FIX: fix time format for BAM and FASTQ extractors

GenomiqueENS · Aug 22, 2024 · 4043ad6 · 4043ad6
1 parent 8d41352
commit 4043ad6
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Showing 2 changed files with 6 additions and 7 deletions.
diff --git a/toulligqc/extractor_common.py b/toulligqc/extractor_common.py
@@ -432,9 +432,11 @@ def add_image_to_result(quiet, image_list, start_time, image):
 def timeISO_to_float(iso_datetime, format):
         """
         """
-        if '+' in iso_datetime:
-            iso_datetime = iso_datetime.split('+')[0]
-        dt = datetime.strptime(iso_datetime, format)
+        try:
+            dt = datetime.strptime(iso_datetime, format)
+        except:
+            format = '%Y-%m-%dT%H:%M:%SZ'
+            dt = datetime.strptime(iso_datetime, format)
         unix_timestamp = dt.timestamp()
         return unix_timestamp
 

diff --git a/toulligqc/fastq_extractor.py b/toulligqc/fastq_extractor.py
@@ -375,10 +375,7 @@ def _extract_info_from_name(self, name):
         """
         """
         metadata = dict(x.split("=") for x in name.split(" ")[1:])
-        try:
-            start_time = timeISO_to_float(metadata['start_time'], '%Y-%m-%dT%H:%M:%SZ')
-        except:
-            start_time = timeISO_to_float(metadata['start_time'], '%Y-%m-%dT%H:%M:%S.%f')
+        start_time = timeISO_to_float(metadata['start_time'],  '%Y-%m-%dT%H:%M:%S.%f%z')
         if self.is_barcode:
             return  start_time, metadata['ch'], metadata['barcode']
         return  start_time, metadata['ch']