seqalign
Manage sequence alignments
Installation
pip install seqalign
or
pip install --user seqalign
If you have not already installed picardtools, you will also need to run:
picardtools-download
Examples
with SequenceAlignment(<path to input BAM or FASTQ file>) as sa:
sa.cleans_up_bam = False
sa.remove_supplementary_alignments()
sa.samtools_sort(memory_limit=10)
sa.samtools_index()
sa.write(<path to output BAM file>)
Notes
The input_file argument to SequenceAlignment() should be a string for
single-end reads or for data that is already aligned. For raw paired-end reads,
it should be a tuple containing two strings giving the paths to the two
FASTA / FASTQ files.
Command line usage
seqalign includes a couple of pre-built pipelines for aligning ChIP-seq and ATAC-seq data.
They rely on certain environment variables being set, as described here
To see the basic command line documentation, simply enter seqalign at the terminal:
seqalign
There are two commands for aligning sequencing data:
`seqalign-chip-seq` and `seqalign-atac-seq`. See their
respective documentation by running:
seqalign-chip-seq --help
seqalign-atac-seq --help
1 maintainer
Release files for seqalign 0.1.15
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| seqalign-0.1.15.tar.gz | 12.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| seqalign-0.1.15-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 27.3 kB
Release files / seqalign-0.1.15.tar.gz
| Download URL | seqalign-0.1.15.tar.gz |
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| Size | 12.7 kB |
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| Download URL | seqalign-0.1.15-py3-none-any.whl |
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| Size | 14.5 kB |
| Tags | Python 3 |
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