fixed fastx uppercase

Author: lmdu

docs/source/changelog.rst

@@ -1,6 +1,11 @@
 Changelog
 =========
 
+Version 1.0.1 (2023-03-28)
+--------------------------
+
+- Fixed invalid uppercase when iterating fastx
+
 Version 1.0.0 (2023-03-24)
 --------------------------
 

src/fastx.c

@@ -12,6 +12,7 @@ PyObject *pyfastx_fastx_fasta_comment(kseq_t* kseqs) {
 }
 
 PyObject *pyfastx_fastx_fasta_upper(kseq_t* kseqs) {
+	upper_string(kseqs->seq.s, kseqs->seq.l);
 	return pyfastx_fastx_fasta(kseqs);
 }
 

src/version.h

@@ -1,2 +1,2 @@
-#define PYFASTX_VERSION "1.0.0"
+#define PYFASTX_VERSION "1.0.1"
 #define ZRAN_VERSION "1.7.0"

tests/test_fasta.py

@@ -165,12 +165,25 @@ def test_iter_tuple(self):
 			expect = str(self.faidx[name])
 			self.assertEqual(expect, seq)
 
+	def test_iter_upper(self):
+		fa = pyfastx.Fasta(flat_fasta, build_index=False, uppercase=True)
+
+		for name, seq in fa:
+			self.assertEqual(seq, self.faidx[name.split()[0]][:].seq)
+
 	def test_iter_full_name(self):
 		fa = pyfastx.Fasta(flat_fasta, build_index=False, full_name=True)
 
 		for name, _ in fa:
 			self.assertTrue(name, self.fastx[name.split()[0]].description)
 
+	def test_iter_upper_full_name(self):
+		fa = pyfastx.Fasta(flat_fasta, build_index=False, uppercase=True, full_name=True)
+
+		for name, seq in fa:
+			self.assertEqual(name, self.fastx[name.split()[0]].description)
+			self.assertEqual(seq, self.fastx[name.split()[0]].seq)
+
 	def test_key_func(self):
 		del self.fastx
 
@@ -301,10 +314,13 @@ def test_exception(self):
 			self.fastx.nl(101)
 
 		with self.assertRaises(RuntimeError):
-			with open('non.fa', 'w') as fw:
+			non_fa = 'non.fa'
+			with open(non_fa, 'w') as fw:
 				fw.write('abc')
 
-			pyfastx.Fasta('non.fa')
+			pyfastx.Fasta(non_fa)
+
+			os.remove(non_fa)
 
 if __name__ == '__main__':
 	unittest.main()

tests/test_fastq.py

@@ -102,6 +102,55 @@ def test_fastq(self):
 		self.assertEqual(self.fastq.maxqual, 70)
 		self.assertEqual(self.fastq.minqual, 35)
 
+	def test_platform(self):
+		#test unknown
+		fqfile = 'test.fq'
+		with open(fqfile, 'w') as fw:
+			fw.write("@read1\n")
+			fw.write("AAAAAAAAAA\n")
+			fw.write("+\n")
+			fw.write("          \n")
+		fq = pyfastx.Fastq(fqfile)
+		self.assertEqual(fq.encoding_type, ['Unknown'])
+		os.remove("{}.fxi".format(fqfile))
+
+		with open(fqfile, 'w') as fw:
+			fw.write("@read1\n")
+			qs = []
+			for i in range(59, 105):
+				qs.append(chr(i))
+			fw.write("{}\n".format('A'*len(qs)))
+			fw.write("+\n")
+			fw.write("{}\n".format(''.join(qs)))
+		fq = pyfastx.Fastq(fqfile)
+		self.assertIn("Solexa Solexa+64", fq.encoding_type)
+		os.remove("{}.fxi".format(fqfile))
+
+		with open(fqfile, 'w') as fw:
+			fw.write("@read1\n")
+			qs = []
+			for i in range(64, 105):
+				qs.append(chr(i))
+			fw.write("{}\n".format('A'*len(qs)))
+			fw.write("+\n")
+			fw.write("{}\n".format(''.join(qs)))
+		fq = pyfastx.Fastq(fqfile)
+		self.assertIn("Illumina 1.3+ Phred+64", fq.encoding_type)
+		os.remove("{}.fxi".format(fqfile))
+
+		with open(fqfile, 'w') as fw:
+			fw.write("@read1\n")
+			qs = []
+			for i in range(66, 105):
+				qs.append(chr(i))
+			fw.write("{}\n".format('A'*len(qs)))
+			fw.write("+\n")
+			fw.write("{}\n".format(''.join(qs)))
+		fq = pyfastx.Fastq(fqfile)
+		self.assertIn("Illumina 1.5+ Phred+64", fq.encoding_type)
+		os.remove("{}.fxi".format(fqfile))
+		os.remove(fqfile)
+
 	def test_negative(self):
 		read = self.fastq[-1]
 		self.assertEqual(read.name, self.reads[len(self.reads)-1][0])

tests/test_fqkeys.py

@@ -52,4 +52,4 @@ def test_fastq_key(self):
 
 	def test_exception(self):
 		with self.assertRaises(IndexError):
-			_ = self.keys[self.count]
+			_ = self.keys[self.count*2]

tests/test_sequence.py

@@ -183,8 +183,9 @@ def test_seq_repr(self):
 		self.assertEqual(s.name, "{}:{}-{}".format(n, s.start, s.end))
 
 	def test_full_compo(self):
+		idx = self.get_random_index()
 		fas = pyfastx.Fasta(flat_fasta, full_index=True)
-		self.assertEqual(self.fastx[0].composition, fas[0].composition)
+		self.assertEqual(self.fastx[idx].composition, fas[idx].composition)
 
 	def test_seq_exception(self):
 		with self.assertRaises(RuntimeError):