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visualizeSpecies.py
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visualizeSpecies.py
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import os
from .visualize import Visualize
from Bayegy.ampliconLibs.libShell import qiime2, lefse
class VisualizeSpecies(Visualize):
"""docstring for VisualizeSpecies"""
def __init__(self, abundance_table, mapping_file, categories=False, prefix=False, out_dir=False, filter_species="exclude:Environmentalsamples", normalize_sp_name=True, tmp_dir='./'):
super(VisualizeSpecies, self).__init__(
abundance_table, mapping_file, categories, prefix, out_dir,
filter_abc_description=filter_species,
normalize_abc_description=normalize_sp_name)
self.set_attr(
sample_name=os.path.basename(self.abundance_table).rstrip('.txt'),
# exclude_species=exclude_species
)
def __visualize_with_group__(self, exclude='none', run_ancom=True, frequency=1000, orders=[]):
ancom_spec = """
echo -e "\n############################################Converting qzv files to html"
for f in $(find {tmp_dir}/ -type f -name "*.qzv"); do echo $f; base=$(basename $f .qzv); dir=$(dirname $f); new=${{dir}}/${{base}}; qiime tools export --input-path $f --output-path ${{new}}; done
for f in $(find {tmp_dir}/ -type f -name "index.html") ; do echo $f; base=$(basename $f .html); dir=$(dirname $f); new=${{dir}}/Summary_请点此文件查看.html; mv $f $new; done
""".format(**self.context) if not run_ancom else """
echo "ANCOM analaysis for differential OTU"
mkdir {tmp_dir}/ANCOM
for n2 in "Phylum" "Class" "Order" "Family" "Genus" "Species";
do echo $n2;
for category_1 in {category_set};
do echo $category_1;
{R_path} {bayegy_home}/clean_na_of_inputs.R -m {mapping_file} --group $category_1 -t {tmp_dir}/collapsed/{sample_name}-${{n2}}.qza -o {tmp_dir}
qiime composition add-pseudocount --i-table {tmp_dir}/filtered_feature_table.qza --o-composition-table {tmp_dir}/ANCOM/composition.${{n2}}.qza;
qiime composition ancom --i-table {tmp_dir}/ANCOM/composition.${{n2}}.qza --m-metadata-file {tmp_dir}/cleaned_map.txt --m-metadata-column $category_1 --o-visualization {tmp_dir}/ANCOM/${{category_1}}-ANCOM-${{n2}}.qzv;
done;
#qiime composition ancom --i-table {tmp_dir}/ANCOM/composition.${{n2}}.qza --m-metadata-file {mapping_file} --m-metadata-column $category_2 --o-visualization {tmp_dir}/ANCOM/SecondaryGroup/ANCOM.${{n2}}.qzv;
done;
echo -e "\n############################################Converting qzv files to html"
for f in $(find {tmp_dir}/ -type f -name "*.qzv"); do echo $f; base=$(basename $f .qzv); dir=$(dirname $f); new=${{dir}}/${{base}}; qiime tools export --input-path $f --output-path ${{new}}; done
for f in $(find {tmp_dir}/ -type f -name "index.html") ; do echo $f; base=$(basename $f .html); dir=$(dirname $f); new=${{dir}}/Summary_请点此文件查看.html; mv $f $new; done
mkdir -p {out_dir}/2-AbundanceComparison/ANCOM;
mv {tmp_dir}/ANCOM/*ANCOM* {out_dir}/2-AbundanceComparison/ANCOM/
""".format(**self.context, category_set=self.categories.replace(',', ' '))
with qiime2():
self.system("""
echo "Check wheather your categories are the following:"
for i in {category_set};do echo $i;done
tax_levels["1"]="Kingdom"
tax_levels["2"]="Phylum"
tax_levels["3"]="Class"
tax_levels["4"]="Order"
tax_levels["5"]="Family"
tax_levels["6"]="Genus"
tax_levels["7"]="Species"
echo "##############################################################\n#Generate the figure for the percentage of annotated level"
{perl_path} {bayegy_home}/stat_otu_tab.pl -unif min {abundance_table} -prefix {tmp_dir}/Relative/otu_table --even {tmp_dir}/Relative/otu_table.even.txt -spestat {tmp_dir}/Relative/classified_stat_relative.xls
{perl_path} {bayegy_home}/stat_otu_tab.pl -unif min {abundance_table} -prefix {tmp_dir}/Absolute/otu_table -nomat -abs -spestat exported/Absolute/classified_stat.xls
{perl_path} {bayegy_home}/bar_diagram.pl -table {tmp_dir}/Relative/classified_stat_relative.xls -style 1 -x_title "Sample Name" -y_title "Sequence Number Percent" -right -textup -rotate='-45' --y_mun 1,7 > {tmp_dir}/Relative/Classified_stat_relative.svg
# source {base_dir}/path/activate_qiime2.sh
echo -e "\n#Convert OTU table to biom format"
biom convert -i {abundance_table} -o {tmp_dir}/{sample_name}.taxonomy.biom --to-hdf5 --table-type="OTU table" --process-obs-metadata taxonomy
echo -e "\n#Generate Qiime2 artifacts"
qiime tools import --input-path {tmp_dir}/{sample_name}.taxonomy.biom --type 'FeatureTable[Frequency]' --input-format BIOMV210Format --output-path {tmp_dir}/{sample_name}.count.qza
qiime tools import --input-path {tmp_dir}/{sample_name}.taxonomy.biom --type "FeatureData[Taxonomy]" --input-format BIOMV210Format --output-path {tmp_dir}/{sample_name}.taxonomy.qza
echo -e "\n#Filter OTU table by taxonomy"
qiime feature-table filter-features --i-table {tmp_dir}/{sample_name}.count.qza --p-min-frequency 10 --o-filtered-table {tmp_dir}/{sample_name}.count.filtered.qza
echo -e "\n#Generate barplot"
qiime taxa barplot --i-table {tmp_dir}/{sample_name}.count.filtered.qza --i-taxonomy {tmp_dir}/{sample_name}.taxonomy.qza --m-metadata-file {mapping_file} --o-visualization {tmp_dir}/{sample_name}.taxa-bar-plots.qzv
qiime feature-table filter-features --i-table {tmp_dir}/{sample_name}.count.filtered.qza --p-min-frequency {frequency} --o-filtered-table {tmp_dir}/{sample_name}.count.filtered.{frequency}.qza
qiime taxa barplot --i-table {tmp_dir}/{sample_name}.count.filtered.{frequency}.qza --i-taxonomy {tmp_dir}/{sample_name}.taxonomy.qza --m-metadata-file {mapping_file} --o-visualization {tmp_dir}/{sample_name}.taxa-bar-plots.{frequency}.qzv
echo -e "Conduct non-phylogenetic diversity analysis"
depth=$({R_path} {bayegy_home}/min.R {abundance_table})
echo "depth is $depth"
qiime diversity core-metrics --i-table {tmp_dir}/{sample_name}.count.qza --p-sampling-depth $depth --m-metadata-file {mapping_file} --output-dir {tmp_dir}/core-metrics
mkdir {tmp_dir}/collapsed
for n2 in 2 3 4 5 6 7;
do echo $n2; qiime taxa collapse --i-table {tmp_dir}/{sample_name}.count.filtered.qza --i-taxonomy {tmp_dir}/{sample_name}.taxonomy.qza --p-level $n2 --o-collapsed-table {tmp_dir}/collapsed/{sample_name}-${{tax_levels[${{n2}}]}}.qza;
done;
{ancom_spec}
mv {tmp_dir}/Relative/otu_table.p.relative.mat {tmp_dir}/Relative/otu_table.Phylum.relative.txt
mv {tmp_dir}/Relative/otu_table.c.relative.mat {tmp_dir}/Relative/otu_table.Class.relative.txt
mv {tmp_dir}/Relative/otu_table.o.relative.mat {tmp_dir}/Relative/otu_table.Order.relative.txt
mv {tmp_dir}/Relative/otu_table.f.relative.mat {tmp_dir}/Relative/otu_table.Family.relative.txt
mv {tmp_dir}/Relative/otu_table.g.relative.mat {tmp_dir}/Relative/otu_table.Genus.relative.txt
mv {tmp_dir}/Relative/otu_table.s.relative.mat {tmp_dir}/Relative/otu_table.Species.relative.txt
mv {tmp_dir}/Absolute/otu_table.p.absolute.mat {tmp_dir}/Absolute/otu_table.Phylum.absolute.txt
mv {tmp_dir}/Absolute/otu_table.c.absolute.mat {tmp_dir}/Absolute/otu_table.Class.absolute.txt
mv {tmp_dir}/Absolute/otu_table.o.absolute.mat {tmp_dir}/Absolute/otu_table.Order.absolute.txt
mv {tmp_dir}/Absolute/otu_table.f.absolute.mat {tmp_dir}/Absolute/otu_table.Family.absolute.txt
mv {tmp_dir}/Absolute/otu_table.g.absolute.mat {tmp_dir}/Absolute/otu_table.Genus.absolute.txt
mv {tmp_dir}/Absolute/otu_table.s.absolute.mat {tmp_dir}/Absolute/otu_table.Species.absolute.txt
""", ancom_spec=ancom_spec, frequency=frequency, category_set=self.categories.replace(',', ' '))
self.system("""
not_rda='{exclude}'
echo "Check CorrelationAnalysis config:"
for i in $not_rda;do echo $i;done
for n in "Phylum" "Class" "Order" "Family" "Genus" "Species";
do echo $n;
for category_1 in {category_set};
do echo $category_1;
{R_path} {bayegy_home}/abundance_heatmap.R -m {mapping_file} -c $category_1 -n 20 -i {tmp_dir}/Absolute/otu_table.${{n}}.absolute.txt -o {tmp_dir}/Heatmap/Heatmap_top20/${{n}}/ -l T -t F -p "${{category_1}}_";
{R_path} {bayegy_home}/abundance_heatmap.R -m {mapping_file} -c $category_1 -n 20 -i {tmp_dir}/Absolute/otu_table.${{n}}.absolute.txt -o {tmp_dir}/Heatmap/Heatmap_top20_clustered/${{n}}/ -l T -t F -u T -p "${{category_1}}_";
{R_path} {bayegy_home}/abundance_heatmap.R -m {mapping_file} -c $category_1 -n 20 -i {tmp_dir}/Absolute/otu_table.${{n}}.absolute.txt -o {tmp_dir}/Heatmap/Heatmap_top20/${{n}}/ -b T -l T -p "${{category_1}}_group_mean_" -t T;
for order in {orders};
do {R_path} {bayegy_home}/abundance_heatmap.R -m {mapping_file} -c $category_1 -n 20 \
-i {tmp_dir}/Absolute/otu_table.${{n}}.absolute.txt -o {tmp_dir}/Heatmap/Heatmap_top20/${{n}}/ \
-l T -t F -p "${{category_1}}_in_${{order}}_" -O $order;
done;
done;
done;
test=${{not_rda// */}}
if [ ! $test == "all" ];then
echo "##############################################################\nCorrelation heatmap analysis"
for nrda in $not_rda;
do echo $nrda;
arr=(${{nrda//:/ }});
nrda=${{arr[0]}};
prefix=${{arr[1]}};
for n7 in "Phylum" "Class" "Order" "Family" "Genus" "Species";
do echo $n7;
{R_path} {bayegy_home}/cor_heatmap.R -i {tmp_dir}/Relative/otu_table.${{n7}}.relative.txt -o {tmp_dir}/CorrelationAnalysis/CorrelationHeatmap/${{n7}}/ -n 25 -m {mapping_file} -e $nrda -p "$prefix";
for category_1 in {category_set};do echo $category_1;{R_path} {bayegy_home}/RDA.R -i {tmp_dir}/Absolute/otu_table.${{n7}}.absolute.txt -m {mapping_file} -c $category_1 -o {tmp_dir}/CorrelationAnalysis/RDA/${{n7}} -n 25 -e $nrda -p "$prefix";done;
done;
done;
fi;
echo "##############################################################\n#Barplot according to group mean"
for n7 in "Phylum" "Class" "Order" "Family" "Genus" "Species";
do echo $n7;
{perl_path} -lane '$,="\t";pop(@F);print(@F)' {tmp_dir}/Relative/otu_table.${{n7}}.relative.txt > {tmp_dir}/Relative/otu_table.${{n7}}.relative.lastcolumn.txt;
{perl_path} {bayegy_home}/get_table_head2.pl {tmp_dir}/Relative/otu_table.${{n7}}.relative.lastcolumn.txt 20 -trantab > {tmp_dir}/Relative/otu_table.${{n7}}.relative.lastcolumn.trans;
{perl_path} {bayegy_home}/bar_diagram.pl -table {tmp_dir}/Relative/otu_table.${{n7}}.relative.lastcolumn.trans -style 1 -x_title "Sample Name" -y_title "Sequence Number Percent (%)" -right -textup -rotate='-45' --y_mun 0.2,5 --micro_scale --percentage > {tmp_dir}/Relative/otu_table.${{n7}}.relative.svg
done;
for svg_file in {tmp_dir}/Relative/*svg; do echo $svg_file; n=$(basename "$svg_file" .svg); echo $n; convert $svg_file {tmp_dir}/Relative/${{n}}.png; done;
for category_1 in {category_set};
do echo $category_1;
for n7 in "Phylum" "Class" "Order" "Family" "Genus" "Species";
do echo $n7;
{R_path} {bayegy_home}/abundance_barplot.R -n 20 -m {mapping_file} -c $category_1 -i {tmp_dir}/Relative/otu_table.${{n7}}.relative.txt -o {tmp_dir}/Taxa-bar-plots-top20/ -p ${{n7}}_${{category_1}}_ -b F;
{R_path} {bayegy_home}/abundance_barplot.R -n 20 -m {mapping_file} -c $category_1 -i {tmp_dir}/Relative/otu_table.${{n7}}.relative.txt -o {tmp_dir}/Barplot-of-Group-Mean/ -p ${{category_1}}_${{n7}}_mean_ -b T;
{R_path} {bayegy_home}/Function_DunnTest.r -m {mapping_file} -c $category_1 -i {tmp_dir}/Relative/otu_table.${{n7}}.relative.txt -o {tmp_dir}/DunnTest/ -p ${{n7}}_ > /dev/null;
{R_path} {bayegy_home}/write_data_for_lefse.R -i {tmp_dir}/Relative/otu_table.${{n7}}.relative.txt -m {mapping_file} -c $category_1 -o {tmp_dir}/Lefse/${{n7}}/${{category_1}}_${{n7}}_lefse.txt -u l;
for order in {orders};
do {R_path} {bayegy_home}/abundance_barplot.R -n 20 -m {mapping_file} -c $category_1 \
-i {tmp_dir}/Relative/otu_table.${{n7}}.relative.txt -o {tmp_dir}/Taxa-bar-plots-top20/ \
-p ${{n7}}_${{category_1}}_in_${{order}}_ -b F -O $order;
done;
done;
done;
echo "############################################Additional R related plot "
sed 's/taxonomy/Consensus Lineage/' < {abundance_table} | sed 's/ConsensusLineage/Consensus Lineage/' > {tmp_dir}/feature-table.ConsensusLineage.txt
for category_1 in {category_set};
do echo $category_1;
{R_path} {bayegy_home}/clean_na_of_inputs.R -m {mapping_file} --group $category_1 -o {tmp_dir}
map="{tmp_dir}/cleaned_map.txt"
{R_path} {bayegy_home}/venn_and_flower_plot.R -s F -i {abundance_table} -m {mapping_file} -c $category_1 -o {tmp_dir}/VennAndFlower;
{R_path} {bayegy_home}/pcoa_and_nmds.R -i {tmp_dir}/feature-table.ConsensusLineage.txt -m $map -c $category_1 -o {tmp_dir}/PCoA-NMDS;
done;
""", category_set=self.categories.replace(',', ' '), exclude=exclude.replace(';', ' '), orders=" ".join(orders))
with lefse():
self.system("""
echo "#####################Run Lefse for taxa abundance";
for n7 in "Phylum" "Class" "Order" "Family" "Genus" "Species";
do echo $n7;
for category_1 in {category_set};
do echo $category_1;
base="{tmp_dir}/Lefse/${{n7}}/${{category_1}}_${{n7}}_lefse_LDA2"; lefse-format_input.py {tmp_dir}/Lefse/${{n7}}/${{category_1}}_${{n7}}_lefse.txt ${{base}}.lefseinput.txt -c 2 -u 1 -o 1000000; run_lefse.py ${{base}}.lefseinput.txt ${{base}}.LDA.txt -l 2;
{bayegy_home}/mod_lefse-plot_res.py --category $category_1 --map {mapping_file} --max_feature_len 200 --orientation h --format pdf --left_space 0.3 --dpi 300 ${{base}}.LDA.txt ${{base}}.pdf; {bayegy_home}/mod_lefse-plot_cladogram.py ${{base}}.LDA.txt --category $category_1 --map {mapping_file} --dpi 300 ${{base}}.cladogram.pdf --format pdf;
base4="{tmp_dir}/Lefse/${{n7}}/${{category_1}}_${{n7}}_lefse_LDA4";
# lefse-format_input.py ${{category_1}}_${{n7}}_lefse.txt ${{base}}.lefseinput.txt -c 2 -u 1 -o 1000000; run_lefse.py ${{base}}.lefseinput.txt ${{base}}.LDA.txt -l 4;
{python3_path} {base_dir}/lda22ldamt.py ${{base}}.LDA.txt ${{base4}}.LDA.txt 4;
{bayegy_home}/mod_lefse-plot_res.py --category $category_1 --map {mapping_file} --max_feature_len 200 --orientation h --format pdf --left_space 0.3 --dpi 300 ${{base4}}.LDA.txt ${{base4}}.pdf; {bayegy_home}/mod_lefse-plot_cladogram.py ${{base4}}.LDA.txt --category $category_1 --map {mapping_file} --dpi 300 ${{base4}}.cladogram.pdf --format pdf;
done;
done;
mkdir -p {out_dir}/1-AbundanceSummary/1-RelativeAbundance \
{out_dir}/1-AbundanceSummary/2-Barplots \
{out_dir}/1-AbundanceSummary/3-Heatmaps \
{out_dir}/2-AbundanceComparison/VennAndFlower \
{out_dir}/2-AbundanceComparison/LEfSe \
{out_dir}/3-DiversityAnalysis \
mv {tmp_dir}/Relative/Classified_stat_relative.png {out_dir}/1-AbundanceSummary/
mv {tmp_dir}/Relative/*relative.txt {out_dir}/1-AbundanceSummary/1-RelativeAbundance/
mv {tmp_dir}/{sample_name}.taxa-bar-plots {tmp_dir}/{sample_name}.taxa-bar-plots.{frequency} {tmp_dir}/Barplot-of-Group-Mean {tmp_dir}/Taxa-bar-plots-top20 {out_dir}/1-AbundanceSummary/2-Barplots/
mv {tmp_dir}/Heatmap/* {out_dir}/1-AbundanceSummary/3-Heatmaps/
mv {tmp_dir}/Lefse/* {out_dir}/2-AbundanceComparison/LEfSe/
mv {tmp_dir}/DunnTest {out_dir}/2-AbundanceComparison/
mv {tmp_dir}/VennAndFlower/* {out_dir}/2-AbundanceComparison/VennAndFlower/
mv {tmp_dir}/core-metrics/bray_curtis_emperor {tmp_dir}/PCoA-NMDS/* {out_dir}/3-DiversityAnalysis/
mv {tmp_dir}/CorrelationAnalysis {out_dir}/4-CorrelationAnalysis
""", frequency=frequency, category_set=self.categories.replace(',', ' '))
def __visualize_without_group__(self, run_ancom=True, frequency=1000):
os.system("bash {}visualize_otu_table_without_group.sh {} {} none {} {} {} {}".format(
self._base_dir, self.abundance_table, self.mapping_file, self.prefix, "NONE", self.path[
'bayegy_home'], self.tmp_dir
))