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Merge pull request #5512 from mvdbeek/fix_new_pysam

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[18.01] Make galaxy compatible with pysam 0.14
This commit is contained in:
John Chilton
2018-02-13 11:22:04 -05:00
committed by GitHub
parent aefe0e1449 3b8a2f9edc
commit 321cd78ad8
2 changed files with 6 additions and 18 deletions
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lib/galaxy/datatypes/binary.py
+5 -17
View File
@@ -12,6 +12,7 @@ import sys
import tarfile
import tempfile
import zipfile
from collections import OrderedDict
from json import dumps
import h5py
@@ -234,10 +235,10 @@ class BamNative(Binary):
# TODO: Reference names, lengths, read_groups and headers can become very large, truncate when necessary
dataset.metadata.reference_names = list(bam_file.references)
dataset.metadata.reference_lengths = list(bam_file.lengths)
dataset.metadata.bam_header = bam_file.header
dataset.metadata.bam_header = OrderedDict((k, v) for k, v in bam_file.header.items())
dataset.metadata.read_groups = [read_group['ID'] for read_group in dataset.metadata.bam_header.get('RG', []) if 'ID' in read_group]
dataset.metadata.sort_order = bam_file.header.get('HD', {}).get('SO', None)
dataset.metadata.bam_version = bam_file.header.get('HD', {}).get('VN', None)
dataset.metadata.sort_order = dataset.metadata.bam_header.get('HD', {}).get('SO', None)
dataset.metadata.bam_version = dataset.metadata.bam_header.get('HD', {}).get('VN', None)
except Exception:
# Per Dan, don't log here because doing so will cause datasets that
# fail metadata to end in the error state
@@ -383,25 +384,12 @@ class Bam(BamNative):
def set_meta(self, dataset, overwrite=True, **kwd):
# These metadata values are not accessible by users, always overwrite
super(Bam, self).set_meta(dataset=dataset, overwrite=overwrite, **kwd)
index_file = dataset.metadata.bam_index
if not index_file:
index_file = dataset.metadata.spec['bam_index'].param.new_file(dataset=dataset)
pysam.index(dataset.file_name, index_file.file_name)
dataset.metadata.bam_index = index_file
# Now use pysam with BAI index to determine additional metadata
try:
bam_file = pysam.AlignmentFile(dataset.file_name, mode='rb', index_filename=index_file.file_name)
# TODO: Reference names, lengths, read_groups and headers can become very large, truncate when necessary
dataset.metadata.reference_names = list(bam_file.references)
dataset.metadata.reference_lengths = list(bam_file.lengths)
dataset.metadata.bam_header = bam_file.header
dataset.metadata.read_groups = [read_group['ID'] for read_group in dataset.metadata.bam_header.get('RG', []) if 'ID' in read_group]
dataset.metadata.sort_order = bam_file.header.get('HD', {}).get('SO', None)
dataset.metadata.bam_version = bam_file.header.get('HD', {}).get('VN', None)
except Exception:
# Per Dan, don't log here because doing so will cause datasets that
# fail metadata to end in the error state
pass
def sniff(self, file_name):
return super(Bam, self).sniff(file_name) and not self.dataset_content_needs_grooming(file_name)
lib/galaxy/dependencies/pinned-requirements.txt
+1 -1
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@@ -11,7 +11,7 @@ mercurial==3.7.3; python_version < '3.0'
pycrypto==2.6.1
uWSGI==2.0.15
# Flexible BAM index naming is new to core pysam
pysam>=0.13
pysam==0.14
# Install python_lzo if you want to support indexed access to lzo-compressed
# locally cached maf files via bx-python