add desc to tqdm

chaochungkuo · Mar 14, 2024 · de57ce8 · de57ce8
1 parent 303ef9c
commit de57ce8
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/genomkit/annotation/gannotation.py b/genomkit/annotation/gannotation.py
@@ -28,7 +28,7 @@ def load_data(self):
         open_func = gzip.open if self.file_path.endswith('.gz') else open
         total_lines = sum(1 for _ in open_func(self.file_path, 'rt'))
         with open_func(self.file_path, 'rt') as f:
-            for line in tqdm(f, total=total_lines, desc="Loading Data"):
+            for line in tqdm(f, total=total_lines, desc="Loading GTF"):
                 if line.startswith('#'):
                     continue
                 fields = line.strip().split('\t')

diff --git a/genomkit/regions/gregions.py b/genomkit/regions/gregions.py
@@ -310,7 +310,7 @@ def intersect(self, target, mode: str = "OVERLAP",
             cont_overlap = False
             # OVERLAP ###############################
             if mode == "OVERLAP":
-                with tqdm(total=len(b)) as pbar:
+                with tqdm(total=len(b), desc="Calculate intersects") as pbar:
                     while cont_loop:
                         # When the regions overlap
                         if s.overlap(b[j]):
@@ -355,7 +355,7 @@ def intersect(self, target, mode: str = "OVERLAP",
                         pbar.update(1)
             # ORIGINAL ###############################
             if mode == "ORIGINAL":
-                with tqdm(total=len(b)) as pbar:
+                with tqdm(total=len(b), desc="Calculate intersects") as pbar:
                     while cont_loop:
                         # When the regions overlap
                         if s.overlap(b[j]):
@@ -382,7 +382,7 @@ def intersect(self, target, mode: str = "OVERLAP",
                         pbar.update(1)
             # COMP_INCL ###############################
             if mode == "COMP_INCL":
-                with tqdm(total=len(b)) as pbar:
+                with tqdm(total=len(b), desc="Calculate intersects") as pbar:
                     while cont_loop:
                         # When the regions overlap
                         if s.overlap(b[j]):

diff --git a/genomkit/sequences/io.py b/genomkit/sequences/io.py
@@ -21,7 +21,7 @@ def load_FASTA_from_file(file):
     current_sequence = ""
     total_lines = sum(1 for line in file if not line.startswith("#"))
     file.seek(0)  # Reset file pointer to the beginning
-    with tqdm(total=total_lines) as pbar:
+    with tqdm(total=total_lines, desc="Load FASTA") as pbar:
         for line in file:
             line = line.strip()
             if line.startswith("#"):
@@ -69,7 +69,7 @@ def load_FASTQ_from_file(file):
     total_records = sum(1 for _ in file) // 4  # Calculate total records
     file.seek(0)  # Reset file pointer to the beginning
 
-    with tqdm(total=total_records) as pbar:
+    with tqdm(total=total_records, desc="Load FASTQ") as pbar:
         for line_num, line in enumerate(file):
             line = line.strip()
             if line.startswith("#"):