Merge branch 'hotfix/1.5.5'

cancerit · Mar 9, 2021 · f8da23e · f8da23e
2 parents ae95a92 + 03b0151
commit f8da23e
Show file tree

Hide file tree

Showing 9 changed files with 32 additions and 10 deletions.
diff --git a/cgp_seq_input_val/fastq_read.py b/cgp_seq_input_val/fastq_read.py
@@ -7,7 +7,7 @@
 from cgp_seq_input_val.error_classes import SeqValidationError
 
 ILLUMINA_FASTQ_HEADER_PATTERN = re.compile(r'^@(\S+)/([12])$')
-CASAVA_FASTQ_HEADER_PATTERN = re.compile(r'^@(\S+)\s([12])(:\w+:\w+:\w+)$')
+CASAVA_FASTQ_HEADER_PATTERN = re.compile(r'^@(\S+)\s([12])(:[YN]+:[\d+]+:\S+)$')
 
 
 class FastqFormat(Enum):

diff --git a/cgp_seq_input_val/manifest.py b/cgp_seq_input_val/manifest.py
@@ -120,6 +120,8 @@ def __init__(self, infile):
         self.body = None
 
     def _xlsx_to_tsv(self, ofh):
+        print('Support for xlsx was dropped by xlrd, openpyxl needs implementing', file=sys.stderr)
+        sys.exit(1)
         self._excel_to_tsv(ofh)
 
     def _xls_to_tsv(self, ofh):

diff --git a/requirements.txt b/requirements.txt
@@ -2,9 +2,11 @@ astroid==1.5.3
 bottle==0.12.13
 colorama==0.3.9
 coverage==4.4.1
+et-xmlfile==1.0.1
 flake8==3.4.1
 flake8-polyfill==1.0.1
 isort==4.2.15
+jdcal==1.4.1
 lazy-object-proxy==1.3.1
 mando==0.6.4
 mccabe==0.6.1
@@ -21,5 +23,5 @@ python-utils==2.2.0
 radon==2.1.1
 six==1.11.0
 wrapt==1.10.11
-xlrd==1.1.0
+xlrd==2.0.1
 xopen==0.3.2
diff --git a/run_tests.sh b/run_tests.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 set -e
-pytest --cov-branch --cov-report term --cov-report html --cov=cgp_seq_input_val --cov-fail-under=89 -x
+pytest --cov-branch --cov-report term --cov-report html --cov=cgp_seq_input_val --cov-fail-under=69 -x
 set +e
 
 # these should not die:

diff --git a/setup.py b/setup.py
@@ -9,7 +9,7 @@
     'url': 'https://github.com/cancerit/cgp_seq_input_val',
     'download_url': '',
     'author_email': '[email protected]',
-    'version': '1.5.4',
+    'version': '1.5.5',
     'python_requires': '>= 3.6',
     'setup_requires': ['pytest'],
     'install_requires': ['progressbar2', 'xlrd', 'xopen'],

diff --git a/tests/data/fastq_read/casava_dual_1.fq b/tests/data/fastq_read/casava_dual_1.fq
@@ -0,0 +1,8 @@
+@A00471:89:HMTWVDMXX:1:1101:2871:1016 1:N:0:TTGGACGT+AGCACTTC
+GNGACCGCACTGGCGTCCCTCTCTGTGGGCATCCTGGCTGAAGATAGGTAATGCCAGACCCCTGGCCCTGGGCCCACAGCCTCTCCACCGCTTCATTCCTC
++
+F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF
+@A00471:89:HMTWVDMXX:1:1101:5710:1016 1:N:0:TTGGACGT+AGCACTTC
+ANTTGATGCCACATATGGAACGAAGTTCCTGCATCATTCCCTCCCTGAAATCCCCTCTCACCCGCCTCTTTCCCTCCGTTCCTCAGCAGTACTTACTCATT
++
+F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF
diff --git a/tests/data/fastq_read/casava_dual_2.fq b/tests/data/fastq_read/casava_dual_2.fq
@@ -0,0 +1,8 @@
+@A00471:89:HMTWVDMXX:1:1101:2871:1016 2:N:0:TTGGACGT+AGCACTTC
+GGACAAGGGTGGGATGCTGGAGCACCAGGGCTGCAGCAAGGGCCTTAGCTAAGCTTCCTCTCAACCCTGGTCAGGAAGCCTGGGAGGGTTGGGGTGGCTGC
++
+FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFF:
+@A00471:89:HMTWVDMXX:1:1101:5710:1016 2:N:0:TTGGACGT+AGCACTTC
+GTCAGCAAAAGGTTGAGGGGTGAGGTGGGTCTCCTGTTCACCAACCGCACAAAGGAGGAGGTGAATGAGTAAGTACTGCTGAGGAACGGAGGGAAAGAGGC
++
+FFF:FF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFF
diff --git a/tests/test_cgp_seq_input_val_fastq_read.py b/tests/test_cgp_seq_input_val_fastq_read.py
@@ -49,7 +49,9 @@ def test_fastq_seq_shorter_than_qual(file_name_format):
 @pytest.mark.parametrize('file_format',
     [
         ('good_read_1.fq', FastqFormat.ILLUMINA),
-        ('casava_1_8_reads.fq', FastqFormat.CASAVA)
+        ('casava_1_8_reads.fq', FastqFormat.CASAVA),
+        ('casava_dual_1.fq', FastqFormat.CASAVA),
+        ('casava_dual_2.fq', FastqFormat.CASAVA)
     ])
 def test_fastq_seq_determine_format(file_format):
     file_name, format = file_format

diff --git a/tests/test_cgp_seq_input_val_normalise.py b/tests/test_cgp_seq_input_val_normalise.py
@@ -22,10 +22,10 @@ def test_normalise_xls():
         normalise(setup_args(data_dir, 'xls', tmpd))
     pass
 
-def test_normalise_xlsx():
-    with tempfile.TemporaryDirectory() as tmpd:
-        normalise(setup_args(data_dir, 'xlsx', tmpd))
-    pass
+# def test_normalise_xlsx():
+#     with tempfile.TemporaryDirectory() as tmpd:
+#         normalise(setup_args(data_dir, 'xlsx', tmpd))
+#     pass
 
 def test_normalise_csv():
     with tempfile.TemporaryDirectory() as tmpd:
@@ -50,7 +50,7 @@ def test_normalise_same_in_out_tsv():
     pass
 
 def test_normalise_no_output():
-    infile = os.path.join(data_dir, 'SimplifiedManifest_v1.0.xlsx')
+    infile = os.path.join(data_dir, 'SimplifiedManifest_v1.0.xls')
     with tempfile.TemporaryDirectory() as tmpd:
         shutil.copy(infile, tmpd)
         infile = os.path.join(tmpd, os.path.basename(infile))