Other tools

On top of the pipelines described in the major sections of the documentation, the pipeline comes bundled with several other, smaller tools, all accessible via the ‘paleomix’ command. These tools are (briefly) described in this section.

paleomix cleanup

paleomix coverage

paleomix depths

paleomix rmdup_collapsed

paleomix genotype

paleomix gtf_to_bed

paleomix vcf_filter

paleomix vcf_to_fasta

paleomix cat

The ‘paleomix cat’ command provides a simple wrapper around the commands ‘cat’, ‘gzip’, and ‘bzip2’, calling each as appropriate depending on the files listed on the command-line. This tool is primarily used in order to allow the on-the-fly decompression of input for various programs that do not support both gzip and bzip2 compressed input.

Usage:

usage: paleomix cat [options] files

positional arguments:
files One or more input files; these may be uncompressed,
compressed using gzip, or compressed using bzip2.
optional arguments:
-h, --help show this help message and exit
--output OUTPUT
 Write output to this file; by default, output written to STDOUT.

Example:

$ echo "Simple file" > file1.txt
$ echo "Gzip'ed file" | gzip > file2.txt.gz
$ echo "Bzip2'ed file" | bzip2  > file3.txt.bz2
$ paleomix cat file1.txt file2.txt.gz file3.txt.bz2
Simple file
Gzip'ed file
Bzip2'ed file