/usr/share/doc/last-align/maf-convert.txt is in last-align 490-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 | 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.
|