Pysam
This applet performs a SAMtools count on an input BAM using Pysam, a python wrapper for SAMtools.
View full source code on GitHub
How is Pysam provided?
Pysam is provided through a pip3 install
using the pip3 package manager in the dxapp.json
's runSpec.execDepends
property:
{
"runSpec": {
...
"execDepends": [
{"name": "pysam",
"package_manager": "pip3",
"version": "0.15.4"
}
]
...
}
The execDepends
value is a JSON array of dependencies to resolve before the applet source code is run. In this applet, we specify pip3
as our package manager and pysam version 0.15.4
as the dependency to resolve.
Downloading Input
The fields mappings_sorted_bam
and mappings_sorted_bai
are passed to the main function as parameters for our job. These parameters are dictionary objects with key-value pair {"$dnanexus_link": "<file>-<xxxx>"}
. We handle file objects from the platform through DXFile
handles. If an index file is not supplied, then a *.bai
index will be created.
print(mappings_sorted_bai)
print(mappings_sorted_bam)
mappings_sorted_bam = dxpy.DXFile(mappings_sorted_bam)
sorted_bam_name = mappings_sorted_bam.name
dxpy.download_dxfile(mappings_sorted_bam.get_id(),
sorted_bam_name)
ascii_bam_name = unicodedata.normalize( # Pysam requires ASCII not Unicode string.
'NFKD', sorted_bam_name).encode('ascii', 'ignore')
if mappings_sorted_bai is not None:
mappings_sorted_bai = dxpy.DXFile(mappings_sorted_bai)
dxpy.download_dxfile(mappings_sorted_bai.get_id(),
mappings_sorted_bai.name)
else:
pysam.index(ascii_bam_name)
Working with Pysam
Pysam provides key methods that mimic SAMtools commands. In our applet example, we want to focus only on canonical chromosomes. The Pysam object representation of a BAM file is pysam.AlignmentFile
.
mappings_obj = pysam.AlignmentFile(ascii_bam_name, "rb")
regions = get_chr(mappings_obj, canonical_chr)
The helper function get_chr
def get_chr(bam_alignment, canonical=False):
"""Helper function to return canonical chromosomes from SAM/BAM header
Arguments:
bam_alignment (pysam.AlignmentFile): SAM/BAM pysam object
canonical (boolean): Return only canonical chromosomes
Returns:
regions (list[str]): Region strings
"""
regions = []
headers = bam_alignment.header
seq_dict = headers['SQ']
if canonical:
re_canonical_chr = re.compile(r'^chr[0-9XYM]+$|^[0-9XYM]')
for seq_elem in seq_dict:
if re_canonical_chr.match(seq_elem['SN']):
regions.append(seq_elem['SN'])
else:
regions = [''] * len(seq_dict)
for i, seq_elem in enumerate(seq_dict):
regions[i] = seq_elem['SN']
return regions
Once we establish a list of canonical chromosomes, we can iterate over them and perform the Pysam version of samtools view -c
, pysam.AlignmentFile.count
.
total_count = 0
count_filename = "{bam_prefix}_counts.txt".format(
bam_prefix=ascii_bam_name[:-4])
with open(count_filename, "w") as f:
for region in regions:
temp_count = mappings_obj.count(region=region)
f.write("{region_name}: {counts}\n".format(
region_name=region, counts=temp_count))
total_count += temp_count
f.write("Total reads: {sum_counts}".format(sum_counts=total_count))
Uploading Outputs
Our summarized counts are returned as the job output. We use the dx-toolkit
Python SDK function dxpy.upload_local_file
to upload and generate a DXFile
corresponding to our tabulated result file.
counts_txt = dxpy.upload_local_file(count_filename)
output = {}
output["counts_txt"] = dxpy.dxlink(counts_txt)
return output
Python job outputs have to be a dictionary of key-value pairs, with the keys being job output names as defined in the dxapp.json
file and the values being the output values for corresponding output classes. For files, the output type is a DXLink
. We use the dxpy.dxlink
function to generate the appropriate DXLink
value.
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