How To Transform The Bowtie Tabular Output Into Blast Tabular Output

Question

[2011101101]

I have a perl program SUmirFold13.pl

The SUmirFold13.pl only accept the the blast results in the format tabular (-outformat 6) like this

# Query ID    Subject ID    %    length    mism    gaps    qstart    qend    sstart    send    evalue    bitscore
2-16    contig213144    100.00    23    0    0    1    23    910    888    0.10    38.0
2-16    contig1892305    95.65    23    1    0    1    23    447    469    0.94    34.9

I have the bowtie result(below)

# Query ID length qstart-qend Subject ID Subject-length     sstart-send evalue unknown    bitscore  direction
2-16    23    1..23    contig213144    1892    983..1005    1e-04    1.00    42.1    Plus / Minus
2-16    23    1..23    contig1892305    721    447..469    1e-04    1.00    42.1    Plus / Plus

I think if the SUmirFold13.pl accept the bowtie result,it's good.I don't know how to modify the program，I hope someone give some suggestion.Thank you

[Michael]

Are you referring to: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0040859 ? The code is available in the supplementary material S1 in a PDF file (about the most intelligent way to distribute the code xD). If your code is different, please use a little less intrusive/obstructive site to deposit it, e.g. pastebin or github.

[Sebastian Kurscheid]

not the most intelligent way, but at least they bothered with publishing the code at all, instead of referring to the mysterious "in house script" ;-)

[2011101101]

This perl was Written by Stuart J. Lucas,and I get this from him,there is no problem about it.

[fo3c]

What are the names of the columns in the botwie output? Or, could you produce bowtie output for the same query as in the blast example?

[2011101101]

I have edit it.

[fo3c]

There are columns in the format you want to use that do not exist in the other file (mismatches, gaps). Unless you have the query and subject sequences, and a pairwise alignment of the two, you can't simply transform that bowtie output into the blast one, I'm afraid.

[Dan]

Does the tool use those columns?