Removing adapters, primers and polyA/T tails using Perl?

[xhuister]

Hi all,

I've got many short sequences like the following:
ADAPTER1 (or 2) + insert + Poly(A) + GGGG(n) + ADAPTER 1 ( or 2)

I'd like to get the insert part for mapping. Also I need to record the adapter type, the length of poly(A) tail and length of GGGG(n) part.

Because it is more than just adpater trimming, I think it is better to write a script to record and trim the adapter, poly(A), GGGG(n) by myself. I can only write some Perl scripts.

But there should be some insertions or deletions in the adapter/polyA/GGG. Is there any Perl function or BioPerl function or some tool/package can search substrings with insertion/deletions/substitution?

Thank you!

[sphil]

Maybe you can have a look at http://hannonlab.cshl.edu/fastx_toolkit/. There is trimming as well as clipping of reads in a fasta/q file. Using these and manually (of course using s script) monitor the length should do the job...

[xhuister]

Maybe you can have a look at http://hannonlab.cshl.edu/fastx_toolkit/. There is trimming as well as clipping of reads in a fasta/q file. Using these and manually (of course using s script) monitor the length should do the job...

Thank you, sphil. The FASTX can only trim the adapter, but it cannot trim the polyA tail (A-stretch). I need to get the A-stretch and G-stretch length, is there any function (or regEx) to get this information? Sometimes, the A-stretch also has some deletions or insertions, like AAAAAAGAAAATAAA.

[sphil]

hmmm in python there is a regex moduk named "re" since there are mismatches it will be quite tricky to filter thos except you have defined length, which I highly doubt...