Unable to generate output from ExtractFeature()

[mkay...@gmail.com]

Hi,

I am trying to use mafFilter to extract subregions of a large maf (the one I'm using is the Drosophila 27 species alignment downloaded from UCSC). I am specifying the region in a .gff.gz file. Here is just a test example with one mRNA, but obviously the reason I'd like to use mafFilter is to do this for an arbitrarily large number of genomic regions I'm interested in.

The program runs without throwing any errors but it does not generate an output file and the log file is empty. To my knowledge, the chromosome names in the my .gff.gz file (i.e. 'chr2L') match the name in the .maf.gz file ('dm6.chr2L'). I don't know what else to check.

This is my first time trying to use mafFilter and I have tried to read through the relevant documentation and examples, but I don't know C++.

Thanks for any advice,
Mary

[Julien Yann Dutheil]

Dear Mary,

In order to output the extracted regions into a sequence file, you need to add an output filter (see http://biopp.univ-montp2.fr/manual/html/maffilter/v1.2.1/maffilter.html#Exporting ).

You have basically 3 possibilities:

- Output the regions in a maf file (simple 'Output' filter)

- Output the regions in a single sequence file ('OutputAlignments' filter, with single file name. Several formats supported, including Fasta, Phylip, Clustal...)

- Output each region in a distinct file ('OutputAlignments' filter with special file name, for instance 'block-%i-%c-%b-%e.fasta' will create one fasta file for each block, including the block number, chromosome name, starting and ending positions in reference sequence. %c,%b and %e are optional, but %i is mandatory to create unique file names)

Hope this helps.

Best,

Julien.

[mkay...@gmail.com]

Hi,

I have now tried appending both of the following (Output() or OutputAlignments()) as below and in neither case did it generate an output file. Also, the log file is still empty. Sorry if I am doing something stupid, but I am pretty stumped. Maybe it doesn't like the format of one of the input files? Is there anyway to check whether it has found any matches between my provided annotations and the maf?

Output(\
      file=/Users/maryk.thompson/Desktop/Davislab/C2.21_conservation/datasources/testing.maf.gz,\
      compression=gzip,\
      mask=yes)

OutputAlignments(                                \
        format=Clustal,                              \
        file=testcyceagain.aln,                          \
        compression=none,                            \
        mask=yes)                                    \

[Julien Y. Dutheil]

Passing by the forum I realized I had not seen your answer... really sorry about that :s is the problem still there? One possible issue is that the output path contains a directory that does not exist. Maffilter can only create files, not directories, so all intermediate dirs have to be created prior to launching the program.

Julien.