Add milliseconds to start_time, convert to UTC.

nanoporetech · Sep 21, 2022 · c45905c · c45905c
1 parent 99a1712
commit c45905c
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/bonito/fast5.py b/bonito/fast5.py
@@ -8,7 +8,7 @@
 from itertools import chain
 from functools import partial
 from multiprocessing import Pool
-from datetime import datetime, timedelta
+from datetime import timedelta, timezone
 
 import numpy as np
 import bonito.reader
@@ -68,7 +68,7 @@ def __init__(self, read, filename, meta=False, do_trim=True):
 
         exp_start_dt = parser.parse(self.exp_start_time)
         start_time = exp_start_dt + timedelta(seconds=self.start)
-        self.start_time = start_time.replace(microsecond=0).isoformat()
+        self.start_time = start_time.astimezone(timezone.utc).isoformat(timespec="milliseconds")
 
         raw = read.handle[read.raw_dataset_name][:]
         self.scaled = np.array(self.scaling * (raw + self.offset), dtype=np.float32)

diff --git a/bonito/pod5.py b/bonito/pod5.py
@@ -5,7 +5,7 @@
 from glob import glob
 from uuid import UUID
 from pathlib import Path
-from datetime import timedelta
+from datetime import timedelta, timezone
 
 import numpy as np
 import bonito.reader
@@ -47,7 +47,7 @@ def __init__(self, read, filename, meta=False, do_trim=True):
         self.duration = self.num_samples / self.sample_rate
 
         start_time = self.acquisition_start_time + timedelta(seconds=self.start)
-        self.start_time = start_time.replace(microsecond=0).isoformat()
+        self.start_time = start_time.astimezone(timezone.utc).isoformat(timespec="milliseconds")
 
         self.raw = read.signal
 

diff --git a/documentation/SAM.md b/documentation/SAM.md
@@ -46,7 +46,7 @@ $ bonito basecaller $model $data --reference ref.fasta > aligned.cram
 | mx:i:	 | read mux                                                   |
 | ch:i:  | read channel                                               |
 | rn:i:	 | read number                                                |
-| st:Z:	 | read start time                                            |
+| st:Z:	 | read start time (in UTC)                                   |
 | f5:Z:	 | fast5 file name                                            |
 | sm:f:	 | scaling midpoint/mean/median (pA to ~0-mean/1-sd)          |
 | sd:f:	 | scaling dispersion  (pA to ~0-mean/1-sd)                   |