_containment_internal:
input:
paf="{filename}.paf"
output:
gfa="{filename}.containment.internal.gfa"
shell:
config['paf2gfa']['bin'] + " {input.paf} {output.gfa}"
ruleorder: bandage_colo > bandage
......@@ -52,6 +62,6 @@ rule generate_search_path:
search = "{prefix}_{name}_extremity_search.csv"
run:
if wildcards.name == "canu":
canu_utils.generate_output_extract_graph(canu_read2tig, canu_bog_readname, config['canu']['ov_dump_bin'], canu_ovl_store, canu_gkp_store, canu_search_path_prefix)
canu_utils.generate_output_extract_graph(canu_read2tig, canu_bog_readname, canu_search_path_prefix)
else:
canu_utils.generate_output_extract_graph(canu_read2tig, canu_bog_readname, config['canu']['ov_dump_bin'], canu_ovl_store, canu_gkp_store, minimap_search_path_prefix)
canu_utils.generate_output_extract_graph(canu_read2tig, canu_bog_readname, minimap_search_path_prefix)
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