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Merge pull request #15972 from wm75/fast-bam-chunks

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Improve display chunk generation for BAMs
This commit is contained in:
Dannon
2023-04-26 10:22:34 -04:00
committed by GitHub
parent de488f145a 999162c884
commit 0a47a7eb97
1 changed files with 17 additions and 13 deletions
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lib/galaxy/datatypes/binary.py
+17 -13
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@@ -609,30 +609,34 @@ class BamNative(CompressedArchive, _BamOrSam):
try:
with pysam.AlignmentFile(dataset.file_name, "rb", check_sq=False) as bamfile:
ck_size = 300 # 300 lines
ck_data = ""
header_line_count = 0
if offset == 0:
ck_data = bamfile.text.replace("\t", " ") # type: ignore[attr-defined]
header_line_count = bamfile.text.count("\n") # type: ignore[attr-defined]
offset = bamfile.tell()
ck_lines = bamfile.text.strip().replace("\t", " ").splitlines() # type: ignore[attr-defined]
else:
bamfile.seek(offset)
for line_number, alignment in enumerate(bamfile):
ck_lines = []
for line_number, alignment in enumerate(bamfile, len(ck_lines)):
# return only Header lines if 'header_line_count' exceeds 'ck_size'
# FIXME: Can be problematic if bam has million lines of header
offset = bamfile.tell()
if (line_number + header_line_count) > ck_size:
if line_number > ck_size:
break
else:
bamline = alignment.tostring(bamfile)
# Galaxy display each tag as separate column because 'tostring()' funcition put tabs in between each tag of tags column.
# Below code will remove spaces between each tag.
bamline_modified = ("\t").join(bamline.split()[:11] + [(" ").join(bamline.split()[11:])])
ck_data = f"{ck_data}\n{bamline_modified}"
offset = bamfile.tell()
bamline = alignment.tostring(bamfile)
# With multiple tags, Galaxy would display each as a separate column
# because the 'tostring()' function uses tabs also between tags.
# Below code will turn these extra tabs into spaces.
n_tabs = bamline.count("\t")
if n_tabs > 11:
bamline, *extra_tags = bamline.rsplit("\t", maxsplit=n_tabs - 11)
bamline = f"{bamline} {' '.join(extra_tags)}"
ck_lines.append(bamline)
else:
# Nothing to enumerate; we've either offset to the end
# of the bamfile, or there is no data. (possible with
# header-only bams)
offset = -1
ck_data = "\n".join(ck_lines)
except Exception as e:
offset = -1
ck_data = f"Could not display BAM file, error was:\n{e}"