From 2b651306c155f22afa8d80842f319d601fe6c905 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 14 Jan 2019 07:41:54 -0600
Subject: [PATCH] Update tests and output file names.
---
workflow/scripts/call_peaks_macs.py | 2 +-
workflow/scripts/map_reads.py | 4 ++--
workflow/scripts/trim_reads.py | 6 +++---
workflow/tests/test_convert_reads.py | 4 ++--
workflow/tests/test_trim_reads.py | 8 ++++----
workflow/tests/test_xcor.py | 4 ++--
6 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/workflow/scripts/call_peaks_macs.py b/workflow/scripts/call_peaks_macs.py
index 69a5968..99e2900 100644
--- a/workflow/scripts/call_peaks_macs.py
+++ b/workflow/scripts/call_peaks_macs.py
@@ -126,7 +126,7 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
# Remove coordinates outside chromosome sizes
int_narrowpeak_fn = '%s_peaks.narrowPeak' % (prefix)
- narrowpeak_fn = '%s_peaks.narrowPeak' % (prefix)
+ narrowpeak_fn = '%s.narrowPeak' % (prefix)
clipped_narrowpeak_fn = 'clipped-%s' % (narrowpeak_fn)
diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py
index 3c20ac8..a1f8161 100644
--- a/workflow/scripts/map_reads.py
+++ b/workflow/scripts/map_reads.py
@@ -104,7 +104,7 @@ def generate_sa(fastq, reference):
def align_se(fastq, sai, reference, fastq_basename):
'''Use BWA to align SE data.'''
- bam_filename = '%s.srt.bam' % (fastq_basename)
+ bam_filename = '%s.bam' % (fastq_basename)
steps = [
"bwa samse %s %s %s"
@@ -125,7 +125,7 @@ def align_pe(fastq, sai, reference, fastq_basename):
sam_filename = "%s.sam" % (fastq_basename)
badcigar_filename = "%s.badReads" % (fastq_basename)
- bam_filename = '%s.srt.bam' % (fastq_basename)
+ bam_filename = '%s.bam' % (fastq_basename)
# Remove read pairs with bad CIGAR strings and sort by position
steps = [
diff --git a/workflow/scripts/trim_reads.py b/workflow/scripts/trim_reads.py
index e31ec93..bf5f901 100644
--- a/workflow/scripts/trim_reads.py
+++ b/workflow/scripts/trim_reads.py
@@ -76,15 +76,15 @@ def rename_reads(fastq, sample, paired):
if paired: # paired-end data
# Set file names
- renamed_fastq.append(cwd + '/' + sample + '_R1.fastq.gz')
- renamed_fastq.append(cwd + '/' + sample + '_R2.fastq.gz')
+ renamed_fastq.append(cwd + '/' + sample + '_R1.fq.gz')
+ renamed_fastq.append(cwd + '/' + sample + '_R2.fq.gz')
# Great symbolic links
os.symlink(fastq[0], renamed_fastq[0])
os.symlink(fastq[1], renamed_fastq[1])
else:
# Set file names
- renamed_fastq.append(cwd + '/' + sample + '_R1.fastq.gz')
+ renamed_fastq.append(cwd + '/' + sample + '_R1.fq.gz')
# Great symbolic links
os.symlink(fastq[0], renamed_fastq[0])
diff --git a/workflow/tests/test_convert_reads.py b/workflow/tests/test_convert_reads.py
index 753b54b..d1ef045 100644
--- a/workflow/tests/test_convert_reads.py
+++ b/workflow/tests/test_convert_reads.py
@@ -9,8 +9,8 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_convert_reads_singleend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.tagAlign.gz'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.bedse.gz'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI.tagAlign.gz'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI.bedse.gz'))
@pytest.mark.pairedend
diff --git a/workflow/tests/test_trim_reads.py b/workflow/tests/test_trim_reads.py
index aeb3eb3..5220f18 100644
--- a/workflow/tests/test_trim_reads.py
+++ b/workflow/tests/test_trim_reads.py
@@ -13,9 +13,9 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_trim_reads_singleend():
raw_fastq = test_data_path + 'ENCFF833BLU.fastq.gz'
- trimmed_fastq = test_output_path + 'ENCLB144FDT_trimmed.fq.gz'
+ trimmed_fastq = test_output_path + 'ENCLB144FDT_R1_trimmed.fq.gz'
trimmed_fastq_report = test_output_path + \
- 'ENCLB144FDT.fastq.gz_trimming_report.txt'
+ 'ENCLB144FDT_R1_trimmed.fq.gz_trimming_report.txt'
assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
assert os.path.getsize(trimmed_fastq) == 2512853101
assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]
@@ -24,9 +24,9 @@ def test_trim_reads_singleend():
@pytest.mark.pairedend
def test_trim_reads_pairedend():
raw_fastq = test_data_path + 'ENCFF582IOZ.fastq.gz'
- trimmed_fastq = test_output_path + 'ENCFF582IOZ_val_2.fq.gz'
+ trimmed_fastq = test_output_path + 'ENCLB637LZP_R2_trimmed.fq.gz'
trimmed_fastq_report = test_output_path + \
- 'ENCLB637LZP.fastq.gz_trimming_report.txt'
+ 'ENCLB637LZP_R2_trimmed.fq.gz_trimming_report.txt'
assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
assert os.path.getsize(trimmed_fastq) == 2229312710
assert 'Trimming mode: paired-end' in open(trimmed_fastq_report).readlines()[4]
diff --git a/workflow/tests/test_xcor.py b/workflow/tests/test_xcor.py
index 69006a0..40548cf 100644
--- a/workflow/tests/test_xcor.py
+++ b/workflow/tests/test_xcor.py
@@ -10,8 +10,8 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_cross_singleend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCFF833BLU.cc.plot.pdf'))
- qc_file = os.path.join(test_output_path,"ENCFF833BLU.cc.qc")
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.cc.plot.pdf'))
+ qc_file = os.path.join(test_output_path,"ENCLB144FDT.cc.qc")
df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
assert df_xcor[2].iloc[0] == '190,200,210'
assert df_xcor[8].iloc[0] == 1.025906
--
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