Hi, When I try to running the './jupyter/transformers_glanville_classifier_and_clustering.ipynb', there is a error on figs = [motif_from_cluster(c, fname=os.path.join(PLOT_DIR, f"glanville_embed_cluster_motif_{c}.pdf")) for c in ['25', '22', '20']]:
FileNotFoundError Traceback (most recent call last)
Cell In[14], line 22
19 fig.savefig(fname, bbox_inches='tight')
20 return fig
---> 22 figs = [motif_from_cluster(c, fname=os.path.join(PLOT_DIR, f"glanville_embed_cluster_motif_{c}.pdf")) for c in ['25', '22', '20']]
23 for f in figs:
24 f.show()
Cell In[14], line 22, in <listcomp>(.0)
19 fig.savefig(fname, bbox_inches='tight')
20 return fig
---> 22 figs = [motif_from_cluster(c, fname=os.path.join(PLOT_DIR, f"glanville_embed_cluster_motif_{c}.pdf")) for c in ['25', '22', '20']]
23 for f in figs:
24 f.show()
Cell In[14], line 13, in motif_from_cluster(cluster, fname)
7 logo_kwargs = {
8 "color_scheme": "dmslogo_funcgroup",
9 "show_spines": False,
10 "alpha": 0.9,
11 }
12 fig, ax = plt.subplots(figsize=(4, 1.3), dpi=300)
---> 13 custom_metrics.motif_from_sequences(cluster_of_interest['CDR3b'], normalize_pwm=False, ax=ax, **logo_kwargs)[1]
14 ax.set(
15 xticks=[],
16 yticks=[],
17 )
18 if fname is not None:
File ~/tcr-bert/tcr/custom_metrics.py:214, in motif_from_sequences(sequences, normalize_pwm, dedup, **kwargs)
212 if dedup:
213 sequences = utils.dedup(sequences)
--> 214 msa_seqs = Muscle.run_muscle(sequences)
215 msa_pwm = per_position_aa_count(msa_seqs, normalize=normalize_pwm)
216 logo = logomaker.Logo(msa_pwm, **kwargs)
File ~/tcr-bert/tcr/Muscle.py:39, in run_muscle(sequences, fast)
37 print(subprocess.DEVNULL)
38 print(shlex.split(muscle_cmd))
---> 39 retval = subprocess.call(
40 shlex.split(muscle_cmd),
41 stdout=subprocess.DEVNULL,
42 stderr=subprocess.DEVNULL,
43 )
44 assert retval == 0, f"Exit code {retval} when running muscle"
45 msa_seqs = list(utils.read_fasta(muscle_output_fname).values())
File ~/.conda/envs/tcrbert/lib/python3.9/subprocess.py:349, in call(timeout, *popenargs, **kwargs)
341 def call(*popenargs, timeout=None, **kwargs):
342 """Run command with arguments. Wait for command to complete or
343 timeout, then return the returncode attribute.
344
(...)
347 retcode = call(["ls", "-l"])
348 """
--> 349 with Popen(*popenargs, **kwargs) as p:
350 try:
351 return p.wait(timeout=timeout)
File ~/.conda/envs/tcrbert/lib/python3.9/subprocess.py:951, in Popen.__init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask)
947 if self.text_mode:
948 self.stderr = io.TextIOWrapper(self.stderr,
949 encoding=encoding, errors=errors)
--> 951 self._execute_child(args, executable, preexec_fn, close_fds,
952 pass_fds, cwd, env,
953 startupinfo, creationflags, shell,
954 p2cread, p2cwrite,
955 c2pread, c2pwrite,
956 errread, errwrite,
957 restore_signals,
958 gid, gids, uid, umask,
959 start_new_session)
960 except:
961 # Cleanup if the child failed starting.
962 for f in filter(None, (self.stdin, self.stdout, self.stderr)):
File ~/.conda/envs/tcrbert/lib/python3.9/subprocess.py:1823, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session)
1821 if errno_num != 0:
1822 err_msg = os.strerror(errno_num)
-> 1823 raise child_exception_type(errno_num, err_msg, err_filename)
1824 raise child_exception_type(err_msg)
FileNotFoundError: [Errno 2] No such file or directory: 'muscle'
I found that if using it in Shell, it will be worked. But I want to see it in jupyter... What Can I solve it?
Hi, When I try to running the './jupyter/transformers_glanville_classifier_and_clustering.ipynb', there is a error on
figs = [motif_from_cluster(c, fname=os.path.join(PLOT_DIR, f"glanville_embed_cluster_motif_{c}.pdf")) for c in ['25', '22', '20']]:I found that if using it in Shell, it will be worked. But I want to see it in jupyter... What Can I solve it?
Thank you.