import module in needed functions to fix circular import

Last-Update: 2021-06-30


Gbp-Pq: Name fix-circular-import.patch

1 files changed, 2 insertions, 1 deletions

diff --git a/mirtop/bam/bam.py b/mirtop/bam/bam.py
index 1528b6a..1295729 100644
--- a/mirtop/bam/bam.py
+++ b/mirtop/bam/bam.py
@@ -15,7 +15,6 @@ import mirtop.libs.logger as mylog
 from mirtop.mirna.realign import isomir, hits, reverse_complement
 from mirtop.mirna.mapper import get_primary_transcript, guess_database
 from mirtop.bam import filter
-from mirtop.gff import body
 from mirtop.mirna.annotate import annotate
 from mirtop.libs import sql
 
@@ -72,6 +71,7 @@ def read_bam(bam_fn, args, clean=True):
 def low_memory_bam(bam_fn, sample, out_handle, args):
     if args.genomic:
         raise ValueError("low-memory option is not compatible with genomic coordinates.")
+    from mirtop.gff import body
     precursors = args.precursors
     bam_fn = _sam_to_bam(bam_fn)
     bam_fn = _bam_sort(bam_fn)
@@ -100,6 +100,7 @@ def low_memory_bam(bam_fn, sample, out_handle, args):
 def low_memory_genomic_bam(bam_fn, sample, out_handle, args):
     logger.info("Reading BAM file in low memory mode.")
     logger.warning("This is under development and variants can be unexact.")
+    from mirtop.gff import body
     precursors = args.precursors
     bam_fn = _sam_to_bam(bam_fn)
     bam_fn = _bam_sort(bam_fn)