mirror of
https://github.com/biopython/biopython.git
synced 2025-10-20 13:43:47 +08:00
black v23.9.1
Had to tweak four conflicts with D202
This commit is contained in:
Peter Cock
@ -378,7 +378,7 @@ class SummaryInfo:
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# fill in the ic_vector member: holds IC for each column
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# reset ic_vector to empty list at each call
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self.ic_vector = []
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for (i, k) in enumerate(info_content):
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for i, k in enumerate(info_content):
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self.ic_vector.append(info_content[i + start])
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return total_info
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@ -1191,7 +1191,6 @@ class _ExtraIndex:
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class _ExtraIndices(list):
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formatter = struct.Struct("=HHQ52x")
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def __init__(self, names, declaration):
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@ -1244,7 +1243,6 @@ class _ZoomLevel:
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class _ZoomLevels(list):
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bbiResIncrement = 4
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bbiMaxZoomLevels = 10
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size = _ZoomLevel.formatter.size * bbiMaxZoomLevels
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@ -1352,7 +1350,6 @@ class _Region:
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class _RegionSummary(_Summary):
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__slots__ = _Region.__slots__ + _Summary.__slots__
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formatter = struct.Struct("=IIIIffff")
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@ -1678,7 +1675,6 @@ class _RedBlackTreeNode:
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class _RTreeFormatter:
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signature = 0x2468ACE0
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def __init__(self, byteorder="="):
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@ -2019,11 +2015,9 @@ class _RTreeFormatter:
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class _BPlusTreeFormatter:
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signature = 0x78CA8C91
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def __init__(self, byteorder="="):
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# Supplemental Table 8: Chromosome B+ tree header
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# magic 4 bytes, unsigned
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# blockSize 4 bytes, unsigned
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@ -543,9 +543,7 @@ class AlignmentIterator(interfaces.AlignmentIterator):
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coordinates[1, 0] = qs
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operations = bytearray(n)
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i = 0
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for (operation, query_step, target_step) in zip(
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ops, words[10::3], words[11::3]
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):
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for operation, query_step, target_step in zip(ops, words[10::3], words[11::3]):
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query_step = int(query_step)
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target_step = int(target_step)
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if operation == "M": # Match
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@ -184,7 +184,7 @@ def MafIterator(handle, seq_count=None):
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ref = records[0].seq
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new = []
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for (letter, ref_letter) in zip(sequence, ref):
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for letter, ref_letter in zip(sequence, ref):
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new.append(ref_letter if letter == "." else letter)
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sequence = "".join(new)
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@ -469,7 +469,6 @@ class StockholmIterator(AlignmentIterator):
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self.seq_col_annotation = gr
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if ids and seqs:
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if (
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self.records_per_alignment is not None
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and self.records_per_alignment != len(ids)
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@ -165,7 +165,6 @@ def __read(handle):
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record = None
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for line in handle:
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key, value = line[:2], line[5:].rstrip()
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if key == "ID":
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record = Record()
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@ -350,7 +350,7 @@ class Chromosome(_ChromosomeComponent):
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"start",
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),
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]:
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for (y1, y2, color, back_color, name) in labels:
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for y1, y2, color, back_color, name in labels:
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cur_drawing.add(
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Line(x1, y1, x2, y2, strokeColor=color, strokeWidth=0.25)
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)
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@ -494,7 +494,6 @@ class ChromosomeSegment(_ChromosomeComponent):
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This may be overlapped by any sub-feature labels on other segments!
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"""
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if self.label is not None:
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label_x = 0.5 * (self.start_x_position + self.end_x_position) + (
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self.chr_percent + 0.05
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) * (self.end_x_position - self.start_x_position)
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@ -203,7 +203,7 @@ def draw_polygon(
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strokecolor, color = _stroke_and_fill_colors(color, border)
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xy_list = []
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for (x, y) in list_of_points:
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for x, y in list_of_points:
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xy_list.append(x)
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xy_list.append(y)
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@ -193,6 +193,5 @@ class Feature:
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################################################################################
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if __name__ == "__main__":
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# Test code
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gdf = Feature()
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@ -93,7 +93,7 @@ class GraphData:
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def set_data(self, data):
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"""Add data as a list of (position, value) tuples."""
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for (pos, val) in data: # Fill data dictionary
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for pos, val in data: # Fill data dictionary
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self.data[pos] = val
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def get_data(self):
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@ -231,7 +231,7 @@ class KGMLCanvas:
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else:
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self.drawing.setLineWidth(1)
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p.moveTo(x, y)
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for (x, y) in graphics.coords:
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for x, y in graphics.coords:
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p.lineTo(x, y)
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self.drawing.drawPath(p)
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self.drawing.setLineWidth(1) # Return to default
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@ -607,7 +607,7 @@ class Graphics:
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"fgcolor": fghex,
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"bgcolor": bghex,
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}
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for (n, attr) in [
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for n, attr in [
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("x", "_x"),
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("y", "_y"),
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("width", "_width"),
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@ -850,7 +850,7 @@ class Relation:
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"entry2": str(self._entry2),
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"type": self.type,
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}
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for (name, value) in self.subtypes:
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for name, value in self.subtypes:
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subtype = ET.Element("subtype")
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subtype.attrib = {"name": name, "value": str(value)}
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relation.append(subtype)
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@ -200,7 +200,6 @@ def kegg_get(dbentries, option=None):
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#
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# <option> = aaseq | ntseq | mol | kcf | image
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if option in ["aaseq", "ntseq", "mol", "kcf", "image", "kgml", "json"]:
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resp = _q("get", dbentries, option)
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elif option:
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raise ValueError("Invalid option arg for kegg get request.")
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@ -265,7 +264,6 @@ def kegg_conv(target_db, source_db, option=None):
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and source_db in ["drug", "compound", "glycan"]
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)
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):
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if option:
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resp = _q("conv", target_db, source_db, option)
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else:
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@ -95,7 +95,6 @@ class Peaklist:
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def __init__(self, infn):
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"""Initialize the class."""
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with open(infn) as infile:
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# Read in the header lines
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self.firstline = infile.readline().split("\012")[0]
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self.axislabels = infile.readline().split("\012")[0]
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@ -441,8 +441,8 @@ class Tree(Nodes.Chain):
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and tree2.node(n).data.support >= threshold
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]
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conflict = []
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for (st1, sup1) in t1:
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for (st2, sup2) in t2:
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for st1, sup1 in t1:
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for st2, sup2 in t2:
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if not st1.issubset(st2) and not st2.issubset(
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st1
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): # don't hiccup on upstream nodes
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@ -586,7 +586,7 @@ class Tree(Nodes.Chain):
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terminals.remove(newsplit)
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# distribute taxon labels randomly
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random.shuffle(taxon_list)
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for (node, name) in zip(terminals, taxon_list):
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for node, name in zip(terminals, taxon_list):
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self.node(node).data.taxon = name
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def display(self):
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@ -226,7 +226,7 @@ class HSExposureCA(_AbstractHSExposure):
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fp.write("obj=[\n")
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fp.write("BEGIN, LINES,\n")
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fp.write(f"COLOR, {1.0:.2f}, {1.0:.2f}, {1.0:.2f},\n")
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for (ca, cb) in self.ca_cb_list:
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for ca, cb in self.ca_cb_list:
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x, y, z = ca.get_array()
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fp.write(f"VERTEX, {x:.2f}, {y:.2f}, {z:.2f},\n")
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x, y, z = cb.get_array()
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@ -72,7 +72,7 @@ class MMCIF2Dict(dict):
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# quote character of the currently open quote, or None if no quote open
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quote_open_char = None
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start_i = 0
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for (i, c) in enumerate(line):
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for i, c in enumerate(line):
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if c in self.whitespace_chars:
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if in_token and not quote_open_char:
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in_token = False
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@ -135,7 +135,6 @@ class MMCIFParser:
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return self.header
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def _build_structure(self, structure_id):
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# two special chars as placeholders in the mmCIF format
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# for item values that cannot be explicitly assigned
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# see: pdbx/mmcif syntax web page
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@ -203,7 +202,6 @@ class MMCIFParser:
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current_model_id = -1
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current_serial_id = -1
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for i in range(0, len(atom_id_list)):
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# set the line_counter for 'ATOM' lines only and not
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# as a global line counter found in the PDBParser()
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structure_builder.set_line_counter(i)
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@ -399,7 +397,6 @@ class FastMMCIFParser:
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# Private methods
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def _build_structure(self, structure_id, filehandle):
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# two special chars as placeholders in the mmCIF format
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# for item values that cannot be explicitly assigned
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# see: pdbx/mmcif syntax web page
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@ -502,7 +499,6 @@ class FastMMCIFParser:
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current_model_id = -1
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current_serial_id = -1
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for i in range(0, len(atom_id_list)):
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# set the line_counter for 'ATOM' lines only and not
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# as a global line counter found in the PDBParser()
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structure_builder.set_line_counter(i)
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@ -58,7 +58,7 @@ class NeighborSearch:
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# pairs.
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# o pair_list - a list of (entity, entity) tuples
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parent_pair_list = []
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for (e1, e2) in pair_list:
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for e1, e2 in pair_list:
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p1 = e1.get_parent()
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p2 = e2.get_parent()
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if p1 == p2:
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@ -668,7 +668,6 @@ class PDBList:
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if __name__ == "__main__":
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doc = """PDBList.py
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(c) Kristian Rother 2003, Wiktoria Karwicka & Jacek Smietanski 2016
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Contributed to Biopython
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@ -450,6 +450,8 @@ def read_PIC(
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def dihedra_check(ric: IC_Residue) -> None:
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"""Look for required dihedra in residue, generate defaults if set."""
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# This method has some internal functions
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# rnext should be set
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def ake_recurse(akList: List) -> List:
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"""Bulid combinatorics of AtomKey lists."""
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@ -206,7 +206,6 @@ class ShrakeRupley:
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asa_array = np.zeros((n_atoms, 1), dtype=np.int64)
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ptset = set(range(self.n_points))
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for i in range(n_atoms):
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r_i = radii[i]
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# Move sphere to atom
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@ -341,7 +341,7 @@ class PrintFormat:
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resultKeys = sorted(str(x) for x, y in ls)
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map = title or ""
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enzymemap = {}
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for (enzyme, cut) in ls:
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for enzyme, cut in ls:
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for c in cut:
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if c in enzymemap:
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enzymemap[c].append(str(enzyme))
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@ -258,7 +258,6 @@ class Scop:
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n = sunidDict[record.sunid]
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if record.parent != "": # Not root node
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if record.parent not in sunidDict:
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raise ValueError("Incomplete data?")
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@ -175,7 +175,6 @@ def _compute_gapopen_num(hsp):
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def _augment_blast_hsp(hsp, attr):
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"""Calculate the given HSP attribute, for writing (PRIVATE)."""
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if not hasattr(hsp, attr) and not attr.endswith("_pct"):
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# aln_span is number of identical matches + mismatches + gaps
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if attr == "aln_span":
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hsp.aln_span = hsp.ident_num + hsp.mismatch_num + hsp.gap_num
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@ -290,7 +290,6 @@ class BlastXmlParser:
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# </Iteration> marks the end of a single query
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# which means we can process it
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if event == "end" and qresult_elem.tag == "Iteration":
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# we'll use the following schema
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# <!ELEMENT Iteration (
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# Iteration_iter-num,
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@ -417,7 +416,6 @@ class BlastXmlParser:
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root_hit_elem = []
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for hit_elem in root_hit_elem:
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# BLAST sometimes mangles the sequence IDs and descriptions, so we need
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# to extract the actual values.
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raw_hit_id = hit_elem.findtext("Hit_id")
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@ -674,7 +674,6 @@ class BlatPslWriter:
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for hit in qresult:
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for hsp in hit.hsps:
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query_is_protein = getattr(hsp, "query_is_protein", False)
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blocksize_multiplier = 3 if query_is_protein else 1
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|
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|
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@ -188,7 +188,6 @@ def _split_fragment(frag):
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abs_pos = 0
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# split according to hit, then query
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while simil:
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try:
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shifts = re.search(_RE_SHIFTS, simil).group(1)
|
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s_start = simil.find(shifts)
|
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|
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@ -401,7 +401,6 @@ class ExonerateTextParser(_BaseExonerateParser):
|
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|
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# compute start and end coords for each block
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for seq_type in ("query", "hit"):
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|
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# ner blocks and intron blocks require different adjustments
|
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if not has_ner:
|
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opp_type = "hit" if seq_type == "query" else "query"
|
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@ -449,7 +448,6 @@ class ExonerateTextParser(_BaseExonerateParser):
|
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# flag for vulgar line, if present, we can parse coordinates from it
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vulgar_comp = None
|
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while True:
|
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|
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match = re.search(_RE_ALN_ROW, self.line.strip())
|
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# if we have a match, set flags and values
|
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if match and not in_aln_row:
|
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|
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@ -325,7 +325,6 @@ class FastaM10Parser:
|
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line = self.line
|
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|
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while True:
|
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|
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# one line before the hit table
|
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if line.startswith("The best scores are:"):
|
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qres_state = state_QRES_HITTAB
|
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|
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@ -301,7 +301,6 @@ class Hmmer3DomtabHmmhitWriter:
|
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qresult_acc = "-"
|
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|
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for hit in qresult:
|
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|
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# try to get hit accession
|
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try:
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hit_acc = hit.accession
|
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|
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@ -100,7 +100,6 @@ class Hmmer3TextParser:
|
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self._read_until(lambda line: line.startswith("Query:"))
|
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|
||||
while self.line:
|
||||
|
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regx = re.search(_QRE_ID_LEN, self.line)
|
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|
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while not regx:
|
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@ -251,7 +250,6 @@ class Hmmer3TextParser:
|
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or self.line.startswith(" Alignments for each domain:")
|
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or self.line.startswith(">>")
|
||||
):
|
||||
|
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hit_attr = hit_attrs.pop(0)
|
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hit = Hit(hsp_list)
|
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for attr, value in hit_attr.items():
|
||||
@ -348,7 +346,6 @@ class Hmmer3TextParser:
|
||||
|
||||
# parse all the alignment blocks in the hsp
|
||||
while True:
|
||||
|
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regx = None
|
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|
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# check for hit or query line
|
||||
|
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@ -561,7 +561,6 @@ class SeqXmlWriter(SequenceWriter):
|
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|
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# The local species definition is only written if it differs from the global species definition
|
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if local_org != self.species or local_ncbi_taxid != self.ncbiTaxId:
|
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|
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attr = {"name": local_org, "ncbiTaxID": str(local_ncbi_taxid)}
|
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self.xml_generator.startElement("species", AttributesImpl(attr))
|
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self.xml_generator.endElement("species")
|
||||
@ -569,7 +568,6 @@ class SeqXmlWriter(SequenceWriter):
|
||||
def _write_description(self, record):
|
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"""Write the description if given (PRIVATE)."""
|
||||
if record.description:
|
||||
|
||||
if not isinstance(record.description, str):
|
||||
raise TypeError("Description should be of type string")
|
||||
|
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@ -612,9 +610,7 @@ class SeqXmlWriter(SequenceWriter):
|
||||
def _write_dbxrefs(self, record):
|
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"""Write all database cross references (PRIVATE)."""
|
||||
if record.dbxrefs is not None:
|
||||
|
||||
for dbxref in record.dbxrefs:
|
||||
|
||||
if not isinstance(dbxref, str):
|
||||
raise TypeError("dbxrefs should be of type list of string")
|
||||
if dbxref.find(":") < 1:
|
||||
@ -631,17 +627,13 @@ class SeqXmlWriter(SequenceWriter):
|
||||
def _write_properties(self, record):
|
||||
"""Write all annotations that are key value pairs with values of a primitive type or list of primitive types (PRIVATE)."""
|
||||
for key, value in record.annotations.items():
|
||||
|
||||
if key not in ("organism", "ncbi_taxid", "source"):
|
||||
|
||||
if value is None:
|
||||
|
||||
attr = {"name": key}
|
||||
self.xml_generator.startElement("property", AttributesImpl(attr))
|
||||
self.xml_generator.endElement("property")
|
||||
|
||||
elif isinstance(value, list):
|
||||
|
||||
for v in value:
|
||||
if v is None:
|
||||
attr = {"name": key}
|
||||
@ -653,7 +645,6 @@ class SeqXmlWriter(SequenceWriter):
|
||||
self.xml_generator.endElement("property")
|
||||
|
||||
elif isinstance(value, (int, float, str)):
|
||||
|
||||
attr = {"name": key, "value": str(value)}
|
||||
self.xml_generator.startElement("property", AttributesImpl(attr))
|
||||
self.xml_generator.endElement("property")
|
||||
|
||||
@ -318,7 +318,7 @@ class SnapGeneIterator(SequenceIterator):
|
||||
raise ValueError("The file does not start with a SnapGene cookie packet")
|
||||
_parse_cookie_packet(length, data, record)
|
||||
|
||||
for (packet_type, length, data) in packets:
|
||||
for packet_type, length, data in packets:
|
||||
handler = _packet_handlers.get(packet_type)
|
||||
if handler is not None:
|
||||
handler(length, data, record)
|
||||
|
||||
@ -112,7 +112,7 @@ class _RestrictedDict(Dict[str, Sequence[Any]]):
|
||||
|
||||
def update(self, new_dict):
|
||||
# Force this to go via our strict __setitem__ method
|
||||
for (key, value) in new_dict.items():
|
||||
for key, value in new_dict.items():
|
||||
self[key] = value
|
||||
|
||||
|
||||
|
||||
@ -160,7 +160,6 @@ class CodonAdaptationIndex:
|
||||
|
||||
def _count_codons(self, fasta_file):
|
||||
with open(fasta_file) as handle:
|
||||
|
||||
# make the codon dictionary local
|
||||
self.codon_count = CodonsDict.copy()
|
||||
|
||||
|
||||
@ -117,7 +117,7 @@ class ds:
|
||||
if -1 in tagpos:
|
||||
del tagpos[-1]
|
||||
ps = sorted(tagpos) # the keys
|
||||
for (p1, p2) in zip(ps, ps[1:] + [len(line) + 1]):
|
||||
for p1, p2 in zip(ps, ps[1:] + [len(line) + 1]):
|
||||
setattr(
|
||||
self,
|
||||
tagpos[p1].lower(),
|
||||
@ -376,7 +376,6 @@ def parse(source):
|
||||
# encountered at the end of file, to any previous read or contig.
|
||||
# The sort() method deals with that later.
|
||||
while True:
|
||||
|
||||
# each read must have a rd and qa
|
||||
try:
|
||||
while True:
|
||||
|
||||
@ -34,7 +34,6 @@ def read(handle):
|
||||
line = line.strip()
|
||||
if line:
|
||||
if line.startswith(">"):
|
||||
|
||||
if motif_nbr != 0:
|
||||
motif = motifs.Motif(alphabet="GATC", counts=nucleotide_counts)
|
||||
motif.name = motif_name
|
||||
|
||||
@ -30,7 +30,6 @@ if len(sys.argv) != 2:
|
||||
parser = GenBank.FeatureParser(debug_level=2)
|
||||
|
||||
with open(sys.argv[1]) as handle:
|
||||
|
||||
iterator = GenBank.Iterator(handle, parser)
|
||||
|
||||
while True:
|
||||
|
||||
@ -123,9 +123,7 @@ else:
|
||||
residue_list = Selection.unfold_entities(m, "R")
|
||||
|
||||
for r in residue_list:
|
||||
|
||||
if k in r.xtra:
|
||||
|
||||
exposure = r.xtra[k]
|
||||
|
||||
if args.exp == "DSSPR":
|
||||
|
||||
@ -200,7 +200,6 @@ def main(argv):
|
||||
|
||||
|
||||
class TestRunner(unittest.TextTestRunner):
|
||||
|
||||
if __name__ == "__main__":
|
||||
file = sys.argv[0]
|
||||
else:
|
||||
|
||||
@ -24,7 +24,6 @@ test_write_read_align_with_seq_count = test_write_read_alignment_formats + [
|
||||
|
||||
|
||||
class TestAlignIO_exceptions(unittest.TestCase):
|
||||
|
||||
t_formats = list(AlignIO._FormatToWriter) + list(SeqIO._FormatToWriter)
|
||||
|
||||
def test_phylip_reject_duplicate(self):
|
||||
|
||||
@ -20,7 +20,7 @@ class AlignInfoTests(unittest.TestCase):
|
||||
|
||||
def assertAlmostEqualList(self, list1, list2, **kwargs):
|
||||
self.assertEqual(len(list1), len(list2))
|
||||
for (v1, v2) in zip(list1, list2):
|
||||
for v1, v2 in zip(list1, list2):
|
||||
self.assertAlmostEqual(v1, v2, **kwargs)
|
||||
|
||||
def test_nucleotides(self):
|
||||
|
||||
@ -26,7 +26,6 @@ except ImportError:
|
||||
|
||||
|
||||
class TestAlign_dna_rna(unittest.TestCase):
|
||||
|
||||
# The PSL file dna_rna.psl was generated using this command:
|
||||
# blat -mask=lower hg38.2bit rna.fa dna_rna.unsorted.psl
|
||||
# pslSort dirs dna_rna.psl . dna_rna.unsorted.psl
|
||||
@ -1326,7 +1325,6 @@ NR_111921 199 ATTAAAAAA 208
|
||||
|
||||
|
||||
class TestAlign_dna(unittest.TestCase):
|
||||
|
||||
queries = {
|
||||
record.id: str(record.seq)
|
||||
for record in SeqIO.parse("Blat/fasta_34.fa", "fasta")
|
||||
|
||||
@ -17,7 +17,6 @@ except ImportError:
|
||||
|
||||
|
||||
class TestCluster(unittest.TestCase):
|
||||
|
||||
module = "Bio.Cluster"
|
||||
|
||||
def test_matrix_parse(self):
|
||||
|
||||
@ -342,7 +342,6 @@ class TestURLConstruction(unittest.TestCase):
|
||||
for alt_value in [alt_values[param], None]:
|
||||
# Try both altering global variable and also passing parameter directly
|
||||
for set_global in [False, True]:
|
||||
|
||||
variables = dict(vars_base)
|
||||
|
||||
with patch_urlopen() as patched:
|
||||
@ -376,7 +375,6 @@ class TestURLConstruction(unittest.TestCase):
|
||||
}
|
||||
|
||||
for etool in [Entrez.efetch, Entrez.epost]: # Make both GET and POST requests
|
||||
|
||||
with patch_urlopen() as patched:
|
||||
etool(**variables)
|
||||
assert Entrez._has_api_key(get_patched_request(patched, self))
|
||||
|
||||
@ -8132,7 +8132,7 @@ class LineOneTests(unittest.TestCase):
|
||||
None,
|
||||
),
|
||||
]
|
||||
for (line, topo, mol_type, div, warning_list) in tests:
|
||||
for line, topo, mol_type, div, warning_list in tests:
|
||||
with warnings.catch_warnings(record=True) as caught:
|
||||
warnings.simplefilter("always")
|
||||
scanner = GenBank.Scanner.GenBankScanner()
|
||||
@ -8206,7 +8206,7 @@ class LineOneTests(unittest.TestCase):
|
||||
("ID DI500001 STANDARD; PRT; 111 AA.", None, None, None),
|
||||
("ID DI644510 standard; PRT; 1852 AA.", None, None, None),
|
||||
]
|
||||
for (line, topo, mol_type, div) in tests:
|
||||
for line, topo, mol_type, div in tests:
|
||||
scanner = GenBank.Scanner.EmblScanner()
|
||||
consumer = GenBank._FeatureConsumer(1, GenBank.FeatureValueCleaner)
|
||||
scanner._feed_first_line(consumer, line)
|
||||
@ -8230,7 +8230,7 @@ class LineOneTests(unittest.TestCase):
|
||||
("ID HLA00001 standard; DNA; HUM; 3503 BP.", None, "DNA", "HUM"),
|
||||
("ID HLA00001; SV 1; standard; DNA; HUM; 3503 BP.", None, "DNA", "HUM"),
|
||||
]
|
||||
for (line, topo, mol_type, div) in tests:
|
||||
for line, topo, mol_type, div in tests:
|
||||
scanner = GenBank.Scanner._ImgtScanner()
|
||||
consumer = GenBank._FeatureConsumer(1, GenBank.FeatureValueCleaner)
|
||||
scanner._feed_first_line(consumer, line)
|
||||
|
||||
@ -24,7 +24,6 @@ SITECLASSES = {0: None, 1: 2, 2: 3, 3: 3, 7: 10, 8: 11, 22: 3}
|
||||
|
||||
|
||||
class ModTest(unittest.TestCase):
|
||||
|
||||
align_dir = os.path.join("PAML", "Alignments")
|
||||
tree_dir = os.path.join("PAML", "Trees")
|
||||
ctl_dir = os.path.join("PAML", "Control_files")
|
||||
|
||||
@ -14,7 +14,6 @@ import glob
|
||||
|
||||
|
||||
class ModTest(unittest.TestCase):
|
||||
|
||||
align_dir = os.path.join("PAML", "Alignments")
|
||||
tree_dir = os.path.join("PAML", "Trees")
|
||||
ctl_dir = os.path.join("PAML", "Control_files")
|
||||
|
||||
@ -61,7 +61,6 @@ class DSSP_tool_test(unittest.TestCase):
|
||||
|
||||
@classmethod
|
||||
def setUpClass(cls):
|
||||
|
||||
cls.dssp_version = (0, 0, 0)
|
||||
is_dssp_available = False
|
||||
# Check if DSSP is installed
|
||||
|
||||
@ -64,7 +64,6 @@ class NeighborTest(unittest.TestCase):
|
||||
|
||||
|
||||
class KDTreeTest(unittest.TestCase):
|
||||
|
||||
nr_points = 5000 # number of points used in test
|
||||
bucket_size = 5 # number of points per tree node
|
||||
radius = 0.05 # radius of search (typically 0.05 or so)
|
||||
|
||||
@ -148,6 +148,8 @@ class WriteTest(unittest.TestCase):
|
||||
|
||||
def test_mmcifio_select(self):
|
||||
"""Write a selection of the structure using a Select subclass."""
|
||||
# This method has an internal class defined
|
||||
|
||||
# Selection class to filter all alpha carbons
|
||||
class CAonly(Select):
|
||||
"""Accepts only CA residues."""
|
||||
|
||||
@ -233,6 +233,8 @@ class WriteTest(unittest.TestCase):
|
||||
|
||||
def test_pdbio_select(self):
|
||||
"""Write a selection of the structure using a Select subclass."""
|
||||
# This method has an internal class definition
|
||||
|
||||
# Selection class to filter all alpha carbons
|
||||
class CAonly(Select):
|
||||
"""Accepts only CA residues."""
|
||||
|
||||
@ -33,7 +33,6 @@ class CompareStructures(unittest.TestCase):
|
||||
"""Tests for comparing the same structure parsed by PDB and MMCIF parsers."""
|
||||
|
||||
def setUp(self):
|
||||
|
||||
# Silence!
|
||||
warnings.simplefilter("ignore", PDBConstructionWarning)
|
||||
|
||||
|
||||
@ -120,7 +120,6 @@ gi|11464971:4-101 gi|365982352|ref|XM_003667962.1| 30.77 52 27 1 12 54 3181 3336
|
||||
|
||||
|
||||
class BlastTabIndexCases(CheckIndex):
|
||||
|
||||
fmt = "blast-tab"
|
||||
|
||||
def test_blasttab_2226_tblastn_001(self):
|
||||
|
||||
@ -727,7 +727,6 @@ class BlastXmlRawCases(CheckRaw):
|
||||
|
||||
|
||||
class BlastXmlIndexCases(CheckIndex):
|
||||
|
||||
fmt = "blast-xml"
|
||||
|
||||
def test_blastxml_2212L_blastp_001(self):
|
||||
|
||||
@ -12,7 +12,6 @@ from search_tests_common import CheckIndex
|
||||
|
||||
|
||||
class BlatPslIndexCases(CheckIndex):
|
||||
|
||||
fmt = "blat-psl"
|
||||
|
||||
def test_psl_34_001(self):
|
||||
|
||||
@ -21,7 +21,6 @@ def get_file(filename):
|
||||
|
||||
|
||||
class ExonerateSpcCases(unittest.TestCase):
|
||||
|
||||
coord = ("start", "end")
|
||||
coords = ("inter_ranges",)
|
||||
stype = ("hit_", "query_")
|
||||
@ -68,7 +67,6 @@ class ExonerateSpcCases(unittest.TestCase):
|
||||
|
||||
|
||||
class ExonerateTextCases(unittest.TestCase):
|
||||
|
||||
fmt = "exonerate-text"
|
||||
|
||||
def test_exn_22_m_affine_local(self):
|
||||
@ -2396,7 +2394,6 @@ class ExonerateTextCases(unittest.TestCase):
|
||||
|
||||
|
||||
class ExonerateVulgarCases(unittest.TestCase):
|
||||
|
||||
fmt = "exonerate-vulgar"
|
||||
|
||||
def test_exn_22_o_vulgar(self):
|
||||
@ -2586,7 +2583,6 @@ class ExonerateVulgarCases(unittest.TestCase):
|
||||
|
||||
|
||||
class ExonerateCigarCases(unittest.TestCase):
|
||||
|
||||
fmt = "exonerate-cigar"
|
||||
|
||||
def test_exn_22_o_vulgar_cigar(self):
|
||||
|
||||
@ -12,7 +12,6 @@ from search_tests_common import CheckIndex
|
||||
|
||||
|
||||
class ExonerateTextIndexCases(CheckIndex):
|
||||
|
||||
fmt = "exonerate-text"
|
||||
|
||||
def test_exn_22_m_est2genome(self):
|
||||
|
||||
@ -12,7 +12,6 @@ from search_tests_common import CheckIndex
|
||||
|
||||
|
||||
class ExonerateVulgarIndexCases(CheckIndex):
|
||||
|
||||
fmt = "exonerate-vulgar"
|
||||
|
||||
def test_exn_22_m_est2genome(self):
|
||||
|
||||
@ -12,7 +12,6 @@ from search_tests_common import CheckIndex
|
||||
|
||||
|
||||
class FastaM10IndexCases(CheckIndex):
|
||||
|
||||
fmt = "fasta-m10"
|
||||
|
||||
def test_output_002(self):
|
||||
|
||||
@ -13,7 +13,6 @@ from Bio.SearchIO import parse, read
|
||||
|
||||
|
||||
class HmmpfamTests(unittest.TestCase):
|
||||
|
||||
fmt = "hmmer2-text"
|
||||
|
||||
def test_hmmpfam_21(self):
|
||||
@ -353,7 +352,6 @@ class HmmpfamTests(unittest.TestCase):
|
||||
|
||||
|
||||
class HmmsearchTests(unittest.TestCase):
|
||||
|
||||
fmt = "hmmer2-text"
|
||||
|
||||
def test_hmmsearch_20(self):
|
||||
|
||||
@ -12,7 +12,6 @@ from search_tests_common import CheckRaw, CheckIndex
|
||||
|
||||
|
||||
class Hmmer2TextRawCases(CheckRaw):
|
||||
|
||||
fmt = "hmmer2-text"
|
||||
|
||||
def test_hmmer2text_22_single_hmmsearch(self):
|
||||
@ -478,7 +477,6 @@ TFIIB: domain 1 of 1, from 253 to 268: score 2.6, E = 6.1
|
||||
|
||||
|
||||
class Hmmer2TextIndexCases(CheckIndex):
|
||||
|
||||
fmt = "hmmer2-text"
|
||||
|
||||
def test_hmmertext_text_21_hmmpfam_001(self):
|
||||
|
||||
@ -12,7 +12,6 @@ from search_tests_common import CheckRaw, CheckIndex
|
||||
|
||||
|
||||
class HmmerDomtabRawCases(CheckRaw):
|
||||
|
||||
fmt = "hmmscan3-domtab"
|
||||
|
||||
def test_hmmerdomtab_30_multiple_first(self):
|
||||
|
||||
@ -12,7 +12,6 @@ from search_tests_common import CheckRaw, CheckIndex
|
||||
|
||||
|
||||
class Hmmer3TabRawCases(CheckRaw):
|
||||
|
||||
fmt = "hmmer3-tab"
|
||||
|
||||
def test_hmmer3tab_30_multiple_first(self):
|
||||
@ -51,7 +50,6 @@ Ig_2 PF13895.1 gi|126362951:116-221 - 3.5e-05 23.7
|
||||
|
||||
|
||||
class Hmmer3TabIndexCases(CheckIndex):
|
||||
|
||||
fmt = "hmmer3-tab"
|
||||
|
||||
def test_hmmer3tab_30_hmmscan_001(self):
|
||||
|
||||
@ -11,7 +11,6 @@ from search_tests_common import CheckRaw, CheckIndex
|
||||
|
||||
|
||||
class Hmmer3TextRawCases(CheckRaw):
|
||||
|
||||
fmt = "hmmer3-text"
|
||||
|
||||
def test_hmmer3text_30_multiple_first(self):
|
||||
@ -301,7 +300,6 @@ Domain search space (domZ): 1 [number of targets reported over t
|
||||
|
||||
|
||||
class Hmmer3TextIndexCases(CheckIndex):
|
||||
|
||||
fmt = "hmmer3-text"
|
||||
|
||||
def test_hmmertext_text_30_hmmscan_001(self):
|
||||
|
||||
@ -82,7 +82,6 @@ file"""
|
||||
|
||||
class TestParserSupport(unittest.TestCase):
|
||||
def test_TaggingConsumer(self):
|
||||
|
||||
h = StringIO()
|
||||
tc = ParserSupport.TaggingConsumer(handle=h, colwidth=5)
|
||||
tc.start_section()
|
||||
|
||||
@ -39,7 +39,6 @@ class WriteCases(SearchTestBaseClass):
|
||||
|
||||
|
||||
class BlastXmlWriteCases(WriteCases):
|
||||
|
||||
fmt = "blast-xml"
|
||||
out = os.path.join("Blast", "test_write.xml")
|
||||
|
||||
@ -56,7 +55,6 @@ class BlastXmlWriteCases(WriteCases):
|
||||
|
||||
|
||||
class BlastTabWriteCases(WriteCases):
|
||||
|
||||
fmt = "blast-tab"
|
||||
out = os.path.join("Blast", "test_write.txt")
|
||||
|
||||
@ -141,7 +139,6 @@ class BlastTabWriteCases(WriteCases):
|
||||
|
||||
|
||||
class HmmerTabWriteCases(WriteCases):
|
||||
|
||||
fmt = "hmmer3-tab"
|
||||
out = os.path.join("Hmmer", "test_write.txt")
|
||||
|
||||
@ -158,7 +155,6 @@ class HmmerTabWriteCases(WriteCases):
|
||||
|
||||
|
||||
class HmmerDomtabWriteCases(WriteCases):
|
||||
|
||||
out = os.path.join("Hmmer", "test_write.txt")
|
||||
|
||||
def test_write_single_from_hmmscandomtab(self):
|
||||
@ -183,7 +179,6 @@ class HmmerDomtabWriteCases(WriteCases):
|
||||
|
||||
|
||||
class BlatPslWriteCases(WriteCases):
|
||||
|
||||
fmt = "blat-psl"
|
||||
out = os.path.join("Blat", "test_write.txt")
|
||||
|
||||
|
||||
@ -111,7 +111,7 @@ class ConvertTestsInsdc(SeqIOConverterTestBaseClass):
|
||||
("GenBank/cor6_6.gb", "genbank"),
|
||||
]
|
||||
for filename, fmt in tests:
|
||||
for (in_format, out_format) in self.formats:
|
||||
for in_format, out_format in self.formats:
|
||||
if in_format != fmt:
|
||||
continue
|
||||
self.check_conversion(filename, in_format, out_format)
|
||||
|
||||
@ -1069,7 +1069,7 @@ class TestsConverter(SeqIOConverterTestBaseClass, QualityIOTestBaseClass):
|
||||
("Quality/illumina_faked.fastq", "fastq-illumina"),
|
||||
]
|
||||
for filename, fmt in tests:
|
||||
for (in_format, out_format) in self.formats:
|
||||
for in_format, out_format in self.formats:
|
||||
if in_format != fmt:
|
||||
continue
|
||||
self.check_conversion(filename, in_format, out_format)
|
||||
@ -1100,7 +1100,7 @@ class TestsConverter(SeqIOConverterTestBaseClass, QualityIOTestBaseClass):
|
||||
("Quality/error_double_qual.fastq", "fastq"),
|
||||
]
|
||||
for filename, fmt in tests:
|
||||
for (in_format, out_format) in self.formats:
|
||||
for in_format, out_format in self.formats:
|
||||
if in_format != fmt:
|
||||
continue
|
||||
if (
|
||||
|
||||
@ -27,7 +27,6 @@ class TestSimpleRead(unittest.TestCase):
|
||||
|
||||
|
||||
class TestDetailedRead(unittest.TestCase):
|
||||
|
||||
records = {}
|
||||
|
||||
def setUp(self):
|
||||
@ -176,7 +175,6 @@ class TestReadAndWrite(unittest.TestCase):
|
||||
self._write_parse_and_compare(read1_records)
|
||||
|
||||
def _write_parse_and_compare(self, read1_records):
|
||||
|
||||
handle = BytesIO()
|
||||
|
||||
SeqIO.write(read1_records, handle, "seqxml")
|
||||
@ -221,6 +219,7 @@ class TestReadCorruptFiles(unittest.TestCase):
|
||||
# Since one block is likely large enough to cover the first few
|
||||
# entries in the file, the ValueError may be raised after we call
|
||||
# SeqIO.parse, before we start iterating over the file.
|
||||
|
||||
def f(path):
|
||||
records = SeqIO.parse(path, "seqxml")
|
||||
for record in records:
|
||||
|
||||
@ -15,7 +15,6 @@ from Bio.SeqFeature import CompoundLocation
|
||||
|
||||
|
||||
class TestSnapGene(unittest.TestCase):
|
||||
|
||||
sample_data = {
|
||||
"sample-d": {
|
||||
"file": "SnapGene/sample-d.dna",
|
||||
|
||||
@ -19,7 +19,6 @@ from Bio.SeqRecord import SeqRecord
|
||||
|
||||
|
||||
class TestXdna(unittest.TestCase):
|
||||
|
||||
sample_data = {
|
||||
"sample-a": {
|
||||
"file": "Xdna/sample-a.xdna",
|
||||
|
||||
@ -337,7 +337,6 @@ if sqlite3:
|
||||
|
||||
|
||||
class IndexDictTests(SeqRecordTestBaseClass, SeqIOTestBaseClass):
|
||||
|
||||
tests = [
|
||||
("Ace/contig1.ace", "ace"),
|
||||
("Ace/consed_sample.ace", "ace"),
|
||||
|
||||
@ -295,7 +295,7 @@ class WriterTests(SeqIOTestBaseClass):
|
||||
self.assertEqual(1, SeqIO.write(records, handle, fmt))
|
||||
|
||||
def test_alignment_formats(self):
|
||||
for (records, descr, errs) in test_records:
|
||||
for records, descr, errs in test_records:
|
||||
for fmt in test_write_read_alignment_formats:
|
||||
for err_formats, err_type, err_msg in errs:
|
||||
if fmt in err_formats:
|
||||
|
||||
@ -10,11 +10,9 @@ import unittest
|
||||
|
||||
class TestUniGene(unittest.TestCase):
|
||||
def test_parse(self):
|
||||
|
||||
# Start of the UniGene file for Equus caballus downloaded from:
|
||||
# ftp://ftp.ncbi.nih.gov/repository/UniGene/Equus_caballus
|
||||
with open("UniGene/Eca.1.2425.data") as handle:
|
||||
|
||||
records = UniGene.parse(handle)
|
||||
|
||||
# First record
|
||||
@ -863,7 +861,6 @@ class TestUniGene(unittest.TestCase):
|
||||
)
|
||||
|
||||
def test_read(self):
|
||||
|
||||
# Start of the UniGene file for Homo sapiens downloaded from:
|
||||
# ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens
|
||||
with open("UniGene/Hs.2.data") as handle:
|
||||
@ -1201,7 +1198,6 @@ class TestUniGene(unittest.TestCase):
|
||||
)
|
||||
|
||||
def test_read_value_error(self):
|
||||
|
||||
# Test More than one SwissProt record found
|
||||
with open("UniGene/Eca.1.2425.data") as handle:
|
||||
self.assertRaises(ValueError, UniGene.read, handle)
|
||||
|
||||
@ -56,7 +56,7 @@ class TestBasics(unittest.TestCase):
|
||||
self.assertEqual(msa[0].id, "mixed")
|
||||
self.assertEqual(msa[1].id, "lower")
|
||||
self.assertEqual(msa[2].id, "upper")
|
||||
for (col, letter) in enumerate(letters):
|
||||
for col, letter in enumerate(letters):
|
||||
self.assertEqual(msa[:, col], letter + letter.lower() + letter.upper())
|
||||
# Check row extractions:
|
||||
self.assertEqual(msa[0].id, "mixed")
|
||||
@ -75,7 +75,7 @@ class TestBasics(unittest.TestCase):
|
||||
self.assertEqual(alignment.sequences[0].id, "mixed")
|
||||
self.assertEqual(alignment.sequences[1].id, "lower")
|
||||
self.assertEqual(alignment.sequences[2].id, "upper")
|
||||
for (col, letter) in enumerate(letters):
|
||||
for col, letter in enumerate(letters):
|
||||
self.assertEqual(
|
||||
alignment[:, col], letter + letter.lower() + letter.upper()
|
||||
)
|
||||
|
||||
@ -279,7 +279,6 @@ Z 0.0
|
||||
class TestScoringMatrices(unittest.TestCase):
|
||||
@classmethod
|
||||
def setUpClass(cls):
|
||||
|
||||
from Bio import SeqIO
|
||||
from Bio.Align import PairwiseAligner
|
||||
|
||||
|
||||
@ -369,7 +369,6 @@ class BgzfTests(unittest.TestCase):
|
||||
self.assertNotEqual(offset3, h.tell())
|
||||
|
||||
with bgzf.open(temp_file, "r") as h: # Text mode!
|
||||
|
||||
h.seek(offset) # i.e. End of first BGZF block
|
||||
self.assertEqual(offset1, h.tell()) # Note *not* seek offset
|
||||
# Now at start of second BGZF block
|
||||
|
||||
@ -1744,7 +1744,6 @@ query 5 GTCCT 0
|
||||
|
||||
|
||||
class TestPairwiseMatchDictionary(unittest.TestCase):
|
||||
|
||||
match_dict = {("A", "A"): 1.5, ("A", "T"): 0.5, ("T", "A"): 0.5, ("T", "T"): 1.0}
|
||||
|
||||
def test_match_dictionary1(self):
|
||||
|
||||
@ -193,7 +193,6 @@ class SamtoolsTestCase(unittest.TestCase):
|
||||
# TODO: def test_fixmate(self):
|
||||
|
||||
def test_sort(self):
|
||||
|
||||
cmdline = SamtoolsVersion0xSortCommandline(samtools_exe)
|
||||
cmdline.set_parameter("input", self.bamfile1)
|
||||
cmdline.set_parameter("out_prefix", "SamBam/out")
|
||||
|
||||
Reference in New Issue
Block a user