/usr/share/doc/python-pysam/tests/00README.txt is in python-pysam-tests 0.7.7-1ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | File ex1.fa contains two sequences cut from the human genome
build36. They were exatracted with command:
samtools faidx human_b36.fa 2:2043966-2045540 20:67967-69550
Sequence names were changed manually for simplicity. File ex1.sam.gz
contains MAQ alignments exatracted with:
(samtools view NA18507_maq.bam 2:2044001-2045500;
samtools view NA18507_maq.bam 20:68001-69500)
and processed with `samtools fixmate' to make it self-consistent as a
standalone alignment.
To try samtools, you may run the following commands:
samtools faidx ex1.fa # index the reference FASTA
samtools import ex1.fa.fai ex1.sam.gz ex1.bam # SAM->BAM
samtools index ex1.bam # index BAM
samtools tview ex1.bam ex1.fa # view alignment
samtools pileup -cf ex1.fa ex1.bam # pileup and consensus
samtools pileup -cf ex1.fa -t ex1.fa.fai ex1.sam.gz
In order for the script pysam_test.py to work, you will need pysam
in your PYTHONPATH.
In order for the script example.py to work, you will need pysam
in your PYTHONPATH and run
make all
beforehand.
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