From 276dac3b112928c1aaf4696ad234328995095008 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Thu, 7 Mar 2019 13:33:22 -0600
Subject: [PATCH] Fix rename.
---
workflow/scripts/pool_and_psuedoreplicate.py | 23 +++++++++++++++-----
1 file changed, 17 insertions(+), 6 deletions(-)
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 94b5d12..0f2c295 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -5,6 +5,9 @@
import argparse
import logging
import os
+import subprocess
+import shutil
+import shlex
import pandas as pd
import numpy as np
import utils
@@ -140,21 +143,29 @@ def self_psuedoreplication(tag_file, prefix, paired):
splits_prefix = 'temp_split'
- out, err = utils.run_pipe([
- 'gzip -dc %s' % (tag_file),
- 'shuf --random-source=<(openssl enc -aes-256-ctr -pass pass:$(zcat -f %s | wc -c) -nosalt </dev/zero 2>/dev/null)' % (tag_file),
- 'split -d -l %d - %s' % (lines_per_rep, splits_prefix)])
+ psuedo_command = 'bash -c "zcat {} | shuf --random-source=<(openssl enc -aes-256-ctr -pass pass:$(zcat -f {} | wc -c) -nosalt </dev/zero 2>/dev/null) | '
+ psuedo_command += 'split -d -l {} - {}."'
+ psuedo_command = psuedo_command.format(
+ tag_file,
+ tag_file,
+ int(lines_per_rep),
+ splits_prefix)
+ logger.info("Running psuedo with %s", psuedo_command)
+ subprocess.check_call(shlex.split(psuedo_command))
+
+ logger.info("Running bwa with %s", bwa_command)
+ subprocess.check_call(shlex.split(bwa_command), stdout=sai_file)
+
# Convert read pairs to reads into standard tagAlign file
for i, index in enumerate([0, 1]):
- string_index = '0' + str(index)
+ string_index = '.0' + str(index)
steps = ['cat %s' % (splits_prefix + string_index)]
if paired:
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}'"""])
steps.extend(['gzip -cn'])
out, err = utils.run_pipe(steps, outfile=pseudoreplicate_dict[i])
- os.remove(splits_prefix + string_index)
return pseudoreplicate_dict
--
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