For when you just need a coverage plot.
Just throw in your indexed bamfiles, done. Will process the files in parallel. Uses the first reference of the first file if you don't give a specific genomic position.
Feature requests welcome!
fastcov.py my_alignment.bam another_alignment.bam
generates a coverage plot called fastcov_output.pdf
Get a logplot of some SARS-CoV-2 direct RNA sequencing data
./fastcov.py -l -o example.png flowcell*.bam
makes use of
pysamnumpypandasseaborn
usage: fastcov.py [-h] [-p POSITION] [-l] [-o OUTPUT_FILE] [-c CSV_OUT]
[--csv_no_header]
bamfile [bamfile ...]
Plot the coverage based on some bam files.
positional arguments:
bamfile Alignment files to include in the coverage plot.
optional arguments:
-h, --help show this help message and exit
-p POSITION, --position POSITION
Specify a genomic position to plot exclusively.
Format: <ref_name>[:<start>-<stop>] Coordinates are
1-based and inclusive. Start and/or stop are optional
with fallbacks 1 and <length_of_ref> respectively
(i.e. 'chr1', 'chr1:-200', 'chr1:100-' and
'chr1:100-200 are legal)
-l, --logscale Use logarithmic scale on y-axis.
-o OUTPUT_FILE, --output_file OUTPUT_FILE
Specify plot output filename. File extension defines
the format (default: fastcov_output.pdf)
-c CSV_OUT, --csv_out CSV_OUT
Specify csv data output filename. Use '-' to write to
stdout. Will disable plot output by default, specify
--output_file to re-enable plot output.
--csv_no_header Suppress column names in csv output.