Anurag Priyam

Hi, Currently the 'download' helper in 'tasks/libs.rake' fails behind proxy. This commit fixes it by using http_proxy environment variable if set.

How to add arrows to features?

2

Like in https://www.biodalliance.org/ss/cview1.png, or as on biodalliance.org.

Sending commands to bots from the right-click menu causes ShakesPeer to be disconnected from the Hub. From the logs: ``` 10/09/13 10:01:02.898 PM ShakesPeer[169]: instantiating usercommand [To: [BOT]Info From: yeban...

And how it is addressed in the http module. Maybe relevant for #10

Check for `md5sum` & `md5` on startup and accordingly define a `verify_checksum` method that can be called in an OS independent manner.

gt gff3 -sort doesn't work on some gff files in one go

4

Sometimes you have to run the GFF3 through `gt gff3 -sort` a few times before it's really sorted and will be accepted by `gt extractfeat`, like with NCBI's fire ant...

extractfeat: option to add attributes from 9th column to defline of resulting FASTA

15

Much like `-seqid` option, it would be great if other attributes like 'Name', 'Dbxref', etc. can be added to the defline of the extracted sequence.

extractfeat: -matchdescstart should probably be set by default

6

From #592 extractfeat tries to pick reference sequences using MD5 tag by default. To look up by id, `-matchdescstart` option must be used. I am not sure if it's common...

This came up in #417.