We are currently solving the following issue within our repository. Here is the issue text:
--- BEGIN 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)
    ...
```

--- END ISSUE ---

Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
--- BEGIN FILES ---
Path: `Bio/PDB/PSEA.py`
Content:
```
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 FILES ---

Please first localize the bug based on the issue statement, and then generate a patch according to the `git diff` format fenced by three backticks.

Here is an example:

```diff
diff --git a/examples/server_async.py b/examples/server_async.py
--- a/examples/server_async.py
+++ b/examples/server_async.py
@@ -313,4 +313,4 @@
 
 
 if __name__ == "__main__":
-    asyncio.run(run_async_server("."), debug=True)
+    asyncio.run(run_async_server(), debug=True)
diff --git a/examples/server_sync.py b/examples/server_sync.py
--- a/examples/server_sync.py
+++ b/examples/server_sync.py
@@ -313,5 +313,5 @@
 
 
 if __name__ == "__main__":
-    server = run_sync_server(".")
+    server = run_sync_server()
     server.shutdown()

```

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):

{"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"}], "after_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\nimport os\n\nfrom Bio.PDB.Polypeptide import is_aa\n\n\ndef 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    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 not write output to the terminal while run unless\n     verbose is set to True.\n    \"\"\"\n    last = fname.split(\"/\")[-1]\n    base = last.split(\".\")[0]\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\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"}]}