From 87f907089fb432c11e5d6f70cbacfef0a6309440 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 27 Jun 2018 17:12:28 -0500
Subject: [PATCH] Fix paired end.
---
workflow/main.nf | 8 +--
workflow/scripts/pool_and_psuedoreplicate.py | 53 +++++++++++++++++++-
2 files changed, 55 insertions(+), 6 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 9cd780d..4fa5d9f 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -239,7 +239,7 @@ process crossReads {
output:
- set sampleId, tagAlign, file('*.cc.qc'), experimentId, biosample, factor, treatment, replicate, controlId into xcorReads
+ set sampleId, seTagAlign, tagAlign, file('*.cc.qc'), experimentId, biosample, factor, treatment, replicate, controlId into xcorReads
set file('*.cc.qc'), file('*.cc.plot.pdf') into xcorReadsStats
script:
@@ -259,9 +259,9 @@ process crossReads {
// Define channel collecting tagAlign and xcor into design file
xcorDesign = xcorReads
- .map{ sampleId, tagAlign, xcor, experimentId, biosample, factor, treatment, replicate, controlId ->
- "$sampleId\t$tagAlign\t$xcor\t$experimentId\t$biosample\t$factor\t$treatment\t$replicate\t$controlId\n"}
- .collectFile(name:'design_xcor.tsv', seed:"sample_id\ttag_align\txcor\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$baseDir/output/design")
+ .map{ sampleId, seTagAlign, tagAlign, xcor, experimentId, biosample, factor, treatment, replicate, controlId ->
+ "$sampleId\t$seTagAlign\t$tagAlign\t$xcor\t$experimentId\t$biosample\t$factor\t$treatment\t$replicate\t$controlId\n"}
+ .collectFile(name:'design_xcor.tsv', seed:"sample_id\tse_tag_align\ttag_align\txcor\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$baseDir/output/design")
// Make Experiment design files to be read in for downstream analysis
process defineExpDesignFiles {
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 72a2558..3481495 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -98,6 +98,20 @@ def pool(tag_files, outfile, paired):
return pooled_filename
+def bedpe_to_tagalign(tag_file, outfile):
+ '''Convert read pairs to reads itno standard tagAlign file.'''
+
+ se_tag_filename = outfile + "bedse.tagAlign.gz"
+
+ # Convert read pairs to reads into standard tagAlign file
+ tag_steps = ["zcat -f %s" % (tag_file)]
+ tag_steps.extend([r"""awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}'"""])
+ tag_steps.extend(['gzip -cn'])
+ out, err = utils.run_pipe(tag_steps, outfile=se_tag_filename)
+
+ return se_tag_filename
+
+
def self_psuedoreplication(tag_file, prefix, paired):
'''Make 2 self-psuedoreplicates.'''
@@ -183,13 +197,24 @@ def main():
else:
pool_control = design_df.control_tag_align.unique()[0]
+ # if paired_end make tagAlign
+ if paired:
+ pool_control_tmp = bedpe_to_tagalign(pool_control, "pool_control")
+ pool_control = pool_control_tmp
+
# Psuedoreplicate and update design accordingly
if not replicated:
- # Duplicate rows and update for pool and psuedoreplicates
+ # Duplicate rows and update for pool and psuedoreplicates and update tagAlign with single end data
experiment_id = design_df.at[0, 'experiment_id']
replicate = design_df.at[0, 'replicate']
design_new_df = design_df.loc[np.repeat(design_df.index, 4)].reset_index()
+
+ # Update tagAlign with single end data
+ if paired:
+ design_new_df['tag_align'] = design_new_df['se_tag_align']
+ design_new_df.drop(labels = 'se_tag_align', axis = 1, inplace = True)
+
design_new_df['replicate'] = design_new_df['replicate'].astype(str)
design_new_df.at[1, 'sample_id'] = experiment_id + '_pr1'
design_new_df.at[1, 'replicate'] = '1_pr'
@@ -200,6 +225,7 @@ def main():
design_new_df.at[3, 'sample_id'] = experiment_id + '_pooled'
design_new_df.at[3, 'replicate'] = 'pooled'
design_new_df.at[3, 'xcor'] = 'Calculate'
+ design_new_df.at[3, 'tag_align'] = design_new_df.at[0, 'tag_align']
# Make 2 self psuedoreplicates
self_pseudoreplicates_dict = {}
@@ -217,12 +243,20 @@ def main():
# Drop index column
design_new_df.drop(labels='index', axis=1, inplace=True)
+
+
else:
# Make pool of replicates
replicate_files = design_df.tag_align.unique()
experiment_id = design_df.at[0, 'experiment_id']
pool_experiment = pool(replicate_files, experiment_id + "_pooled", paired)
+ # If paired change to single End
+ if paired:
+ pool_experiment_se = bedpe_to_tagalign(pool_experiment, experiment_id + "_pooled")
+ else:
+ pool_experiment_se = pool_experiment
+
# Make self psuedoreplicates equivalent to number of replicates
pseudoreplicates_dict = {}
for rep, tag_file in zip(design_df['replicate'], design_df['tag_align']):
@@ -240,6 +274,10 @@ def main():
pool_pseudoreplicates_dict[replicate_id] = pool_replicate
design_new_df = design_df
+ # Update tagAlign with single end data
+ if paired:
+ design_new_df['tag_align'] = design_new_df['se_tag_align']
+ design_new_df.drop(labels = 'se_tag_align', axis = 1, inplace = True)
# Check controls against cutoff_ratio
# if so replace with pool_control
# unless single control was used
@@ -260,6 +298,16 @@ def main():
% row['replicate'])
design_new_df.loc[index, 'control_tag_align'] = \
path_to_pool_control
+ else:
+ if paired:
+ control = row['control_tag_align']
+ control_basename = os.path.basename(
+ utils.strip_extensions(control, ['.filt.nodup.bedpe.gz']))
+ control_tmp = bedpe_to_tagalign(control , "control_basename")
+ path_to_control = cwd + '/' + control_tmp
+ design_new_df.loc[index, 'control_tag_align'] = \
+ path_to_control
+
else:
path_to_pool_control = pool_control
@@ -278,10 +326,11 @@ def main():
tmp_metadata['sample_id'] = experiment_id + '_pooled'
tmp_metadata['replicate'] = 'pooled'
tmp_metadata['xcor'] = 'Calculate'
- path_to_file = cwd + '/' + pool_experiment
+ path_to_file = cwd + '/' + pool_experiment_se
tmp_metadata['tag_align'] = path_to_file
design_new_df = design_new_df.append(tmp_metadata)
+
# Write out new dataframe
design_new_df.to_csv(experiment_id + '_ppr.tsv',
header=True, sep='\t', index=False)
--
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