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Commit 882bba33 authored by Yohan Jarosz's avatar Yohan Jarosz
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try redefine analysis rules

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rules/Analysis/MGMT.rules
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− 48
View file @ 882bba33
......@@ -461,54 +461,6 @@ rule ANALYSIS_VIZBIN:
paste {AN_OUT}/MGMT.vizbin.contigs {output[0]} | sed -e 's/,/\t/g' > {output[2]}
"""
def analysis_plot_files_output():
return expand('{dir}/{name}', name=[
"IMP-reads_density.png",
"IMP-rpkm_density.png",
"IMP-coverage_density.png",
"IMP-depth_density.png",
"IMP-var_count.png",
"IMP-var_density.png",
"IMP-vizbin_length.png",
"IMP-vizbin_length_GC.png",
"IMP-vizbin_length_MGcov.png",
"IMP-vizbin_length_MGdepth.png",
"IMP-vizbin_length_MGvardens.png",
"IMP-vizbin_length_MTcov.png",
"IMP-vizbin_length_MTdepth.png",
"IMP-vizbin_length_MTvardens.png",
"IMP-vizbin_length_covRatio.png",
"IMP-vizbin_length_depthRatio.png",
"IMP-vizbin_length_geneDensity.png",
"IMP-vizbin_length_rpkmRatio.png",
"IMP-vizbin_standard.png",
"MG.read_stats.html",
"MG.read_stats.txt",
"MG_mapping_stats.html",
"MG_mapping_stats.txt",
"MT.read_stats.html",
"MT.read_stats.txt",
"MT_mapping_stats.html",
"MT_mapping_stats.txt",
"assembly_stats.html",
"assembly_stats.txt"], dir='%s/results' % AN_OUT)
def analysis_stats_files_output():
return expand([
'{dir}/{stat_flag}/{rtype}/cycle_composition_{n}.{ext}',
'{dir}/{stat_flag}/{rtype}/cycle_quality_{n}.{ext}',
'{dir}/{stat_flag}/{rtype}/cycle_quality_box_{n}.{ext}',
'{dir}/{stat_flag}/{rtype}/info.tab',
'{dir}/{stat_flag}/{rtype}/lane_tile_quality_{n}.{ext}',
'{dir}/{stat_flag}/{rtype}/quality_QQ.{ext}',
'{dir}/{stat_flag}/{rtype}/reads_length.{ext}',
'{dir}/{stat_flag}/{rtype}/reads_quality.{ext}'],
n = ['1', '2'],
ext = ['gnuplot', 'png', 'tab'],
dir = P_OUT,
stat_flag = ['stats', 'stats_after_preprocessing'],
rtype = ['MG', 'MT'])
rule ANALYSIS_PLOT:
log:
AN_LOG
......
rules/Analysis/master.rules
+ 155
− 68
View file @ 882bba33
# output directory and log
AN_OUT, AN_LOG = prepare_environment('Analysis')
# DEFINE OUTPUT FILES DEPENDING GIVEN PARAMETERS
PLOT_OUTPUT_FILES = {
'default': [
"IMP-vizbin_length.png",
"IMP-vizbin_length_GC.png",
"IMP-vizbin_length_geneDensity.png",
"IMP-vizbin_standard.png",
"assembly_stats.html",
"assembly_stats.txt"
],
'mgmt': [
"IMP-reads_density.png",
"IMP-rpkm_density.png",
"IMP-coverage_density.png",
"IMP-depth_density.png",
"IMP-var_count.png",
"IMP-var_density.png",
"IMP-vizbin_length_MGcov.png",
"IMP-vizbin_length_MGdepth.png",
"IMP-vizbin_length_MGvardens.png",
"IMP-vizbin_length_MTcov.png",
"IMP-vizbin_length_MTdepth.png",
"IMP-vizbin_length_MTvardens.png",
"IMP-vizbin_length_covRatio.png",
"IMP-vizbin_length_depthRatio.png",
"IMP-vizbin_length_rpkmRatio.png",
"MG.read_stats.html",
"MG.read_stats.txt",
"MG_mapping_stats.html",
"MG_mapping_stats.txt",
"MT.read_stats.html",
"MT.read_stats.txt",
"MT_mapping_stats.html",
"MT_mapping_stats.txt",
],
'mg': [
"IMP-MG_var_count.png",
"IMP-MG_coverage_density.png",
"IMP-MG_reads_density.png",
"IMP-MG_vizbin_length_cov.png",
"IMP-MG_vizbin_length_depth.png",
"IMP-MG_vizbin_length_vardens.png",
"MG.read_stats.html",
"MG.read_stats.txt",
"MG_mapping_stats.html",
"MG_mapping_stats.txt",
],
'mt': [
"IMP-MT_var_count.png",
"IMP-MT_coverage_density.png",
"IMP-MT_reads_density.png",
"IMP-MT_vizbin_length_cov.png",
"IMP-MT_vizbin_length_depth.png",
"IMP-MT_vizbin_length_vardens.png",
"MT.read_stats.html",
"MT.read_stats.txt",
"MT_mapping_stats.html",
"MT_mapping_stats.txt",
]
}
ANALYSIS_OUTPUT_FILES = {
'mgmt': [
"MGMT.assembly.length.txt",
"MGMT.assembly.gc_content.txt",
"MGMT.vizbin.points",
"MGMT.vizbin.filtered.fa",
"MGMT.vizbin.with-contig-names.points"
],
'mg': [
"MG.read_counts.txt",
"MG.annotation.bed",
"MG.gene_depth.hist",
"MG.gene_depth.avg",
"MG.gene.len",
"MG.prokkaID2ec.txt",
"MG.variants.isec.vcf.gz",
"MG.assembly.contig_coverage.txt",
"MG.assembly.contig_depth.txt",
"MG.assembly.contig_flagstat.txt",
],
'mt': [
"MT.read_counts.txt",
"MT.annotation.bed",
"MT.gene_depth.hist",
"MT.gene_depth.avg",
"MT.gene.len",
"MT.prokkaID2ec.txt",
"MT.variants.isec.vcf.gz",
"MT.assembly.contig_coverage.txt",
"MT.assembly.contig_depth.txt",
"MT.assembly.contig_flagstat.txt",
],
'mg_only': [
"MG.assembly.length.txt",
"MG.assembly.gc_content.txt",
"MG.vizbin.points",
"MG.vizbin.filtered.fa",
"MG.vizbin.with-contig-names.points"
],
'mt_only': [
"MT.assembly.length.txt",
"MT.assembly.gc_content.txt",
"MT.vizbin.points",
"MT.vizbin.filtered.fa",
"MT.vizbin.with-contig-names.points"
]
}
def analysis_stats_files_output(rtype):
return expand([
'{dir}/{stat_flag}/{rtype}/cycle_composition_{n}.{ext}',
'{dir}/{stat_flag}/{rtype}/cycle_quality_{n}.{ext}',
'{dir}/{stat_flag}/{rtype}/cycle_quality_box_{n}.{ext}',
'{dir}/{stat_flag}/{rtype}/info.tab',
'{dir}/{stat_flag}/{rtype}/lane_tile_quality_{n}.{ext}',
'{dir}/{stat_flag}/{rtype}/quality_QQ.{ext}',
'{dir}/{stat_flag}/{rtype}/reads_length.{ext}',
'{dir}/{stat_flag}/{rtype}/reads_quality.{ext}'],
n=['1', '2'],
ext=['gnuplot', 'png', 'tab'],
dir=P_OUT,
stat_flag=['stats', 'stats_after_preprocessing'],
rtype=rtype)
def analysis_plot_files_output():
if MG and MT:
addon = PLOT_OUTPUT_FILES['mgmt']
elif MG:
addon = PLOT_OUTPUT_FILES['mg']
elif MT:
addon = PLOT_OUTPUT_FILES['mt']
return expand('%s/results/{name}' % AN_OUT, name=PLOT_OUTPUT_FILES['default'] + addon)
def analysis_output_files():
if MG and MT:
addon = ANALYSIS_OUTPUT_FILES['mgmt'] + ANALYSIS_OUTPUT_FILES['mg'] + ANALYSIS_OUTPUT_FILES['mt']
stats = analysis_stats_files_output(['MG', 'MT'])
elif MG:
addon = ANALYSIS_OUTPUT_FILES['mg'] + ANALYSIS_OUTPUT_FILES['mg_only']
stats = analysis_stats_files_output(['MG'])
elif MT:
addon = ANALYSIS_OUTPUT_FILES['mt'] + ANALYSIS_OUTPUT_FILES['mt_only']
stats = analysis_stats_files_output('MT')
all = expand('%s/{name}' % AN_OUT, name=addon)
plots = analysis_plot_files_output()
return all + plots + stats
# include sub rules
if MG and MT:
......@@ -13,74 +168,6 @@ elif MT:
include:
"MT.rules"
def analysis_MGMT_output_files():
all = expand("{dir}/{name}", name=[
"MT.read_counts.txt",
"MG.read_counts.txt",
#### Added this ####
"MG.annotation.bed",
"MG.gene_depth.hist",
"MG.gene_depth.avg",
"MG.gene.len",
"MG.prokkaID2ec.txt",
"MT.annotation.bed",
"MT.gene_depth.hist",
"MT.gene_depth.avg",
"MT.gene.len",
"MT.prokkaID2ec.txt",
#####################
"MG.variants.isec.vcf.gz",
"MT.variants.isec.vcf.gz",
"MGMT.assembly.length.txt",
"MGMT.assembly.gc_content.txt",
"MT.assembly.contig_coverage.txt",
"MT.assembly.contig_depth.txt",
"MT.assembly.contig_flagstat.txt",
"MG.assembly.contig_coverage.txt",
"MG.assembly.contig_depth.txt",
"MG.assembly.contig_flagstat.txt",
"MGMT.vizbin.points",
"MGMT.vizbin.filtered.fa",
#### Added this ####
#"results/MT.gene_kegg_krona.txt",
#"results/MT.gene_kegg_krona.html",
#"results/MG.gene_kegg_krona.txt",
#"results/MG.gene_kegg_krona.html",
#####################
"MGMT.vizbin.with-contig-names.points"], dir=AN_OUT)
plots = analysis_plot_files_output()
stats = analysis_stats_files_output()
return all + plots + stats
## Define MG output files
def analysis_MG_output_files():
all = expand("{dir}/{name}", name=[
"MG.read_counts.txt",
#### Added this ####
"MG.annotation.bed",
"MG.gene_depth.hist",
"MG.gene_depth.avg",
"MG.gene.len",
"MG.prokkaID2ec.txt",
#####################
"MG.variants.isec.vcf.gz",
"MG.assembly.length.txt",
"MG.assembly.gc_content.txt",
"MG.assembly.contig_coverage.txt",
"MG.assembly.contig_depth.txt",
"MG.assembly.contig_flagstat.txt",
"MG.vizbin.points",
"MG.vizbin.filtered.fa",
#### Added this ####
#"results/MG.gene_kegg_krona.txt",
#"results/MG.gene_kegg_krona.html",
#####################
"MG.vizbin.with-contig-names.points"], dir=AN_OUT)
plots = analysis_plot_files_output()
stats = analysis_stats_files_output()
return all + plots + stats
# master command
rule ANALYSIS:
input:
......
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