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separating fingerprint plots; merging inputnorm heatmaps
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@tovahmarkowitz
tovahmarkowitz committed Nov 13, 2018
1 parent def151e commit dff8bae
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Showing 3 changed files with 55 additions and 39 deletions.
88 changes: 52 additions & 36 deletions Rules/InitialChIPseqQC.snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ def outputfiles(groupslist):
groups2input = _findinputs()
dtoolgroups, dtoolext, dtoolinorm = [], [], []
inputnorm = ["", ".inputnorm"]
extensions = ["sorted.RPGC", "sorted.Q5DD.RPGC"] # Change from normalized to RPGC
extensions = ["sorted.RPGC", "sorted.Q5DD.RPGC"]
for group in groupslist:
if groups2input[group]:
dtoolgroups.extend([group]*3)
Expand All @@ -52,6 +52,24 @@ def outputfiles(groupslist):
dtoolinorm.extend([inputnorm[0], inputnorm[0]])
return dtoolgroups, dtoolext, dtoolinorm

def outputfiles2(groupslist):
'''
Produces correct output filenames based on group information.
Names witll be:
Inputnorm.sorted.Q5DD.RPGC.metagene_heatmap.pdf
{groupName}.sorted.Q5DD.RPGC.metagene_heatmap.pdf
{groupName}.sorted.RPGC.metagene_heatmap.pdf
'''
dtoolgroups, dtoolext = [], []
extensions = ["sorted.RPGC", "sorted.Q5DD.RPGC"]
dtoolgroups.extend(["InputNorm"])
dtoolext.extend([extensions[1]])
for group in groupslist:
dtoolgroups.extend([group] * 2)
dtoolext.extend([extensions[1], extensions[0]])
return dtoolgroups, dtoolext


se=""
pe=""

Expand Down Expand Up @@ -93,7 +111,7 @@ for group, chips in groupdata.items() :
groupdatawinput[group]=set(tmp)

groups = list(groupdatawinput.keys())
deepgroups, deepexts, deepnorm = outputfiles(groups)
deepgroups, deepexts = outputfiles2(groups)

trim_dir='trim'
kraken_dir='kraken'
Expand All @@ -107,7 +125,7 @@ for d in [trim_dir,kraken_dir,bam_dir,bw_dir,deeptools_dir,preseq_dir]:
os.mkdir(join(workpath,d))

# Checking to see if output filenames are files are being generated correctly
print("DEEPTOOLS OUTPUT FILESNAMES\n",[file.split('/')[-1] for file in expand(join(workpath,deeptools_dir,"{group}.metagene_heatmap.{ext}{norm}.pdf"), zip, group=deepgroups,ext=deepexts,norm=deepnorm)])
print("DEEPTOOLS OUTPUT FILESNAMES\n",[file.split('/')[-1] for file in expand(join(workpath,deeptools_dir,"{group}.metagene_heatmap.{ext}.pdf"), zip, group=deepgroups,ext=deepexts)])
#print(samples)

if se == 'yes' :
Expand Down Expand Up @@ -143,12 +161,12 @@ if se == 'yes' :
expand(join(workpath,deeptools_dir,"spearman_heatmap.{ext}.pdf"),ext=extensions),
expand(join(workpath,deeptools_dir,"spearman_scatterplot.{ext}.pdf"),ext=extensions),
expand(join(workpath,deeptools_dir,"pca.{ext}.pdf"),ext=extensions),
expand(join(workpath,deeptools_dir,"fingerprint.{ext}.pdf"),ext=extensions2),
expand(join(workpath,deeptools_dir,"fingerprint.metrics.{ext}.tsv"),ext=extensions2),
expand(join(workpath,deeptools_dir,"{group}.metagene_heatmap.{ext}{norm}.pdf"), zip, group=deepgroups,ext=deepexts,norm=deepnorm),
expand(join(workpath,deeptools_dir,"{group}.TSS_heatmap.{ext}{norm}.pdf"), zip, group=deepgroups,ext=deepexts,norm=deepnorm),
expand(join(workpath,deeptools_dir,"{group}.metagene_profile.{ext}{norm}.pdf"), zip, group=deepgroups,ext=deepexts,norm=deepnorm),
expand(join(workpath,deeptools_dir,"{group}.TSS_profile.{ext}{norm}.pdf"), zip, group=deepgroups,ext=deepexts,norm=deepnorm),
expand(join(workpath,deeptools_dir,"{group}.fingerprint.{ext}.pdf"),ext=extensions2,group=groups),
expand(join(workpath,deeptools_dir,"{group}.fingerprint.metrics.{ext}.tsv"),ext=extensions2,group=groups),
expand(join(workpath,deeptools_dir,"{group}.metagene_heatmap.{ext}.pdf"), zip, group=deepgroups,ext=deepexts),
expand(join(workpath,deeptools_dir,"{group}.TSS_heatmap.{ext}.pdf"), zip, group=deepgroups,ext=deepexts),
expand(join(workpath,deeptools_dir,"{group}.metagene_profile.{ext}.pdf"), zip, group=deepgroups,ext=deepexts),
expand(join(workpath,deeptools_dir,"{group}.TSS_profile.{ext}.pdf"), zip, group=deepgroups,ext=deepexts),
# preseq
expand(join(workpath,preseq_dir,"{name}.ccurve"),name=samples),
# QC Table
Expand Down Expand Up @@ -304,12 +322,12 @@ if pe == 'yes':
expand(join(workpath,deeptools_dir,"spearman_heatmap.{ext}.pdf"),ext=extensions),
expand(join(workpath,deeptools_dir,"spearman_scatterplot.{ext}.pdf"),ext=extensions),
expand(join(workpath,deeptools_dir,"pca.{ext}.pdf"),ext=extensions),
expand(join(workpath,deeptools_dir,"fingerprint.{ext}.pdf"),ext=extensions2),
expand(join(workpath,deeptools_dir,"fingerprint.metrics.{ext}.tsv"),ext=extensions2),
expand(join(workpath,deeptools_dir,"{group}.metagene_heatmap.{ext}{norm}.pdf"), zip, group=deepgroups,ext=deepexts,norm=deepnorm),
expand(join(workpath,deeptools_dir,"{group}.TSS_heatmap.{ext}{norm}.pdf"), zip, group=deepgroups,ext=deepexts,norm=deepnorm),
expand(join(workpath,deeptools_dir,"{group}.metagene_profile.{ext}{norm}.pdf"), zip, group=deepgroups,ext=deepexts,norm=deepnorm),
expand(join(workpath,deeptools_dir,"{group}.TSS_profile.{ext}{norm}.pdf"), zip, group=deepgroups,ext=deepexts,norm=deepnorm),
expand(join(workpath,deeptools_dir,"{group}.fingerprint.{ext}.pdf"),group=groups,ext=extensions2),
expand(join(workpath,deeptools_dir,"{group}.fingerprint.metrics.{ext}.tsv"),group=groups,ext=extensions2),
expand(join(workpath,deeptools_dir,"{group}.metagene_heatmap.{ext}.pdf"), zip, group=deepgroups,ext=deepexts),
expand(join(workpath,deeptools_dir,"{group}.TSS_heatmap.{ext}.pdf"), zip, group=deepgroups,ext=deepexts),
expand(join(workpath,deeptools_dir,"{group}.metagene_profile.{ext}.pdf"), zip, group=deepgroups,ext=deepexts),
expand(join(workpath,deeptools_dir,"{group}.TSS_profile.{ext}.pdf"), zip, group=deepgroups,ext=deepexts),
# preseq
expand(join(workpath,preseq_dir,"{name}.ccurve"),name=samples),
# QC Table
Expand Down Expand Up @@ -553,8 +571,8 @@ rule deeptools_prep:
bw2=expand(join(workpath,bw_dir,"{name}.sorted.Q5DD.RPGC.inputnorm.bw"),name=sampleswinput)
output:
expand(join(workpath,bw_dir,"{ext}.deeptools_prep"),ext=extensions),
expand(join(workpath,bam_dir,"{ext}.deeptools_prep"),ext=extensions2),
expand(join(workpath,bw_dir,"{group2}.{ext2}{norm2}.deeptools_prep"), zip, group2=deepgroups,ext2=deepexts,norm2=deepnorm),
expand(join(workpath,bam_dir,"{group}.{ext}.deeptools_prep"),group=groups,ext=extensions2),
expand(join(workpath,bw_dir,"{group2}.{ext2}.deeptools_prep"), zip, group2=deepgroups,ext2=deepexts),
params:
rname="pl:deeptools_prep",
batch="--mem=10g --time=1:00:00",
Expand All @@ -573,29 +591,27 @@ rule deeptools_prep:
o.write("%s\n"%(" ".join(bws)))
o.write("%s\n"%(" ".join(labels)))
o.close()
o2=open(join(workpath,bam_dir,x+".deeptools_prep"),'w')
o2.write("%s\n"%(x))
o2.write("%s\n"%(" ".join(bams)))
o2.write("%s\n"%(" ".join(labels)))
o2.close()
if len(bws2) > 0:
o4=open(join(workpath,bw_dir,"InputNorm."+x+".RPGC.deeptools_prep"),'w')
o4.write("%s\n"%(x+".RPGC.inputnorm"))
o4.write("%s\n"%(" ".join(bws2)))
o4.write("%s\n"%(" ".join(labels2)))
o4.close()
for group in groups:
iter = [ i for i in range(len(labels)) if labels[i] in groupdatawinput[group] ]
bws3 = [ bws[i] for i in iter ]
labels3 = [ labels[i] for i in iter ]
bams3 = [ bams[i] for i in iter ]
o2=open(join(workpath,bam_dir,group+"."+x+".deeptools_prep"),'w')
o2.write("%s\n"%(x))
o2.write("%s\n"%(" ".join(bams3)))
o2.write("%s\n"%(" ".join(labels3)))
o2.close()
o3=open(join(workpath,bw_dir,group+"."+x+".RPGC.deeptools_prep"),'w')
o3.write("%s\n"%(x+".RPGC"))
o3.write("%s\n"%(" ".join(bws3)))
o3.write("%s\n"%(" ".join(labels3)))
o3.close()
iter2 = [ i for i in range(len(labels2)) if labels2[i] in groupdatawinput[group] ]
bws4 = [ bws2[i] for i in iter2 ]
labels4 = [ labels2[i] for i in iter2 ]
if len(bws4) > 0:
o4=open(join(workpath,bw_dir,group+"."+x+".RPGC.inputnorm.deeptools_prep"),'w')
o4.write("%s\n"%(x+".RPGC.inputnorm"))
o4.write("%s\n"%(" ".join(bws4)))
o4.write("%s\n"%(" ".join(labels4)))
o4.close()

rule deeptools_QC:
input:
Expand Down Expand Up @@ -626,11 +642,11 @@ rule deeptools_QC:

rule deeptools_fingerprint:
input:
join(workpath,bam_dir,"{ext}.deeptools_prep")
join(workpath,bam_dir,"{group}.{ext}.deeptools_prep")
output:
image=join(workpath,deeptools_dir,"fingerprint.{ext}.pdf"),
raw=temp(join(workpath,deeptools_dir,"fingerprint.raw.{ext}.tab")),
metrics=join(workpath,deeptools_dir,"fingerprint.metrics.{ext}.tsv"),
image=join(workpath,deeptools_dir,"{group}.fingerprint.{ext}.pdf"),
raw=temp(join(workpath,deeptools_dir,"{group}.fingerprint.raw.{ext}.tab")),
metrics=join(workpath,deeptools_dir,"{group}.fingerprint.metrics.{ext}.tsv"),
params:
rname="pl:deeptools_fingerprint",
deeptoolsver=config['bin'][pfamily]['tool_versions']['DEEPTOOLSVER'],
Expand Down Expand Up @@ -861,7 +877,7 @@ rule multiqc:
join(workpath,"QCTable.txt"),
join(workpath,"rawQC"),
join(workpath,"QC"),
expand(join(workpath,deeptools_dir,"fingerprint.raw.{ext}.tab"),ext=extensions2),
expand(join(workpath,deeptools_dir,"{group}.fingerprint.raw.{ext}.tab"),group=groups,ext=extensions2),
output:
join(workpath,"Reports","multiqc_report.html")
params:
Expand Down
4 changes: 2 additions & 2 deletions cluster.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"__default__": {
"mem": "48g",
"time": "4-00:00:00",
"time": "1-00:00:00",
"partition": "norm",
"threads": "4",
"gres": "lscratch:256"
Expand Down Expand Up @@ -833,4 +833,4 @@
"threads": "32",
"mem": "32g"
}
}
}
2 changes: 1 addition & 1 deletion slurm.template
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Original file line number Diff line number Diff line change
Expand Up @@ -34,4 +34,4 @@ mv $R/HPCusagetable.txt.tmp $R/HPC_usage_table.txt
cd $R/Reports && $R/Reports/ngser.pl ../QC ./
#cd $R/Reports && $R/Reports/stats2html.py
rm -rf $R/bamstats
rm -rf $R/*bam.cnt
rm -rf $R/*bam.cnt

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