maf-convert

This script reads alignments in maf format, and writes them in another format. It can write them in these formats: axt, blast, 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

The input should be "multiple alignment format" as described in the UCSC Genome FAQ (not "MIRA assembly format" or any other maf).

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).

-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

To run fast on multiple CPUs, and get a correct header at the top, this may be the least-awkward way. First, make a header (perhaps by using CreateSequenceDictionary). Then, concatenate the output of a command like this:
```
parallel-fastq "... | maf-convert -n sam" < q.fastq
```
Here is yet another way to get a sequence dictionary, using samtools (http://samtools.sourceforge.net/). Assume the reference sequences are in ref.fa. These commands convert x.sam to y.bam while adding a sequence dictionary:
```
samtools faidx ref.fa
samtools view -bt ref.fa.fai x.sam > y.bam
```
If a query name ends in "/1" or "/2", maf-convert interprets it as a paired sequence. (This affects sam format only.) However, it does not calculate all of the sam pairing information (because it's hard and better done by specialized sam manipulators).

Fix the pair information in y.sam, putting the output in z.bam. Using picard:
```
java -jar FixMateInformation.jar I=y.sam O=z.bam VALIDATION_STRINGENCY=SILENT
```
Using samtools:
```
samtools sort -n y.bam ysorted
samtools fixmate ysorted.bam z.bam
```

"Bugs"

For sam: the QUAL field (column 11) is simply copied from the maf q line. The QUAL is supposed to be encoded as ASCII(phred+33), whereas maf q lines are encoded differently according to the UCSC Genome FAQ. However, if you run lastal with option -Q1, the maf q lines will in fact be ASCII(phred+33).
The blast format is merely blast-like: it is not identical to NCBI BLAST.

`-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).
`-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.