From c84c66cc5bb388262ee1eda181feac94449eef3f Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 12 Feb 2020 00:25:08 -0600
Subject: [PATCH] Solve the minimum fragment length to be at least 50bp or
through an error.
---
.gitignore | 1 -
test_data/test_cross.qc | 1 +
workflow/scripts/call_peaks_macs.py | 18 ++++++++++++++----
workflow/tests/test_call_peaks_macs.py | 19 +++++++++++++++++++
4 files changed, 34 insertions(+), 5 deletions(-)
create mode 100644 test_data/test_cross.qc
diff --git a/.gitignore b/.gitignore
index bf385c6..7756350 100644
--- a/.gitignore
+++ b/.gitignore
@@ -108,5 +108,4 @@ report*.html*
timeline*.html*
/workflow/output/*
/work/*
-/test_data/*
/.nextflow/*
diff --git a/test_data/test_cross.qc b/test_data/test_cross.qc
new file mode 100644
index 0000000..6fbc0ad
--- /dev/null
+++ b/test_data/test_cross.qc
@@ -0,0 +1 @@
+Test.20.tagAlign.gz 18588987 0,20,33 0.211525291335199,0.211232019956852,0.211139666755398 35 0.2123067 1500 0.209429 1.01001 0.7284536 0
diff --git a/workflow/scripts/call_peaks_macs.py b/workflow/scripts/call_peaks_macs.py
index 6981262..f7527eb 100644
--- a/workflow/scripts/call_peaks_macs.py
+++ b/workflow/scripts/call_peaks_macs.py
@@ -138,10 +138,20 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
with open(xcor, 'r') as xcor_fh:
firstline = xcor_fh.readline()
frag_lengths = firstline.split()[2] # third column
- fragment_length = frag_lengths.split(',')[0] # grab first value
- logger.info("Fraglen %s", fragment_length)
- if int(fragment_length) < 1:
- fragment_length = "200"
+ frag_lengths_array = frag_lengths.split(',')
+ fragment_length = 0
+ fragment = False
+ # Loop through all values of fragment length
+ for f in frag_lengths.split(','):
+ fragment_length = f
+ logger.info("Fraglen %s", fragment_length)
+ if int(fragment_length) > 50:
+ fragment = True
+ break
+
+ if fragment == False:
+ logger.info('Error in cross-correlation analysis: %s', frag_lengths_array)
+ raise Exception("Error in cross-correlation analysis: %s" % frag_lengths_array)
# Generate narrow peaks and preliminary signal tracks
diff --git a/workflow/tests/test_call_peaks_macs.py b/workflow/tests/test_call_peaks_macs.py
index cd94e17..3b4404d 100644
--- a/workflow/tests/test_call_peaks_macs.py
+++ b/workflow/tests/test_call_peaks_macs.py
@@ -3,10 +3,29 @@
import pytest
import os
import utils
+from io import StringIO
+import call_peaks_macs
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/callPeaksMACS/'
+test_data_path = os.path.dirname(os.path.abspath(__file__)) + \
+ '/../../test_data/'
+
+
+@pytest.mark.unit
+def test_fragment_length():
+ experiment = "experiment.tagAlign.gz"
+ control = "control.tagAlign.gz"
+ prefix = 'test'
+ genome_size = 'hs'
+ chrom_sizes = 'genomefile.txt'
+ cross_qc = os.path.join(test_data_path, 'test_cross.qc')
+ with pytest.raises(Exception) as excinfo:
+ call_peaks_macs.call_peaks_macs(experiment, cross_qc, control, prefix, genome_size, chrom_sizes)
+ assert str(excinfo.value) == "Error in cross-correlation analysis: ['0', '20', '33']"
+
+
@pytest.mark.singleend
def test_fc_signal_singleend():
--
GitLab