Esempi in Python per pysam

Esempio n. 1

File: bam_to_wiggle.py Progetto: vipints/gx-utils

#!/usr/bin/env python
"""
Convert BAM files to BigWig file format in a specified region.

Usage:
bam_to_wiggle.py <BAM file> [<YAML config>]
[--outfile=<output file name>
--chrom=<chrom>
--start=<start>
--end=<end>
--normalize]

chrom start and end are optional, in which case they default to everything.
The normalize flag adjusts counts to reads per million.

The config file is in YAML format and specifies the location of the wigToBigWig
program from UCSC:

program:
ucsc_bigwig: wigToBigWig

If not specified, these will be assumed to be present in the system path.

The script requires:
pysam (http://code.google.com/p/pysam/)
wigToBigWig from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
If a configuration file is used, then PyYAML is also required (http://pyyaml.org/)
"""
import os
import sys
import subprocess

Esempio n. 2

#!/usr/bin/env python
"""Convert BAM files to BigWig file format in a specified region.

Usage:
bam_to_wiggle.py <BAM file> [<YAML config>]
[--outfile=<output file name>
--chrom=<chrom>
--start=<start>
--end=<end>
--normalize]

chrom start and end are optional, in which case they default to everything.
The normalize flag adjusts counts to reads per million.

The config file is in YAML format and specifies the location of the wigToBigWig
program from UCSC:

program:
ucsc_bigwig: wigToBigWig

If not specified, these will be assumed to be present in the system path.

The script requires:
pysam (http://code.google.com/p/pysam/)
wigToBigWig from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
If a configuration file is used, then PyYAML is also required (http://pyyaml.org/)
"""
import os
import sys
import subprocess
import tempfile

Esempio n. 3

File: bam_to_wiggle.py Progetto: abdo3a/converters

#!/usr/bin/env python
"""Convert BAM files to BigWig file format in a specified region.

Usage:
bam_to_wiggle.py <BAM file> [<YAML config>]
[--outfile=<output file name>
--chrom=<chrom>
--start=<start>
--end=<end>
--normalize]

chrom start and end are optional, in which case they default to everything.
The normalize flag adjusts counts to reads per million.

The config file is in YAML format and specifies the location of the wigToBigWig
program from UCSC:

program:
ucsc_bigwig: wigToBigWig

If not specified, these will be assumed to be present in the system path.

The script requires:
pysam (http://code.google.com/p/pysam/)
wigToBigWig from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
If a configuration file is used, then PyYAML is also required (http://pyyaml.org/)
"""
import os
import sys
import subprocess
import tempfile