mashmap into pipeline

marbl · May 31, 2024 · 2aba44e · 2aba44e
1 parent f6da468
commit 2aba44e
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/src/Snakefiles/8-hicPipeline.sm b/src/Snakefiles/8-hicPipeline.sm
@@ -78,9 +78,11 @@ chmod +x ./prepare_hic.sh
 
 rule runMashMap:
     input:
-        unitigs_hpc = '8-hicPipeline/unitigs.hpc.fasta'
+        unitigs_hpc = '8-hicPipeline/unitigs.hpc.fasta',
+        unitigs = '8-hicPipeline/unitigs.fasta'
     output:
-        unitigs_matches = '8-hicPipeline/unitigs.matches'
+        unitigs_matches = '8-hicPipeline/unitigs.matches',
+        unitigs_nohpc50 = '8-hicPipeline/unitigs_nonhpc50.mashmap'
     log:
         err    = '8-hicPipeline/run_mashmap.err'
     params:
@@ -104,6 +106,8 @@ set -e
 echo "---Running MashMap"
 {params.MASHMAP} -r ../{input.unitigs_hpc} -q ../{input.unitigs_hpc} -t {threads} -f none --pi {params.MASHMAP_DIV} -s 10000 -o mashmap.out
 cat mashmap.out |awk '{{if (\$4-\$3 > 100000 && \$1 != \$6) print \$1"\\t"\$6"\\t"\$4-\$3}}'|sort |uniq > ../{output.unitigs_matches}
+{params.MASHMAP} -r ../{input.unitigs_hpc} -q ../{input.unitigs_hpc} -t {threads} -f none --pi {params.MASHMAP_DIV} -s 10000 -o unitigs_nonhpc.mashmap 
+awk '$11 >= 50000' unitigs_nonhpc.mashmap > ../{output.unitigs_nohpc50}
 EOF
 
 chmod +x ./run_mashmap.sh

diff --git a/src/scripts/rdna_scaff.py b/src/scripts/rdna_scaff.py
@@ -59,6 +59,6 @@
 rukki_paths = sf.read_rukki_paths(old_rukki_tsv_file, G)
 gf.load_indirect_graph(gfa_file, indirectG)
 #sf.try_to_scaff(rukki_paths, telomere_locations_file, os.path.join(hicrun_dir, "hic_mapping.byread.output"), os.path.join(hicrun_dir, "unitigs.matches"), G, indirectG, uncompressed_nodes)
-sg = scaffold_graph.ScaffoldGraph(rukki_paths, telomere_locations_file, os.path.join(hicrun_dir, "hic_mapping.byread.output"), os.path.join(hicrun_dir, "mashmap_nonhpc50.out"), G, uncompressed_nodes, logger) 
+sg = scaffold_graph.ScaffoldGraph(rukki_paths, telomere_locations_file, os.path.join(hicrun_dir, "hic_mapping.byread.output"), os.path.join(hicrun_dir, "unitigs_nonhpc50.mashmap"), G, uncompressed_nodes, logger) 
 res = sg.generateScaffolds()