prompt: You will be provided with a partial code base and an issue statement explaining a problem to resolve.
  <issue>
  Add option to silence/capture stdout/stderr from Bio.PDB.PSEA
  Spun from #3980.
  
  Running `p-sea` through `Bio.PDB.PSEA` will always print output to standard out. We should refactor the code to use `subprocess.run` and add a keyword to the top-level `run_psea` function to control whether to print or capture the tool's output.
  
  A mock implementation that adds some better error handling would be:
  
  ```import subprocess
  
  def run_psea(pname, verbose=True):
      cmd = [...]
      try:
          p = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True)
      except subprocess.CalledProcessError as err:
          print(f"Command {cmd} failed")
          raise
  
      if verbose:
          print(p.stdout)
      ...
  ```
  
  </issue>
  <code>
  [start of Bio/PDB/PSEA.py]
  1 # Copyright (C) 2006, Thomas Hamelryck (thamelry@binf.ku.dk)
  2 #
  3 # This file is part of the Biopython distribution and governed by your
  4 # choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
  5 # Please see the LICENSE file that should have been included as part of this
  6 # package.
  7 
  8 """Wrappers for PSEA, a program for secondary structure assignment.
  9 
  10 See this citation for P-SEA, PMID: 9183534
  11 
  12 Labesse G, Colloc'h N, Pothier J, Mornon J-P:  P-SEA: a new efficient
  13 assignment of secondary structure from C_alpha.
  14 Comput Appl Biosci 1997 , 13:291-295
  15 
  16 ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/
  17 """
  18 
  19 import subprocess
  20 
  21 from Bio.PDB.Polypeptide import is_aa
  22 
  23 
  24 def run_psea(fname):
  25     """Run PSEA and return output filename.
  26 
  27     Note that this assumes the P-SEA binary is called "psea" and that it is
  28     on the path.
  29 
  30     Note that P-SEA will write an output file in the current directory using
  31     the input filename with extension ".sea".
  32 
  33     Note that P-SEA will write output to the terminal while run.
  34     """
  35     subprocess.call(["psea", fname])
  36     last = fname.split("/")[-1]
  37     base = last.split(".")[0]
  38     return base + ".sea"
  39 
  40 
  41 def psea(pname):
  42     """Parse PSEA output file."""
  43     fname = run_psea(pname)
  44     start = 0
  45     ss = ""
  46     with open(fname) as fp:
  47         for l in fp:
  48             if l[0:6] == ">p-sea":
  49                 start = 1
  50                 continue
  51             if not start:
  52                 continue
  53             if l[0] == "\n":
  54                 break
  55             ss = ss + l[0:-1]
  56     return ss
  57 
  58 
  59 def psea2HEC(pseq):
  60     """Translate PSEA secondary structure string into HEC."""
  61     seq = []
  62     for ss in pseq:
  63         if ss == "a":
  64             n = "H"
  65         elif ss == "b":
  66             n = "E"
  67         elif ss == "c":
  68             n = "C"
  69         seq.append(n)
  70     return seq
  71 
  72 
  73 def annotate(m, ss_seq):
  74     """Apply secondary structure information to residues in model."""
  75     c = m.get_list()[0]
  76     all = c.get_list()
  77     residues = []
  78     # Now remove HOH etc.
  79     for res in all:
  80         if is_aa(res):
  81             residues.append(res)
  82     L = len(residues)
  83     if not L == len(ss_seq):
  84         raise ValueError("Length mismatch %i %i" % (L, len(ss_seq)))
  85     for i in range(0, L):
  86         residues[i].xtra["SS_PSEA"] = ss_seq[i]
  87     # subprocess.call(["rm", fname])
  88 
  89 
  90 class PSEA:
  91     """Define PSEA class.
  92 
  93     PSEA object is a wrapper to PSEA program for secondary structure assignment.
  94     """
  95 
  96     def __init__(self, model, filename):
  97         """Initialize the class."""
  98         ss_seq = psea(filename)
  99         ss_seq = psea2HEC(ss_seq)
  100         annotate(model, ss_seq)
  101         self.ss_seq = ss_seq
  102 
  103     def get_seq(self):
  104         """Return secondary structure string."""
  105         return self.ss_seq
  106
  [end of Bio/PDB/PSEA.py]
  </code>
  
  I need you to solve this issue by generating a single patch file that I can apply directly to this repository using git apply. Please respond with a single patch file in the following format.
  <patch>
  diff --git a/file.py b/file.py
  --- a/file.py
  +++ b/file.py
  @@ -1,27 +1,35 @@
   def euclidean(a, b):
  -    while b:
  -        a, b = b, a % b
  -    return a
  +    if b == 0:
  +        return a
  +    return euclidean(b, a % b)
   
   
   def bresenham(x0, y0, x1, y1):
       points = []
       dx = abs(x1 - x0)
       dy = abs(y1 - y0)
  -    sx = 1 if x0 < x1 else -1
  -    sy = 1 if y0 < y1 else -1
  -    err = dx - dy
  +    x, y = x0, y0
  +    sx = -1 if x0 > x1 else 1
  +    sy = -1 if y0 > y1 else 1
   
  -    while True:
  -        points.append((x0, y0))
  -        if x0 == x1 and y0 == y1:
  -            break
  -        e2 = 2 * err
  -        if e2 > -dy:
  -            err -= dy
  -            x0 += sx
  -        if e2 < dx:
  -            err += dx
  -            y0 += sy
  +    if dx > dy:
  +        err = dx / 2.0
  +        while x != x1:
  +            points.append((x, y))
  +            err -= dy
  +            if err < 0:
  +                y += sy
  +                err += dx
  +            x += sx
  +    else:
  +        err = dy / 2.0
  +        while y != y1:
  +            points.append((x, y))
  +            err -= dx
  +            if err < 0:
  +                x += sx
  +                err += dy
  +            y += sy
  +
  +    points.append((x, y))
       return points
  
  </patch>
golden_diff: diff --git a/Bio/PDB/PSEA.py b/Bio/PDB/PSEA.py
  --- a/Bio/PDB/PSEA.py
  +++ b/Bio/PDB/PSEA.py
  @@ -17,11 +17,12 @@
   """
   
   import subprocess
  +import os
   
   from Bio.PDB.Polypeptide import is_aa
   
   
  -def run_psea(fname):
  +def run_psea(fname, verbose=False):
       """Run PSEA and return output filename.
   
       Note that this assumes the P-SEA binary is called "psea" and that it is
  @@ -30,12 +31,22 @@
       Note that P-SEA will write an output file in the current directory using
       the input filename with extension ".sea".
   
  -    Note that P-SEA will write output to the terminal while run.
  +    Note that P-SEA will not write output to the terminal while run unless
  +     verbose is set to True.
       """
  -    subprocess.call(["psea", fname])
       last = fname.split("/")[-1]
       base = last.split(".")[0]
  -    return base + ".sea"
  +    cmd = ["psea", fname]
  +
  +    p = subprocess.run(cmd, capture_output=True, universal_newlines=True)
  +
  +    if verbose:
  +        print(p.stdout)
  +
  +    if not p.stderr.strip() and os.path.exists(base + ".sea"):
  +        return base + ".sea"
  +    else:
  +        raise RuntimeError(f"Error running p-sea: {p.stderr}")
   
   
   def psea(pname):
  
verification_info: {"golden_diff": "diff --git a/Bio/PDB/PSEA.py b/Bio/PDB/PSEA.py\n--- a/Bio/PDB/PSEA.py\n+++ b/Bio/PDB/PSEA.py\n@@ -17,11 +17,12 @@\n \"\"\"\n \n import subprocess\n+import os\n \n from Bio.PDB.Polypeptide import is_aa\n \n \n-def run_psea(fname):\n+def run_psea(fname, verbose=False):\n     \"\"\"Run PSEA and return output filename.\n \n     Note that this assumes the P-SEA binary is called \"psea\" and that it is\n@@ -30,12 +31,22 @@\n     Note that P-SEA will write an output file in the current directory using\n     the input filename with extension \".sea\".\n \n-    Note that P-SEA will write output to the terminal while run.\n+    Note that P-SEA will not write output to the terminal while run unless\n+     verbose is set to True.\n     \"\"\"\n-    subprocess.call([\"psea\", fname])\n     last = fname.split(\"/\")[-1]\n     base = last.split(\".\")[0]\n-    return base + \".sea\"\n+    cmd = [\"psea\", fname]\n+\n+    p = subprocess.run(cmd, capture_output=True, universal_newlines=True)\n+\n+    if verbose:\n+        print(p.stdout)\n+\n+    if not p.stderr.strip() and os.path.exists(base + \".sea\"):\n+        return base + \".sea\"\n+    else:\n+        raise RuntimeError(f\"Error running p-sea: {p.stderr}\")\n \n \n def psea(pname):\n", "issue": "Add option to silence/capture stdout/stderr from Bio.PDB.PSEA\nSpun from #3980.\r\n\r\nRunning `p-sea` through `Bio.PDB.PSEA` will always print output to standard out. We should refactor the code to use `subprocess.run` and add a keyword to the top-level `run_psea` function to control whether to print or capture the tool's output.\r\n\r\nA mock implementation that adds some better error handling would be:\r\n\r\n```import subprocess\r\n\r\ndef run_psea(pname, verbose=True):\r\n    cmd = [...]\r\n    try:\r\n        p = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True)\r\n    except subprocess.CalledProcessError as err:\r\n        print(f\"Command {cmd} failed\")\r\n        raise\r\n\r\n    if verbose:\r\n        print(p.stdout)\r\n    ...\r\n```\n", "before_files": [{"content": "# Copyright (C) 2006, Thomas Hamelryck (thamelry@binf.ku.dk)\n#\n# This file is part of the Biopython distribution and governed by your\n# choice of the \"Biopython License Agreement\" or the \"BSD 3-Clause License\".\n# Please see the LICENSE file that should have been included as part of this\n# package.\n\n\"\"\"Wrappers for PSEA, a program for secondary structure assignment.\n\nSee this citation for P-SEA, PMID: 9183534\n\nLabesse G, Colloc'h N, Pothier J, Mornon J-P:  P-SEA: a new efficient\nassignment of secondary structure from C_alpha.\nComput Appl Biosci 1997 , 13:291-295\n\nftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/\n\"\"\"\n\nimport subprocess\n\nfrom Bio.PDB.Polypeptide import is_aa\n\n\ndef run_psea(fname):\n    \"\"\"Run PSEA and return output filename.\n\n    Note that this assumes the P-SEA binary is called \"psea\" and that it is\n    on the path.\n\n    Note that P-SEA will write an output file in the current directory using\n    the input filename with extension \".sea\".\n\n    Note that P-SEA will write output to the terminal while run.\n    \"\"\"\n    subprocess.call([\"psea\", fname])\n    last = fname.split(\"/\")[-1]\n    base = last.split(\".\")[0]\n    return base + \".sea\"\n\n\ndef psea(pname):\n    \"\"\"Parse PSEA output file.\"\"\"\n    fname = run_psea(pname)\n    start = 0\n    ss = \"\"\n    with open(fname) as fp:\n        for l in fp:\n            if l[0:6] == \">p-sea\":\n                start = 1\n                continue\n            if not start:\n                continue\n            if l[0] == \"\\n\":\n                break\n            ss = ss + l[0:-1]\n    return ss\n\n\ndef psea2HEC(pseq):\n    \"\"\"Translate PSEA secondary structure string into HEC.\"\"\"\n    seq = []\n    for ss in pseq:\n        if ss == \"a\":\n            n = \"H\"\n        elif ss == \"b\":\n            n = \"E\"\n        elif ss == \"c\":\n            n = \"C\"\n        seq.append(n)\n    return seq\n\n\ndef annotate(m, ss_seq):\n    \"\"\"Apply secondary structure information to residues in model.\"\"\"\n    c = m.get_list()[0]\n    all = c.get_list()\n    residues = []\n    # Now remove HOH etc.\n    for res in all:\n        if is_aa(res):\n            residues.append(res)\n    L = len(residues)\n    if not L == len(ss_seq):\n        raise ValueError(\"Length mismatch %i %i\" % (L, len(ss_seq)))\n    for i in range(0, L):\n        residues[i].xtra[\"SS_PSEA\"] = ss_seq[i]\n    # subprocess.call([\"rm\", fname])\n\n\nclass PSEA:\n    \"\"\"Define PSEA class.\n\n    PSEA object is a wrapper to PSEA program for secondary structure assignment.\n    \"\"\"\n\n    def __init__(self, model, filename):\n        \"\"\"Initialize the class.\"\"\"\n        ss_seq = psea(filename)\n        ss_seq = psea2HEC(ss_seq)\n        annotate(model, ss_seq)\n        self.ss_seq = ss_seq\n\n    def get_seq(self):\n        \"\"\"Return secondary structure string.\"\"\"\n        return self.ss_seq\n", "path": "Bio/PDB/PSEA.py"}]}