maf-convert

This script reads alignments in maf format, and writes them in another format. It can write them in these formats: axt, blast, blasttab, chain, html, psl, sam, tab. You can use it like this:

maf-convert psl my-alignments.maf > my-alignments.psl

It's often convenient to pipe in the input, like this:

... | maf-convert psl > my-alignments.psl

This script takes the first (topmost) maf sequence as the "reference" / "subject" / "target", and the second sequence as the "query".

For html: if the input includes probability lines starting with 'p', then the output will be coloured by column probability. (To get lines starting with 'p', run lastal with option -j set to 4 or higher.)

Options

-h, --help Print a help message and exit.
-p, --protein Specify that the alignments are of proteins, rather than nucleotides. This affects psl format only (the first 4 columns).
-j N, --join=N Join neighboring alignments if they are co-linear and separated by at most N letters. This affects psl format only.
-n, --noheader Omit any header lines from the output. This may be useful if you concatenate outputs, e.g. from parallel jobs.
-d, --dictionary Include a dictionary of sequence lengths in the sam header section (lines starting with @SQ). This requires reading the input twice, so it must be a real file (not a pipe). This affects sam format only.
-f DICTFILE, --dictfile=DICTFILE Get a sequence dictionary from DICTFILE. This affects sam format only. You can create a dict file using CreateSequenceDictionary (http://picard.sourceforge.net/).
-r READGROUP, --readgroup=READGROUP Specify read group information. This affects sam format only. Example: -r 'ID:1 PL:ILLUMINA SM:mysample'
-l CHARS, --linesize=CHARS Write CHARS characters per line. This affects blast and html formats only.

Hints for sam/bam

"Bugs"