Mercurial > repos > dereeper > pangenome_explorer
comparison Snakemake_files/Snakefile_wget_panacota_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 name = words[1] | |
21 #words = returned_value.split() | |
22 #SAMPLES.append(words[1]) | |
23 words = gb_path.split("/") | |
24 genbank_file_name = words[-1] | |
25 x = genbank_file_name.replace(".", "_") | |
26 cmd = "sed -i 's/ACCESSION "+name+"/ACCESSION "+x+"/g' "+gb_path | |
27 subprocess.getoutput(cmd) | |
28 | |
29 cmd_locus = "grep 'LOCUS' "+gb_path | |
30 returned_value = subprocess.getoutput(cmd_locus) | |
31 words_locus = returned_value.split() | |
32 name_locus = words_locus[1] | |
33 cmd = "sed -i 's/LOCUS "+name_locus+"/LOCUS "+x+"/' "+gb_path | |
34 subprocess.getoutput(cmd) | |
35 | |
36 cmd = "grep 'ACCESSION' "+gb_path | |
37 returned_value = subprocess.getoutput(cmd) | |
38 words = returned_value.split() | |
39 SAMPLES.append(words[1]) | |
40 | |
41 | |
42 rule final: | |
43 input: | |
44 "outputs/GCskew.txt", | |
45 "outputs/pav_matrix.tsv", | |
46 "outputs/heatmap.svg.gz", | |
47 "outputs/cog_output.txt", | |
48 "outputs/fastani.out", | |
49 "outputs/rarefaction_curves.txt" | |
50 | |
51 | |
52 rule ncbi_datasets: | |
53 input: | |
54 "config.yaml" | |
55 output: | |
56 expand("outputs/genomes/{sample}.fasta", sample=SAMPLES), | |
57 expand("outputs/genomes/{sample}.gb", sample=SAMPLES), | |
58 expand("outputs/genomes/{sample}.prt", sample=SAMPLES), | |
59 genomes="outputs/genomes/genomes.txt" | |
60 shell: | |
61 """ | |
62 perl $PANEX_PATH/Perl/get_data.pl {input} outputs/genomes | |
63 """ | |
64 | |
65 | |
66 rule gcskew: | |
67 input: | |
68 "outputs/genomes/{sample}.fasta" | |
69 output: | |
70 "outputs/genomes/{sample}.fasta.gcskew.txt" | |
71 shell: | |
72 """ | |
73 python3 $PANEX_PATH/SkewIT/src/gcskew.py -i {input} -o {input}.gcskew.txt -k 1000 -w 1000 | |
74 """ | |
75 | |
76 rule concat_gcskew: | |
77 input: | |
78 expand("outputs/genomes/{sample}.fasta.gcskew.txt", sample=SAMPLES) | |
79 output: | |
80 out2="outputs/GCskew.txt" | |
81 shell: | |
82 """ | |
83 cat {input} >>{output.out2} | |
84 """ | |
85 | |
86 rule genbank2gff3: | |
87 input: | |
88 "outputs/genomes/{sample}.gb" | |
89 output: | |
90 gff1="outputs/genomes/{sample}.gb.gff", | |
91 gff2="outputs/genomes/{sample}.gb.rmdup.gff" | |
92 shell: | |
93 """ | |
94 perl $PANEX_PATH/Perl/bp_genbank2gff3.pl -o outputs/genomes {input} | |
95 perl $PANEX_PATH/Perl/remove_duplicates_in_gff.pl {output.gff1} {output.gff2} | |
96 """ | |
97 | |
98 rule panacota: | |
99 input: | |
100 expand("outputs/genomes/{sample}.prt", sample=SAMPLES), | |
101 expand("outputs/genomes/{sample}.gb.gff", sample=SAMPLES) | |
102 output: | |
103 pav="outputs/panacota/PanGenome-mydataset.All.prt.lst" | |
104 params: | |
105 identity=80 | |
106 shell: | |
107 """ | |
108 cat outputs/genomes/*prt >outputs/genomes/mydataset.All.prt | |
109 PanACoTA pangenome -i 0.{params.identity} -l outputs/genomes/mydataset.All.prt -n mydataset -d outputs/genomes -o outputs/panacota | |
110 mv outputs/panacota/PanGenome-mydataset.All.prt-clust-*-mode1.lst {output} | |
111 """ | |
112 | |
113 rule convert_matrix: | |
114 input: | |
115 pav="outputs/panacota/PanGenome-mydataset.All.prt.lst" | |
116 output: | |
117 "outputs/pav_matrix.tsv" | |
118 shell: | |
119 """ | |
120 perl $PANEX_PATH/Perl/ConvertPanacotaMatrix.pl outputs/genomes {input} {output} outputs/genomes/strains.txt | |
121 """ | |
122 | |
123 | |
124 rule cog: | |
125 input: | |
126 pav="outputs/pav_matrix.tsv" | |
127 output: | |
128 cog="outputs/cog_output.txt", | |
129 cogstat="outputs/cog_stats.txt", | |
130 cogstat2="outputs/cog_stats2.txt", | |
131 cogofclusters="outputs/cog_of_clusters.txt" | |
132 shell: | |
133 """ | |
134 perl $PANEX_PATH/Perl/GetCogOfCluster.pl {input} outputs/genomes {output.cog} {output.cogstat} {output.cogstat2} {output.cogofclusters} outputs/genomes/strains.txt | |
135 """ | |
136 | |
137 rule heatmap_upset: | |
138 input: | |
139 pav="outputs/pav_matrix.tsv" | |
140 output: | |
141 heatmap="outputs/heatmap.svg.gz", | |
142 html="outputs/heatmap.svg.heatmap_plotly.html", | |
143 upsetr="outputs/upsetr.svg", | |
144 binpav="outputs/heatmap.svg.pangenes_01matrix.txt" | |
145 shell: | |
146 """ | |
147 perl $PANEX_PATH/Perl/GenerateHeatmapFromPAV.pl {input.pav} outputs/heatmap.svg | |
148 mv outputs/heatmap.svg.upsetr.svg {output.upsetr} | |
149 """ | |
150 | |
151 rule micropan: | |
152 input: | |
153 binpav="outputs/heatmap.svg.pangenes_01matrix.txt" | |
154 output: | |
155 txt="outputs/rarefaction_curves.txt", | |
156 pdf="outputs/rarefaction_curves.pdf", | |
157 svg="outputs/rarefaction_curves.svg", | |
158 heaps="outputs/heaps.tsv" | |
159 shell: | |
160 """ | |
161 Rscript $PANEX_PATH/R/micropan_rarefaction.R -f {input.binpav} -p {output.pdf} -a {output.heaps} -o {output.txt} | |
162 pdf2svg {output.pdf} {output.svg} | |
163 """ | |
164 | |
165 rule fastani: | |
166 input: | |
167 "outputs/genomes/genomes.txt" | |
168 output: | |
169 out="outputs/fastani.out", | |
170 matrix="outputs/fastani.out.matrix", | |
171 completematrix="outputs/fastani.out.matrix.complete", | |
172 pdf="outputs/fastani.out.pdf", | |
173 svg="outputs/fastani.out.svg" | |
174 shell: | |
175 """ | |
176 fastANI --rl {input} --ql {input} -o {output.out} -t 4 --matrix | |
177 perl $PANEX_PATH/Perl/convertANI.pl {output.matrix} outputs/genomes/genomes2.txt >{output.completematrix} | |
178 Rscript $PANEX_PATH/R/heatmap_ani.R -f {output.completematrix} -o {output.pdf} | |
179 pdf2svg {output.pdf} {output.svg} | |
180 """ |