Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Already on GitHub? Sign in to your account

genbank_ref_extractor: new script to make search on entrez gene and retrieve related sequences #23

Merged
merged 1 commit into from Sep 22, 2011

Conversation

2 participants
Owner

carandraug commented Sep 21, 2011

Hi

I wrote a script with bioperl that I would like to share back. It takes a list of searches for Entrez Gene and attempts to retrieve the related sequences (genomic, transcripts and proteins). It is also possible to obtain extra upstream and downstream bp for genomic sequences and control the naming of the files. In the end it can save all the results in a CSV file.

Hope you find it up to your coding standards. Suggestions for improvements are welcome, including for a better name.

Carnë

@bosborne bosborne merged commit 8f9089f into bioperl:master Sep 22, 2011

Member

bosborne commented Sep 22, 2011

Carne,

Wow. Nice looking script!

Did the pull. A couple of minor errors with podchecker, you might want to take a look.

Thank you, I'll mention this in the "Getting Genomic ..." HOWTO.

BIO

On Sep 21, 2011, at 11:25 AM, Carnë Draug wrote:

Hi

I wrote a script with bioperl that I would like to share back. It takes a list of searches for Entrez Gene and attempts to retrieve the related sequences (genomic, transcripts and proteins). It is also possible to obtain extra upstream and downstream bp for genomic sequences and control the naming of the files. In the end it can save all the results in a CSV file.

Hope you find it up to your coding standards. Suggestions for improvements are welcome, including for a better name.

Carnë

You can merge this Pull Request by running:

git pull https://github.com/carandraug/bioperl-live bp_genbank_ref_extractor

Or you can view, comment on it, or merge it online at:

#23

-- Commit Summary --

  • genbank_ref_extractor: new script to make search on entrez gene and retrieve related sequences

-- File Changes --

A scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl (1064)

-- Patch Links --

https://github.com/bioperl/bioperl-live/pull/23.patch
https://github.com/bioperl/bioperl-live/pull/23.diff

Reply to this email directly or view it on GitHub:
#23

Member

bosborne commented Sep 22, 2011

Carne,

This is impressive looking, it is now in scripts/.

Thanks again,

Brian O.

On Sep 21, 2011, at 11:25 AM, Carnë Draug wrote:

Hi

I wrote a script with bioperl that I would like to share back. It takes a list of searches for Entrez Gene and attempts to retrieve the related sequences (genomic, transcripts and proteins). It is also possible to obtain extra upstream and downstream bp for genomic sequences and control the naming of the files. In the end it can save all the results in a CSV file.

Hope you find it up to your coding standards. Suggestions for improvements are welcome, including for a better name.

Carnë

You can merge this Pull Request by running:

git pull https://github.com/carandraug/bioperl-live bp_genbank_ref_extractor

Or you can view, comment on it, or merge it online at:

#23

-- Commit Summary --

  • genbank_ref_extractor: new script to make search on entrez gene and retrieve related sequences

-- File Changes --

A scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl (1064)

-- Patch Links --

https://github.com/bioperl/bioperl-live/pull/23.patch
https://github.com/bioperl/bioperl-live/pull/23.diff

Reply to this email directly or view it on GitHub:
#23

Owner

carandraug commented Sep 22, 2011

Hi Brian,

thank you for the nice words.

I fixed the errors from podchecker. I just used pod2man and saw that a properly formatted man page came out. I'll make another pull request for the fix.

Carnë

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment