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Search: Posts Made By: xApple
Forum: Bioinformatics 07-16-2013, 01:13 PM
Replies: 12
Views: 10,158
Posted By xApple
You're welcome ! It's just a quick hack that has...

You're welcome ! It's just a quick hack that has the advantage to not use any memory but suffers from being extremely slow. Probably not suitable for Illumina sized data.
Forum: Bioinformatics 07-12-2013, 07:25 AM
Replies: 12
Views: 10,158
Posted By xApple
That bioawk command doesn't compute the quality...

That bioawk command doesn't compute the quality score for the entire file as per the question you originally asked. It computes it for every sequence and floods your standard output.

Here is a...
Forum: Bioinformatics 10-22-2012, 09:31 AM
Replies: 2
Views: 1,054
Posted By xApple
Yes, that is correct, my data is exclusively 454....

Yes, that is correct, my data is exclusively 454. But that will probably soon change. It's a pity that this thread did not take up. The last post on cleaning data generated 25 replies.
Forum: Bioinformatics 10-19-2012, 07:34 AM
Replies: 2
Views: 1,054
Posted By xApple
Arrow Cleaning second-generation sequencing data - current situation

Hello everyone,

What was first to be a question on seqanswers or biostars, turned into a long post as I was writting it, so I ended up loading it on a blog. But it's not less of topic I would like...
Forum: Site Feedback/Suggestions 10-12-2012, 04:08 AM
Replies: 4
Views: 6,510
Posted By xApple
If that's the case, then my question would maybe...

If that's the case, then my question would maybe be better suited for seqanswers as it is pretty general. But I have written it now with the biostar markup syntax. Oh well, I'll post it there and...
Forum: Site Feedback/Suggestions 10-12-2012, 12:29 AM
Replies: 4
Views: 6,510
Posted By xApple
I'm happy to hear you are talking with the admin...

I'm happy to hear you are talking with the admin of biostar. Hope you will work something out. But that's probably hard as it would mean one of the two parties has to concede to the other, I guess....
Forum: Site Feedback/Suggestions 10-11-2012, 06:38 AM
Replies: 4
Views: 6,510
Posted By xApple
Cross posting with biostar ?

Hello !

I had this great and fairly long question about 454 pyrosequencing I was going to post; but have difficulty deciding between seqanswers and biostar. Both communities seem to be quite...
Forum: Bioinformatics 10-09-2012, 09:15 AM
Replies: 7
Views: 21,004
Posted By xApple
Here is a script that you can place in your bin/...

Here is a script that you can place in your bin/ directory:


#!/usr/bin/env python

"""
Convert single FASTAQ files to FASTA + QUAL file pairs...
Forum: Bioinformatics 09-13-2012, 05:47 AM
Replies: 9
Views: 15,074
Posted By xApple
Taking on maubp's suggestion and making a better...

Taking on maubp's suggestion and making a better script to place in your ~/bin folder:


#!/usr/bin/env python

"""
Convert FASTA + QUAL file pairs to a single FASTQ file...
Forum: Bioinformatics 02-14-2012, 08:06 AM
Replies: 5
Views: 2,064
Posted By xApple
1. You're welcome to use/steal/take from my...

1. You're welcome to use/steal/take from my implementation. I was thinking of making a generic object called a "tict()" instead of a "dict()" as a play on tictionary. It would be written in C and...
Forum: Bioinformatics 02-13-2012, 07:02 AM
Replies: 5
Views: 2,064
Posted By xApple
Thanks ! If you want to look at the code, it's...

Thanks ! If you want to look at the code, it's all free on github. To answer your questions:

1. The dual tuple/dict hybrid is something I would like to take further. One often needs such an...
Forum: Bioinformatics 02-13-2012, 05:26 AM
Replies: 5
Views: 2,064
Posted By xApple
Easy library to read and write genomic files

Hi guys !

I just finished work on a python package that can read most of the genomic file formats such as BED, WIG, GFF, BedGraph in a simple and standard way. I made a post about in...
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