I think the mafSpeciesSubset program might actually be more what is
wanted. Here's the command line:
mafSpeciesSubset - Extract a maf that just has a subset of species.
usage:
mafSpeciesSubset in.maf species.lst out.maf
Where:
in.maf is a file where the sequence source are either simple
species
names, or species.something. Usually actually it's a genome
database name rather than a species before the dot to tell
the
truth.
species.lst is a file with a list of species to keep
out.maf is the output. It will have columns that are all - or . in
the reduced species set removed, as well as the lines
representing
species not in species.lst removed.
options:
-keepFirst - If set, keep the first 'a' line in a maf no matter what
Useful for mafFrag results where we use this for the
gene name
On Mar 22, 2010, at 12:10 PM, Jennifer Jackson wrote:
> Hello,
>
> The utility mafFilter is the best choice: use option -speciesFilter.
> You
> do not need to set up the entire code tree or a mirror to use the
> utilities in the kent source tree.
>
> http://genomewiki.ucsc.edu/index.php/The_source_tree
> http://hgdownload.cse.ucsc.edu/downloads.html -> Source
>
> mafFilter - Filter out maf files. Output goes to standard out
> usage:
> mafFilter file(s).maf
> options:
> -tolerate - Just ignore bad input rather than aborting.
> -minCol=N - Filter out blocks with fewer than N columns (default 1)
> -minRow=N - Filter out blocks with fewer than N rows (default 2)
> -factor - Filter out scores below -minFactor * (ncol**2) * nrow
> -minFactor=N - Factor to use with -minFactor (default 5)
> -minScore=N - Minimum allowed score (alternative to -minFactor)
> -reject=filename - Save rejected blocks in filename
> -needComp=species - all alignments must have species as one of the
> component
> -overlap - Reject overlapping blocks in reference (assumes ordered
> blocks)
> -componentFilter=filename - Filter out blocks without a component
> listed in filename
> *-speciesFilter=filename* - Filter out blocks without a species
> listed in filename
>
> Hopefully this helps,
> Jennifer
>
> ---------------------------------
> Jennifer Jackson
> UCSC Genome Informatics Group
> http://genome.ucsc.edu/
>
> On 3/22/10 1:42 AM, 董珊 wrote:
>> Dear Genome list,
>>
>> I want to ask a question about creat a multiple alignment from pair-
>> wise
>> alignments from UCSC Genome Blowser.
>> The whole genome multiple alignment I need is from 12 Drosophila
>> species,
>> but the multiple alignment data on UCSC Genome Blowser contain 3
>> excess
>> species (A. gambiae, A. mellifera and T. castaneum).
>>
>> I know there is a complex method to use multiz/TBA to get multiple
>> alignment
>> from pair-wise alignments.
>> However, these pair-wise alignments must in MAF format.
>> But it seems difficult to get the format convert tool on Kent source.
>> Do you know other method to remove the 3 excess species from the
>> multiple
>> alignment from UCSC Genome Blowser?
>>
>> Thank you very much in advance!
>>
>> Best regards!
>> Shan
>> _______________________________________________
>> Genome maillist - [email protected]
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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