Formatting

karel-brinda · Jun 20, 2017 · d79f875 · d79f875
1 parent 82c53e8
commit d79f875
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Showing 8 changed files with 459 additions and 461 deletions.
diff --git a/rnftools/rnfformat/FqCreator.py b/rnftools/rnfformat/FqCreator.py
@@ -2,6 +2,7 @@
 import rnftools
 import os
 
+
 class FqCreator:
 	"""Class for writing RNF reads to FASTQ files.
 
@@ -21,25 +22,25 @@ class FqCreator:
 	"""
 
 	def __init__(
-				self,
-				fastq_fo,
-				read_tuple_id_width=16,
-				genome_id_width=2,
-				chr_id_width=2,
-				coor_width=8,
-				info_reads_in_tuple=True,
-				info_simulator=None,
-			):
-		self._info_simulator=info_simulator
-		self._info_reads_in_tuple=info_reads_in_tuple
-		self._rnf_profile=rnftools.rnfformat.RnfProfile(
-				read_tuple_id_width=read_tuple_id_width,
-				genome_id_width=genome_id_width,
-				chr_id_width=chr_id_width,
-				coor_width=coor_width,
-			)
-		self._fq_file=fastq_fo
-		self.current_read_tuple_id=None
+			self,
+			fastq_fo,
+			read_tuple_id_width=16,
+			genome_id_width=2,
+			chr_id_width=2,
+			coor_width=8,
+			info_reads_in_tuple=True,
+			info_simulator=None,
+	):
+		self._info_simulator = info_simulator
+		self._info_reads_in_tuple = info_reads_in_tuple
+		self._rnf_profile = rnftools.rnfformat.RnfProfile(
+			read_tuple_id_width=read_tuple_id_width,
+			genome_id_width=genome_id_width,
+			chr_id_width=chr_id_width,
+			coor_width=coor_width,
+		)
+		self._fq_file = fastq_fo
+		self.current_read_tuple_id = None
 		self.empty()
 
 	def __del__(self):
@@ -49,35 +50,35 @@ def flush_read_tuple(self):
 		"""Flush the internal buffer of reads.
 		"""
 		if not self.is_empty():
-			suffix_comment_buffer=[]
+			suffix_comment_buffer = []
 			if self._info_simulator is not None:
 				suffix_comment_buffer.append(self._info_simulator)
 			if self._info_reads_in_tuple:
-				#todo: orientation (FF, FR, etc.)
-				#orientation="".join([])
+				# todo: orientation (FF, FR, etc.)
+				# orientation="".join([])
 				suffix_comment_buffer.append("reads-in-tuple:{}".format(len(self.seqs_bases)))
-			if len(suffix_comment_buffer)!=0:
-				suffix_comment="[{}]".format(",".join(suffix_comment_buffer))
+			if len(suffix_comment_buffer) != 0:
+				suffix_comment = "[{}]".format(",".join(suffix_comment_buffer))
 			else:
-				suffix_comment=""
-
-			rnf_name=self._rnf_profile.get_rnf_name(
-						rnftools.rnfformat.ReadTuple(
-								segments=self.segments,
-								read_tuple_id=self.current_read_tuple_id,
-								suffix=suffix_comment,
-							)
-					)
+				suffix_comment = ""
+
+			rnf_name = self._rnf_profile.get_rnf_name(
+				rnftools.rnfformat.ReadTuple(
+					segments=self.segments,
+					read_tuple_id=self.current_read_tuple_id,
+					suffix=suffix_comment,
+				)
+			)
 			fq_reads = [
 				os.linesep.join([
-						"@{rnf_name}{read_suffix}".format(
-								rnf_name=rnf_name,
-								read_suffix="/{}".format(str(i+1)) if len(self.seqs_bases)>1 else "",
-							),
-						self.seqs_bases[i],
-						"+",
-						self.seqs_qualities[i],
-					])
+					"@{rnf_name}{read_suffix}".format(
+						rnf_name=rnf_name,
+						read_suffix="/{}".format(str(i + 1)) if len(self.seqs_bases) > 1 else "",
+					),
+					self.seqs_bases[i],
+					"+",
+					self.seqs_qualities[i],
+				])
 				for i in range(len(self.seqs_bases))
 			]
 			self._fq_file.write(os.linesep.join(fq_reads))
@@ -87,22 +88,21 @@ def flush_read_tuple(self):
 	def empty(self):
 		"""Empty all internal buffers.
 		"""
-		self.seqs_bases=[]
-		self.seqs_qualities=[]
-		self.segments=[]
+		self.seqs_bases = []
+		self.seqs_qualities = []
+		self.segments = []
 
 	def is_empty(self):
 		"""All internal buffer empty?
 		"""
-		return self.seqs_bases==[] and self.seqs_qualities==[] and self.segments==[]
-
+		return self.seqs_bases == [] and self.seqs_qualities == [] and self.segments == []
 
 	def add_read(self,
-				read_tuple_id,
-				bases,
-				qualities,
-				segments,
-			):
+			read_tuple_id,
+			bases,
+			qualities,
+			segments,
+	):
 
 		"""Add a new read to the current buffer. If it is a new read tuple (detected from ID), the buffer will be flushed.
 
@@ -117,9 +117,9 @@ def add_read(self,
 		assert type(qualities) is str, "Wrong type of qualities: '{}'".format(qualities)
 		assert type(segments) is tuple or type(segments) is list
 
-		if self.current_read_tuple_id!=read_tuple_id:
+		if self.current_read_tuple_id != read_tuple_id:
 			self.flush_read_tuple()
-		self.current_read_tuple_id=read_tuple_id
+		self.current_read_tuple_id = read_tuple_id
 
 		self.seqs_bases.append(bases)
 		self.seqs_qualities.append(qualities)