Mercurial > repos > dereeper > pangenome_explorer
comparison Snakemake_files/Snakefile_wget_PGAP_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 rule final: | |
24 input: | |
25 "outputs/pav_matrix.csv", | |
26 "outputs/GCskew.txt", | |
27 "outputs/pav_matrix.tsv", | |
28 "outputs/heatmap.svg", | |
29 "outputs/cog_output.txt" | |
30 | |
31 | |
32 rule ncbi_datasets: | |
33 input: | |
34 "config.yaml" | |
35 output: | |
36 expand("outputs/genomes/{sample}.fasta", sample=SAMPLES), | |
37 expand("outputs/genomes/{sample}.gb", sample=SAMPLES), | |
38 expand("outputs/genomes/{sample}.pep", sample=SAMPLES), | |
39 genomes="outputs/genomes/genomes.txt" | |
40 shell: | |
41 """ | |
42 perl $PANEX_PATH/Perl/get_data.pl {input} outputs/genomes | |
43 """ | |
44 | |
45 | |
46 rule gcskew: | |
47 input: | |
48 "outputs/genomes/{sample}.fasta" | |
49 output: | |
50 "outputs/genomes/{sample}.fasta.gcskew.txt" | |
51 shell: | |
52 """ | |
53 python3 $PANEX_PATH/SkewIT/src/gcskew.py -i {input} -o {input}.gcskew.txt -k 1000 -w 1000 | |
54 """ | |
55 | |
56 rule concat_gcskew: | |
57 input: | |
58 expand("outputs/genomes/{sample}.fasta.gcskew.txt", sample=SAMPLES) | |
59 output: | |
60 out2="outputs/GCskew.txt" | |
61 shell: | |
62 """ | |
63 cat {input} >>{output.out2} | |
64 """ | |
65 | |
66 rule genbank2gff3: | |
67 input: | |
68 "outputs/genomes/{sample}.gb" | |
69 output: | |
70 gff1="outputs/genomes/{sample}.gb.gff", | |
71 gff2="outputs/genomes/{sample}.gb.rmdup.gff" | |
72 shell: | |
73 """ | |
74 perl $PANEX_PATH/Perl/bp_genbank2gff3.pl -o outputs/genomes {input} | |
75 perl $PANEX_PATH/Perl/remove_duplicates_in_gff.pl {output.gff1} {output.gff2} | |
76 """ | |
77 | |
78 | |
79 rule pgap: | |
80 input: | |
81 expand("outputs/genomes/{sample}.pep", sample=SAMPLES) | |
82 params: | |
83 identity=80 | |
84 output: | |
85 pav="outputs/pav_matrix.csv", | |
86 newick="outputs/accessory_binary_genes.fa.newick" | |
87 shell: | |
88 """ | |
89 listforpgap=$(cat genbank_ids | tr '\n' '+') | |
90 alias consense='/usr/bin/phylip consense';alias dnaml='phylip /usr/bin/dnaml' | |
91 cp -rf /usr/local/bin/PGAP-1.2.1/Blast_Filter.pl . | |
92 perl /usr/local/bin/PGAP-1.2.1/PGAP.pl --strains $listforpgap --cluster --evolution --method GF --input outputs/genomes --output outputs/pgap_outdir | |
93 cp -rf outputs/pgap_outdir/1.Orthologs_Cluster.txt {output.pav} | |
94 cp -rf outputs/pgap_outdir/4.PanBased.Neighbor-joining.tree {output.newick} | |
95 """ | |
96 | |
97 rule convert_matrix: | |
98 input: | |
99 pav="outputs/pav_matrix.csv" | |
100 output: | |
101 "outputs/pav_matrix.tsv" | |
102 shell: | |
103 """ | |
104 perl $PANEX_PATH/Perl/ConvertPGAPMatrix.pl outputs/genomes outputs/pav_matrix.csv outputs/pav_matrix.tsv outputs/genomes/strains.txt | |
105 """ | |
106 | |
107 rule heatmap_upset: | |
108 input: | |
109 pav="outputs/pav_matrix.tsv" | |
110 output: | |
111 heatmap="outputs/heatmap.svg", | |
112 upsetr="outputs/upsetr.svg" | |
113 shell: | |
114 """ | |
115 perl $PANEX_PATH/Perl/GenerateHeatmapFromPAV.pl {input.pav} {output.heatmap} | |
116 mv {output.heatmap}.upsetr.svg {output.upsetr} | |
117 """ | |
118 | |
119 rule cog: | |
120 input: | |
121 pav="outputs/pav_matrix.tsv" | |
122 output: | |
123 cog="outputs/cog_output.txt", | |
124 cogstat="outputs/cog_stats.txt", | |
125 cogstat2="outputs/cog_stats2.txt", | |
126 cogofclusters="outputs/cog_of_clusters.txt" | |
127 shell: | |
128 """ | |
129 perl $PANEX_PATH/Perl/GetCogOfCluster.pl {input} outputs/genomes {output.cog} {output.cogstat} {output.cogstat2} {output.cogofclusters} outputs/genomes/strains.txt | |
130 """ | |
131 |