Mercurial > repos > dereeper > pangenome_explorer
comparison Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG @ 3:e42d30da7a74 draft
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author | dereeper |
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date | Thu, 30 May 2024 11:52:25 +0000 |
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2:97e4e3e818b6 | 3:e42d30da7a74 |
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1 import glob | |
2 import os | |
3 import shutil | |
4 | |
5 import yaml | |
6 configfile: "config.yaml" | |
7 | |
8 | |
9 SAMPLES = [] | |
10 with open("config.yaml", "r") as yaml_file: | |
11 genome_data = yaml.safe_load(yaml_file) | |
12 if "ids" in genome_data.keys(): | |
13 for id in genome_data["ids"]: | |
14 SAMPLES.append(id) | |
15 if "input_genbanks" in genome_data.keys(): | |
16 for gb_path in genome_data["input_genbanks"]: | |
17 cmd = "grep 'ACCESSION' "+gb_path | |
18 returned_value = subprocess.getoutput(cmd) | |
19 words = returned_value.split() | |
20 SAMPLES.append(words[1]) | |
21 | |
22 | |
23 | |
24 rule final: | |
25 input: | |
26 "outputs/GCskew.txt", | |
27 "outputs/cactus_outdir/output_cactus.sv.gfa.gz", | |
28 "outputs/cactus_outdir/full.gfa", | |
29 "outputs/cactus_outdir/full.gfa.png", | |
30 "outputs/cactus_outdir/output_cactus.sv.gfa.pangenome.fasta", | |
31 "outputs/pav_matrix.tsv", | |
32 "outputs/heatmap.svg.gz", | |
33 "outputs/cog_output.txt", | |
34 "outputs/rarefaction_curves.txt" | |
35 | |
36 | |
37 rule ncbi_datasets: | |
38 input: | |
39 "config.yaml" | |
40 output: | |
41 expand("outputs/genomes/{sample}.fasta", sample=SAMPLES), | |
42 expand("outputs/genomes/{sample}.gb", sample=SAMPLES), | |
43 expand("outputs/genomes/{sample}.prt", sample=SAMPLES), | |
44 expand("outputs/genomes/{sample}.nuc", sample=SAMPLES), | |
45 genomes="outputs/genomes/genomes.txt", | |
46 strains="outputs/genomes/strains.txt" | |
47 shell: | |
48 """ | |
49 perl $PANEX_PATH/Perl/get_data.pl {input} outputs/genomes | |
50 """ | |
51 | |
52 | |
53 rule gcskew: | |
54 input: | |
55 "outputs/genomes/{sample}.fasta" | |
56 output: | |
57 "outputs/genomes/{sample}.fasta.gcskew.txt" | |
58 shell: | |
59 """ | |
60 python3 $PANEX_PATH/SkewIT/src/gcskew.py -i {input} -o {input}.gcskew.txt -k 1000 -w 1000 | |
61 """ | |
62 | |
63 rule concat_gcskew: | |
64 input: | |
65 expand("outputs/genomes/{sample}.fasta.gcskew.txt", sample=SAMPLES) | |
66 output: | |
67 out2="outputs/GCskew.txt" | |
68 shell: | |
69 """ | |
70 cat {input} >>{output.out2} | |
71 """ | |
72 | |
73 rule genbank2gff3: | |
74 input: | |
75 "outputs/genomes/{sample}.gb" | |
76 output: | |
77 gff1="outputs/genomes/{sample}.gb.gff", | |
78 shell: | |
79 """ | |
80 perl $PANEX_PATH/Perl/bp_genbank2gff3.pl -o outputs/genomes {input} | |
81 """ | |
82 | |
83 rule cactus: | |
84 input: | |
85 expand("outputs/genomes/{sample}.fasta", sample=SAMPLES), | |
86 expand("outputs/genomes/{sample}.gb.gff", sample=SAMPLES), | |
87 params: | |
88 reference=SAMPLES[0] | |
89 output: | |
90 gfasv="outputs/cactus_outdir/output_cactus.sv.gfa.gz", | |
91 gfafull="outputs/cactus_outdir/full.gfa" | |
92 shell: | |
93 """ | |
94 mkdir outputs/cactus_work | |
95 cactus-pangenome outputs/jobstore outputs/genomes/seqfile --outDir outputs/cactus_outdir --outName output_cactus --reference {params.reference} --workDir outputs/cactus_work --vcf --mapCores 12 --gfa clip full --viz | |
96 zcat outputs/cactus_outdir/output_cactus.full.gfa.gz >{output.gfafull} | |
97 """ | |
98 | |
99 | |
100 | |
101 | |
102 rule gfatools: | |
103 input: | |
104 "outputs/cactus_outdir/output_cactus.sv.gfa.gz" | |
105 output: | |
106 "outputs/cactus_outdir/output_cactus.sv.gfa.pangenome.fasta" | |
107 shell: | |
108 """ | |
109 gfatools gfa2fa -s {input} > {output} | |
110 """ | |
111 | |
112 rule minigraph: | |
113 input: | |
114 cds_fasta="outputs/genomes/{sample}.nuc", | |
115 gfa="outputs/cactus_outdir/output_cactus.sv.gfa.gz", | |
116 output: | |
117 gaf="outputs/genomes/{sample}.nuc.pangenome.gaf", | |
118 shell: | |
119 """ | |
120 minigraph -x lr {input.gfa} {input.cds_fasta} > {output.gaf} | |
121 """ | |
122 | |
123 rule odgi: | |
124 input: | |
125 "outputs/cactus_outdir/full.gfa" | |
126 output: | |
127 og="outputs/cactus_outdir/full.gfa.og", | |
128 png="outputs/cactus_outdir/full.gfa.png", | |
129 shell: | |
130 """ | |
131 odgi build -g {input} -o {output.og} | |
132 odgi viz -i {output.og} -o {output.png} | |
133 """ | |
134 | |
135 rule gaf2bed: | |
136 input: | |
137 "outputs/genomes/{sample}.nuc.pangenome.gaf" | |
138 output: | |
139 "outputs/genomes/{sample}.nuc.pangenome.gaf.bed", | |
140 shell: | |
141 """ | |
142 awk '{{print $6"\\t"$8"\\t"$9"\\t"$1}}' {input} >{output} | |
143 """ | |
144 | |
145 rule bedtools_intersect: | |
146 input: | |
147 strains="outputs/genomes/strains.txt", | |
148 bedfiles=expand("outputs/genomes/{sample}.nuc.pangenome.gaf.bed", sample=SAMPLES) | |
149 output: | |
150 "outputs/pav_matrix.tsv", | |
151 shell: | |
152 """ | |
153 perl $PANEX_PATH/Perl/GeneratePAVfromBed.pl {input.strains} outputs/genomes {output} | |
154 """ | |
155 | |
156 | |
157 rule cog: | |
158 input: | |
159 pav="outputs/pav_matrix.tsv" | |
160 output: | |
161 cog="outputs/cog_output.txt", | |
162 cogstat="outputs/cog_stats.txt", | |
163 cogstat2="outputs/cog_stats2.txt", | |
164 cogofclusters="outputs/cog_of_clusters.txt" | |
165 shell: | |
166 """ | |
167 perl $PANEX_PATH/Perl/GetCogOfCluster.pl {input} outputs/genomes {output.cog} {output.cogstat} {output.cogstat2} {output.cogofclusters} outputs/genomes/strains.txt | |
168 """ | |
169 | |
170 rule heatmap_upset: | |
171 input: | |
172 pav="outputs/pav_matrix.tsv" | |
173 output: | |
174 heatmap="outputs/heatmap.svg.gz", | |
175 html="outputs/heatmap.svg.heatmap_plotly.html", | |
176 upsetr="outputs/upsetr.svg", | |
177 binpav="outputs/heatmap.svg.pangenes_01matrix.txt" | |
178 shell: | |
179 """ | |
180 perl $PANEX_PATH/Perl/GenerateHeatmapFromPAV.pl {input.pav} outputs/heatmap.svg | |
181 mv outputs/heatmap.svg.upsetr.svg {output.upsetr} | |
182 """ | |
183 | |
184 rule micropan: | |
185 input: | |
186 binpav="outputs/heatmap.svg.pangenes_01matrix.txt" | |
187 output: | |
188 txt="outputs/rarefaction_curves.txt", | |
189 pdf="outputs/rarefaction_curves.pdf", | |
190 svg="outputs/rarefaction_curves.svg", | |
191 heaps="outputs/heaps.tsv" | |
192 shell: | |
193 """ | |
194 Rscript $PANEX_PATH/R/micropan_rarefaction.R -f {input.binpav} -p {output.pdf} -a {output.heaps} -o {output.txt} | |
195 pdf2svg {output.pdf} {output.svg} | |
196 """ |