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"""
This Snakefile runs the scripts to recreate the plots in
Schultz et al 2019 (in prep).
"""
import multiprocessing
corecount = multiprocessing.cpu_count()
rule all:
"""
The final files to be output at the end of this script.
"""
input:
#"figures/redwood/redwood.png",
#"figures/dirichlet_plot/dirichlet_violins.png",
#"figures/heterogeneity_plot/hetero.pdf",
#"figures/heterogeneity_plot/hetero.csv",
#"figures/synteny_plot/synteny_optimum.pdf",
#"figures/nuc_div/nucdiv.csv",
#"figures/nuc_div/nuc_div_boxplot.png",
#"figures/nuc_div/nuc_div_picheck.png",
"figures/nuc_div_ML/nucdiv.csv",
"figures/nuc_div_ML/nuc_div_boxplot.png",
"figures/nuc_div_ML/nuc_div_picheck.png",
#"figures/codonusage/codonplot.pdf",
#non-beroe
"figures/dirichlet_plot_non_beroe/daphnia/daphnia_violins.png",
"figures/dirichlet_plot_non_beroe/drosophila/drosophila_violins.png",
"figures/dirichlet_plot_non_beroe/human/human_violins.png",
"figures/dirichlet_plot_non_beroe/strongylocentrotus/strongylocentrotus_violins.png",
"figures/dirichlet_plot_non_beroe/chlamydomonas/chlamydomonas_violins.png",
#non-beroe nucdiv
"figures/nuc_div_non_beroe/daphnia/daphnia_nuc_div_boxplot.png",
"figures/nuc_div_non_beroe/drosophila/drosophila_nuc_div_boxplot.png",
"figures/nuc_div_non_beroe/human/human_nuc_div_boxplot.png",
"figures/nuc_div_non_beroe/strongylocentrotus/strongylocentrotus_nuc_div_boxplot.png",
"figures/nuc_div_non_beroe/chlamydomonas/chlamydomonas_nuc_div_boxplot.png",
"figures/nuc_div_non_beroe_ML/daphnia/daphnia_nuc_div_boxplot.png",
"figures/nuc_div_non_beroe_ML/drosophila/drosophila_nuc_div_boxplot.png",
"figures/nuc_div_non_beroe_ML/human/human_nuc_div_boxplot.png",
"figures/nuc_div_non_beroe_ML/strongylocentrotus/strongylocentrotus_nuc_div_boxplot.png",
"figures/nuc_div_non_beroe_ML/chlamydomonas/chlamydomonas_nuc_div_boxplot.png",
rule plot_synteny:
"""Generates the synteny plot of all of the ctenophore mitochondrial genomes.
"""
input:
twelveS = "fasta_sequences/alignments/prot_cteno_aln/12S.fasta",
sixteenS = "fasta_sequences/alignments/prot_cteno_aln/16S.fasta",
COX1 = "fasta_sequences/alignments/prot_cteno_aln/COX1.fasta",
COX2 = "fasta_sequences/alignments/prot_cteno_aln/COX2.fasta",
COX3 = "fasta_sequences/alignments/prot_cteno_aln/COX3.fasta",
CYTB = "fasta_sequences/alignments/prot_cteno_aln/CYTB.fasta",
ND1 = "fasta_sequences/alignments/prot_cteno_aln/ND1.fasta",
ND2 = "fasta_sequences/alignments/prot_cteno_aln/ND2.fasta",
ND3 = "fasta_sequences/alignments/prot_cteno_aln/ND3.fasta",
ND4 = "fasta_sequences/alignments/prot_cteno_aln/ND4.fasta",
ND4L = "fasta_sequences/alignments/prot_cteno_aln/ND4L.fasta",
ND5 = "fasta_sequences/alignments/prot_cteno_aln/ND5.fasta",
ND6 = "fasta_sequences/alignments/prot_cteno_aln/ND6.fasta",
Cloyai = "gff_files/LN898113.gff",
Bforsk = "gff_files/Bf201706.gff",
Pbache = "gff_files/JN392469.gff",
Mleidy = "gff_files/NC016117.gff",
Cyulia = "gff_files/LN898114.gff",
Vmulti = "gff_files/LN898115.gff",
output:
optimum = "figures/synteny_plot/synteny_optimum.pdf"
params:
basename = "figures/synteny_plot/synteny_optimum",
alndir = "fasta_sequences/alignments/prot_cteno_aln/"
shell:
"""
pauvre synplot --aln_dir {params.alndir} \
--fileform pdf \
--gff_paths {input.Cloyai} {input.Bforsk} {input.Pbache} {input.Mleidy} {input.Cyulia} {input.Vmulti} \
--gff_labels "C. loyai" "B. forskalii" "P. bachei" "M. leidyi" "C. yulianicorum" "V. multiformis" \
--optimum_order --no_timestamp \
-o {params.basename}
"""
rule plot_redwood:
"""
Generates the redwood plot of the B. forskalii
mitogenome.
"""
input:
longreads = "figures/redwood/gd122_to_2013_doubled.bam",
RNA = "figures/redwood/R007mergeASgt140.sorted.bam",
gff = "gff_files/Bf201706.gff"
output:
pngout = "figures/redwood/redwood.png"
params:
basename = "figures/redwood/redwood"
shell:
"""
pauvre redwood -M {input.longreads} \
--doubled main -R {input.RNA} \
--gff {input.gff} \
--fileform png --sort ALNLEN \
--query 'ALNLEN >= 10000' 'MAPLEN < reflength' \
--dpi 600 --small_start inside \
--ticks 0 10 100 1000 \
-o {params.basename} --no_timestamp
"""
rule plot_codonusage:
"""
Generates the codon usage plot.
"""
input:
COX1 = "fasta_sequences/coding_seqs/COX1.fasta",
COX2 = "fasta_sequences/coding_seqs/COX2.fasta",
COX3 = "fasta_sequences/coding_seqs/COX3.fasta",
CYTB = "fasta_sequences/coding_seqs/CYTB.fasta",
ND1 = "fasta_sequences/coding_seqs/ND1.fasta",
ND2 = "fasta_sequences/coding_seqs/ND2.fasta",
ND3 = "fasta_sequences/coding_seqs/ND3.fasta",
ND4 = "fasta_sequences/coding_seqs/ND4.fasta",
ND4L = "fasta_sequences/coding_seqs/ND4L.fasta",
ND5 = "fasta_sequences/coding_seqs/ND5.fasta",
ND6 = "fasta_sequences/coding_seqs/ND6.fasta"
output:
cu = "figures/codonusage/codonplot.pdf"
params:
basename = "figures/codonusage/codonplot"
shell:
"""
cuttlery codonplot \
--coding_fasta_dir fasta_sequences/coding_seqs/ \
--fileform pdf \
--tt_code 4 \
-o {params.basename} \
--no_timestamp
"""
rule plot_nucdiv:
"""
Generates the nucleotide diversity plot.
"""
input:
COX1 = "fasta_sequences/coding_seqs/COX1.fasta",
COX2 = "fasta_sequences/coding_seqs/COX2.fasta",
COX3 = "fasta_sequences/coding_seqs/COX3.fasta",
CYTB = "fasta_sequences/coding_seqs/CYTB.fasta",
ND1 = "fasta_sequences/coding_seqs/ND1.fasta",
ND2 = "fasta_sequences/coding_seqs/ND2.fasta",
ND3 = "fasta_sequences/coding_seqs/ND3.fasta",
ND4 = "fasta_sequences/coding_seqs/ND4.fasta",
ND4L = "fasta_sequences/coding_seqs/ND4L.fasta",
ND5 = "fasta_sequences/coding_seqs/ND5.fasta",
ND6 = "fasta_sequences/coding_seqs/ND6.fasta"
output:
csv = "figures/nuc_div/nucdiv.csv",
bp = "figures/nuc_div/nuc_div_boxplot.png",
pc = "figures/nuc_div/nuc_div_picheck.png",
csv2 = "figures/nuc_div_ML/nucdiv.csv",
bp2 = "figures/nuc_div_ML/nuc_div_boxplot.png",
pc2 = "figures/nuc_div_ML/nuc_div_picheck.png"
params:
basename = "figures/nuc_div/nuc_div",
basename2 = "figures/nuc_div_ML/nuc_div",
threads:
corecount
shell:
"""
cuttlery piNpiSsim \
--tt_code 4 \
--numsims 1000 \
--fasta_dir fasta_sequences/coding_seqs/ fasta_sequences/test_seqs/ \
--results_file {output.csv} \
--method NG86 \
-@ {threads} \
-o {params.basename} \
--no_timestamp \
--fileform png pdf jpg
cuttlery piNpiSsim \
--tt_code {params.tt_code} \
--numsims 1000 \
--fasta_dir {params.coding_seqs} \
--results_file {output.csv} \
--method ML \
-@ {threads} \
-o {params.basename2} \
--no_timestamp \
--fileform png pdf jpg
"""
rule plot_nucdiv_human:
"""
Generates the nucleotide diversity plot.
"""
input:
COX1= "fasta_sequences/non-beroe/human/coding/COX1.fasta",
output:
csv = "figures/nuc_div_non_beroe/human/human_nucdiv.csv",
bp = "figures/nuc_div_non_beroe/human/human_nuc_div_boxplot.png",
pc = "figures/nuc_div_non_beroe/human/human_nuc_div_picheck.png",
csv2 = "figures/nuc_div_non_beroe_ML/human/human_nucdiv.csv",
bp2 = "figures/nuc_div_non_beroe_ML/human/human_nuc_div_boxplot.png",
pc2 = "figures/nuc_div_non_beroe_ML/human/human_nuc_div_picheck.png",
params:
coding_seqs = "fasta_sequences/non-beroe/human/coding/",
basename = "figures/nuc_div_non_beroe/human/human_nuc_div",
basename2 = "figures/nuc_div_non_beroe_ML/human/human_nuc_div",
tt_code = 2
threads:
corecount
shell:
"""
cuttlery piNpiSsim \
--tt_code {params.tt_code} \
--numsims 1000 \
--fasta_dir {params.coding_seqs} \
--results_file {output.csv} \
--method NG86 \
-@ {threads} \
-o {params.basename} \
--no_timestamp \
--fileform png pdf jpg
cuttlery piNpiSsim \
--tt_code {params.tt_code} \
--numsims 1000 \
--fasta_dir {params.coding_seqs} \
--results_file {output.csv} \
--method ML \
-@ {threads} \
-o {params.basename2} \
--no_timestamp \
--fileform png pdf jpg
"""
rule plot_nucdiv_chlamydomonas:
"""
Generates the nucleotide diversity plot.
"""
input:
COX1= "fasta_sequences/non-beroe/chlamydomonas/coding/COX1.fasta",
output:
csv = "figures/nuc_div_non_beroe/chlamydomonas/chlamydomonas_nucdiv.csv",
bp = "figures/nuc_div_non_beroe/chlamydomonas/chlamydomonas_nuc_div_boxplot.png",
pc = "figures/nuc_div_non_beroe/chlamydomonas/chlamydomonas_nuc_div_picheck.png",
csv2 = "figures/nuc_div_non_beroe_ML/chlamydomonas/chlamydomonas_nucdiv.csv",
bp2 = "figures/nuc_div_non_beroe_ML/chlamydomonas/chlamydomonas_nuc_div_boxplot.png",
pc2 = "figures/nuc_div_non_beroe_ML/chlamydomonas/chlamydomonas_nuc_div_picheck.png",
params:
coding_seqs = "fasta_sequences/non-beroe/chlamydomonas/coding/",
basename = "figures/nuc_div_non_beroe/chlamydomonas/chlamydomonas_nuc_div",
basename = "figures/nuc_div_non_beroe_ML/chlamydomonas/chlamydomonas_nuc_div",
tt_code = 1
threads:
corecount
shell:
"""
cuttlery piNpiSsim \
--tt_code {params.tt_code} \
--numsims 1000 \
--fasta_dir {params.coding_seqs} \
--results_file {output.csv} \
--method NG86 \
-@ {threads} \
-o {params.basename} \
--no_timestamp \
--fileform png pdf jpg
cuttlery piNpiSsim \
--tt_code {params.tt_code} \
--numsims 1000 \
--fasta_dir {params.coding_seqs} \
--results_file {output.csv} \
--method ML \
-@ {threads} \
-o {params.basename2} \
--no_timestamp \
--fileform png pdf jpg
"""
rule plot_nucdiv_drosophila:
"""
Generates the nucleotide diversity plot.
"""
input:
COX1= "fasta_sequences/non-beroe/drosophila/coding/COX1.fasta",
output:
csv = "figures/nuc_div_non_beroe/drosophila/drosophila_nucdiv.csv",
bp = "figures/nuc_div_non_beroe/drosophila/drosophila_nuc_div_boxplot.png",
pc = "figures/nuc_div_non_beroe/drosophila/drosophila_nuc_div_picheck.png",
csv2 = "figures/nuc_div_non_beroe_ML/drosophila/drosophila_nucdiv.csv",
bp2 = "figures/nuc_div_non_beroe_ML/drosophila/drosophila_nuc_div_boxplot.png",
pc2 = "figures/nuc_div_non_beroe_ML/drosophila/drosophila_nuc_div_picheck.png",
params:
coding_seqs = "fasta_sequences/non-beroe/drosophila/coding/",
basename = "figures/nuc_div_non_beroe/drosophila/drosophila_nuc_div",
basename = "figures/nuc_div_non_beroe_ML/drosophila/drosophila_nuc_div",
tt_code = 5
threads:
corecount
shell:
"""
cuttlery piNpiSsim \
--tt_code {params.tt_code} \
--numsims 1000 \
--fasta_dir {params.coding_seqs} \
--results_file {output.csv} \
--method NG86 \
-@ {threads} \
-o {params.basename} \
--no_timestamp \
--fileform png pdf jpg
cuttlery piNpiSsim \
--tt_code {params.tt_code} \
--numsims 1000 \
--fasta_dir {params.coding_seqs} \
--results_file {output.csv} \
--method ML \
-@ {threads} \
-o {params.basename2} \
--no_timestamp \
--fileform png pdf jpg
"""
rule plot_nucdiv_daphnia:
"""
Generates the nucleotide diversity plot.
"""
input:
COX1= "fasta_sequences/non-beroe/daphnia/coding/COX1.fasta",
output:
csv = "figures/nuc_div_non_beroe/daphnia/daphnia_nucdiv.csv",
bp = "figures/nuc_div_non_beroe/daphnia/daphnia_nuc_div_boxplot.png",
pc = "figures/nuc_div_non_beroe/daphnia/daphnia_nuc_div_picheck.png",
csv2 = "figures/nuc_div_non_beroe_ML/daphnia/daphnia_nucdiv.csv",
bp2 = "figures/nuc_div_non_beroe_ML/daphnia/daphnia_nuc_div_boxplot.png",
pc2 = "figures/nuc_div_non_beroe_ML/daphnia/daphnia_nuc_div_picheck.png",
params:
coding_seqs = "fasta_sequences/non-beroe/daphnia/coding/",
basename = "figures/nuc_div_non_beroe/daphnia/daphnia_nuc_div",
basename = "figures/nuc_div_non_beroe_ML/daphnia/daphnia_nuc_div",
tt_code = 5
threads:
corecount
shell:
"""
cuttlery piNpiSsim \
--tt_code {params.tt_code} \
--numsims 1000 \
--fasta_dir {params.coding_seqs} \
--results_file {output.csv} \
--method NG86 \
-@ {threads} \
-o {params.basename} \
--no_timestamp \
--fileform png pdf jpg
cuttlery piNpiSsim \
--tt_code {params.tt_code} \
--numsims 1000 \
--fasta_dir {params.coding_seqs} \
--results_file {output.csv} \
--method ML \
-@ {threads} \
-o {params.basename2} \
--no_timestamp \
--fileform png pdf jpg
"""
rule plot_nucdiv_strongylocentrotus:
"""
Generates the nucleotide diversity plot.
"""
input:
COX1= "fasta_sequences/non-beroe/strongylocentrotus/coding/COX1.fasta",
output:
csv = "figures/nuc_div_non_beroe/strongylocentrotus/strongylocentrotus_nucdiv.csv",
bp = "figures/nuc_div_non_beroe/strongylocentrotus/strongylocentrotus_nuc_div_boxplot.png",
pc = "figures/nuc_div_non_beroe/strongylocentrotus/strongylocentrotus_nuc_div_picheck.png",
csv2 = "figures/nuc_div_non_beroe_ML/strongylocentrotus/strongylocentrotus_nucdiv.csv",
bp2 = "figures/nuc_div_non_beroe_ML/strongylocentrotus/strongylocentrotus_nuc_div_boxplot.png",
pc2 = "figures/nuc_div_non_beroe_ML/strongylocentrotus/strongylocentrotus_nuc_div_picheck.png"
params:
coding_seqs = "fasta_sequences/non-beroe/strongylocentrotus/coding/",
basename = "figures/nuc_div_non_beroe/strongylocentrotus/strongylocentrotus_nuc_div",
basename2 = "figures/nuc_div_non_beroe_ML/strongylocentrotus/strongylocentrotus_nuc_div",
tt_code = 9
threads:
corecount
shell:
"""
cuttlery piNpiSsim \
--tt_code {params.tt_code} \
--numsims 1000 \
--fasta_dir {params.coding_seqs} \
--results_file {output.csv} \
--method NG86 \
-@ {threads} \
-o {params.basename} \
--no_timestamp \
--fileform png pdf jpg
cuttlery piNpiSsim \
--tt_code {params.tt_code} \
--numsims 1000 \
--fasta_dir {params.coding_seqs} \
--results_file {output.csv} \
--method ML \
-@ {threads} \
-o {params.basename2} \
--no_timestamp \
--fileform png pdf jpg
"""
rule plot_dirichlet:
"""
Generates the dirichlet LOO analysis plot for all genes.
"""
input:
COX1= "fasta_sequences/coding_seqs/COX1.fasta",
COX2= "fasta_sequences/coding_seqs/COX2.fasta",
COX3= "fasta_sequences/coding_seqs/COX3.fasta",
CYTB= "fasta_sequences/coding_seqs/CYTB.fasta",
ND1 = "fasta_sequences/coding_seqs/ND1.fasta",
ND2 = "fasta_sequences/coding_seqs/ND2.fasta",
ND3 = "fasta_sequences/coding_seqs/ND3.fasta",
ND4 = "fasta_sequences/coding_seqs/ND4.fasta",
ND4L = "fasta_sequences/coding_seqs/ND4L.fasta",
ND5 = "fasta_sequences/coding_seqs/ND5.fasta",
ND6 = "fasta_sequences/coding_seqs/ND6.fasta",
nc1 = "fasta_sequences/noncoding_seqs/COX1toND6.fasta",
nc2 = "fasta_sequences/noncoding_seqs/COX3toND3.fasta",
nc3 = "fasta_sequences/noncoding_seqs/URF1toURF2.fasta",
nc4 = "fasta_sequences/noncoding_seqs/ND2toCYTB.fasta",
nc5 = "fasta_sequences/noncoding_seqs/ND5toURF1.fasta",
nc6 = "fasta_sequences/noncoding_seqs/URF2toND2.fasta",
t1 = "fasta_sequences/test_seqs/URF1.fasta",
t2 = "fasta_sequences/test_seqs/URF2.fasta"
output:
fig = "figures/dirichlet_plot/dirichlet_violins.png",
results = "figures/dirichlet_plot/dirichlet_results.csv"
params:
obasename = "figures/dirichlet_plot/dirichlet"
shell:
"""
cuttlery dirichlet \
--coding_dir fasta_sequences/coding_seqs/ \
--noncoding_dir fasta_sequences/noncoding_seqs/ \
--test_dir fasta_sequences/test_seqs/ \
--numsims 5000 \
--results_file \
{output.results} \
-s meandec --fileform png pdf jpg \
--no_timestamp \
-o {params.obasename}
"""
rule plot_dirichlet_daphnia:
"""
Generates the dirichlet LOO analysis plot for daphnia genes.
"""
input:
COX1= "fasta_sequences/non-beroe/daphnia/coding/COX1.fasta",
output:
fig = "figures/dirichlet_plot_non_beroe/daphnia/daphnia_violins.png",
results = "figures/dirichlet_plot_non_beroe/daphnia/daphnia_results.csv"
params:
coding_dir = "fasta_sequences/non-beroe/daphnia/coding/",
noncoding_dir = "fasta_sequences/non-beroe/daphnia/noncoding/",
obasename = "figures/dirichlet_plot_non_beroe/daphnia/daphnia"
shell:
"""
cuttlery dirichlet \
--coding_dir {params.coding_dir} \
--noncoding_dir {params.noncoding_dir} \
--numsims 5000 \
--results_file {output.results} \
-s meandec --fileform png pdf jpg \
--no_timestamp \
-o {params.obasename}
"""
rule plot_dirichlet_strongylocentrotus:
"""
Generates the dirichlet LOO analysis plot for strongylocentrotus genes.
"""
input:
COX1= "fasta_sequences/non-beroe/strongylocentrotus/coding/COX1.fasta",
output:
fig = "figures/dirichlet_plot_non_beroe/strongylocentrotus/strongylocentrotus_violins.png",
results = "figures/dirichlet_plot_non_beroe/strongylocentrotus/strongylocentrotus_results.csv"
params:
coding_dir = "fasta_sequences/non-beroe/strongylocentrotus/coding/",
noncoding_dir = "fasta_sequences/non-beroe/strongylocentrotus/noncoding/",
obasename = "figures/dirichlet_plot_non_beroe/strongylocentrotus/strongylocentrotus"
shell:
"""
cuttlery dirichlet \
--coding_dir {params.coding_dir} \
--noncoding_dir {params.noncoding_dir} \
--numsims 5000 \
--results_file {output.results} \
-s meandec --fileform png pdf jpg \
--no_timestamp \
-o {params.obasename}
"""
rule plot_dirichlet_human:
"""
Generates the dirichlet LOO analysis plot for human genes.
"""
input:
COX1= "fasta_sequences/non-beroe/human/coding/COX1.fasta",
output:
fig = "figures/dirichlet_plot_non_beroe/human/human_violins.png",
results = "figures/dirichlet_plot_non_beroe/human/human_results.csv"
params:
coding_dir = "fasta_sequences/non-beroe/human/coding/",
noncoding_dir = "fasta_sequences/non-beroe/human/noncoding/",
obasename = "figures/dirichlet_plot_non_beroe/human/human"
shell:
"""
cuttlery dirichlet \
--coding_dir {params.coding_dir} \
--noncoding_dir {params.noncoding_dir} \
--numsims 5000 \
--results_file {output.results} \
-s meandec --fileform png pdf jpg \
--no_timestamp \
-o {params.obasename}
"""
rule plot_dirichlet_drosophila:
"""
Generates the dirichlet LOO analysis plot for drosophila genes.
"""
input:
COX1= "fasta_sequences/non-beroe/drosophila/coding/COX1.fasta",
output:
fig = "figures/dirichlet_plot_non_beroe/drosophila/drosophila_violins.png",
results = "figures/dirichlet_plot_non_beroe/drosophila/drosophila_results.csv"
params:
coding_dir = "fasta_sequences/non-beroe/drosophila/coding/",
noncoding_dir = "fasta_sequences/non-beroe/drosophila/noncoding/",
obasename = "figures/dirichlet_plot_non_beroe/drosophila/drosophila"
shell:
"""
cuttlery dirichlet \
--coding_dir {params.coding_dir} \
--noncoding_dir {params.noncoding_dir} \
--numsims 5000 \
--results_file {output.results} \
-s meandec --fileform png pdf jpg \
--no_timestamp \
-o {params.obasename}
"""
rule plot_dirichlet_chlamydomonas:
"""
Generates the dirichlet LOO analysis plot for chlamydomonas genes.
"""
input:
COX1= "fasta_sequences/non-beroe/chlamydomonas/coding/COX1.fasta",
output:
fig = "figures/dirichlet_plot_non_beroe/chlamydomonas/chlamydomonas_violins.png",
results = "figures/dirichlet_plot_non_beroe/chlamydomonas/chlamydomonas_results.csv"
params:
coding_dir = "fasta_sequences/non-beroe/chlamydomonas/coding/",
noncoding_dir = "fasta_sequences/non-beroe/chlamydomonas/noncoding/",
obasename = "figures/dirichlet_plot_non_beroe/chlamydomonas/chlamydomonas"
shell:
"""
cuttlery dirichlet \
--coding_dir {params.coding_dir} \
--noncoding_dir {params.noncoding_dir} \
--numsims 5000 \
--results_file {output.results} \
-s meandec --fileform png pdf jpg \
--no_timestamp \
-o {params.obasename}
"""
rule plot_hetero:
"""
Generates the mutation heterogeneity plot.
"""
input:
COX1= "fasta_sequences/coding_seqs/COX1.fasta",
COX2= "fasta_sequences/coding_seqs/COX2.fasta",
COX3= "fasta_sequences/coding_seqs/COX3.fasta",
CYTB= "fasta_sequences/coding_seqs/CYTB.fasta",
ND1 = "fasta_sequences/coding_seqs/ND1.fasta",
ND2 = "fasta_sequences/coding_seqs/ND2.fasta",
ND3 = "fasta_sequences/coding_seqs/ND3.fasta",
ND4 = "fasta_sequences/coding_seqs/ND4.fasta",
ND4L = "fasta_sequences/coding_seqs/ND4L.fasta",
ND5 = "fasta_sequences/coding_seqs/ND5.fasta",
ND6 = "fasta_sequences/coding_seqs/ND6.fasta",
t1 = "fasta_sequences/test_seqs/URF1.fasta",
t2 = "fasta_sequences/test_seqs/URF2.fasta",
COX1_TM = "fasta_sequences/BF201706_prot/TM_txtfiles/COX1_TM.txt",
COX2_TM = "fasta_sequences/BF201706_prot/TM_txtfiles/COX2_TM.txt",
COX3_TM = "fasta_sequences/BF201706_prot/TM_txtfiles/COX3_TM.txt",
CYTB_TM = "fasta_sequences/BF201706_prot/TM_txtfiles/CYTB_TM.txt",
ND1_TM = "fasta_sequences/BF201706_prot/TM_txtfiles/ND1_TM.txt",
ND2_TM = "fasta_sequences/BF201706_prot/TM_txtfiles/ND2_TM.txt",
ND3_TM = "fasta_sequences/BF201706_prot/TM_txtfiles/ND3_TM.txt",
ND4_TM = "fasta_sequences/BF201706_prot/TM_txtfiles/ND4_TM.txt",
ND4L_TM = "fasta_sequences/BF201706_prot/TM_txtfiles/ND4L_TM.txt",
ND5_TM = "fasta_sequences/BF201706_prot/TM_txtfiles/ND5_TM.txt",
ND6_TM = "fasta_sequences/BF201706_prot/TM_txtfiles/ND6_TM.txt",
t1_TM = "fasta_sequences/BF201706_prot/TM_txtfiles/URF1_TM.txt",
t2_TM = "fasta_sequences/BF201706_prot/TM_txtfiles/URF2_TM.txt",
output:
"figures/heterogeneity_plot/hetero.pdf",
"figures/heterogeneity_plot/hetero.csv",
params:
coding = "fasta_sequences/coding_seqs/",
test = "fasta_sequences/test_seqs/",
basename = "figures/heterogeneity_plot/hetero",
TM = "fasta_sequences/BF201706_prot/TM_txtfiles/"
shell:
"""
cuttlery heterogeneity \
--tt_code 4 \
--fasta_dir {params.coding} {params.test} \
--TM_dir {params.TM} \
--fileform pdf --no_timestamp -o {params.basename}
"""
#rule raxml:
# input:
# "phylogeny/20180609_rooted_tree/nuc_and_prot.phy",
# "phylogeny/20180609_rooted_tree/partition.txt"
# output:
# "phylogeny/20180609_rooted_tree/RAxML_bipartitions.best"
# params:
# wd = "phylogeny/20180609_rooted_tree"
# shell:
# """
# cd {params.wd};\
# raxmlHPC-PTHREADS-SSE3 \
# -m GTRGAMMA \
# -p 12345 -x 12345 \
# -f a -# autoMRE \
# -o FUN_Imsh_alue_NC035550 \
# -s nuc_and_prot.phy \
# -q partition.txt
# -n best -T 4; \
# cd ../../
# """