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hallamlab / FabFos

A python-driven fosmid processing pipeline
GNU General Public License v3.0
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Using fosmid end files #7

Open chklopp opened 3 years ago

chklopp commented 3 years ago

Could you give examples for the file name and sequence names of fosmids ends?

I was rather surprised to read the comment of the get_fosmid_end_name function

def get_fosmid_end_name(string): """ This function is very unstable and currently needs to be manually changed for every FabFos run """

PPSLIBM-08-H17_F.ab1

full_name = string.split('.')[0]
prefix = full_name.split('-')[0]
# print "string= ", string, "\tfull= ", full_name, "\tprefix= ", prefix
name, direction = full_name.split('_')
# name = prefix + '.' + name
return name

Do you mean, we have to create a new Fabfos.py for each run?

cmorganl commented 3 years ago

Hi, sorry about the issues you're having.

This pipeline has only been used internally at the lab and I don't dedicate much time to it's upkeep unless a colleague reports a problem. The pipeline is dependent on some internal formats and so I'm not surprised by it causing you so many issues. The function's docstring is in reference to these internal standard formats.

Is there a reason you've chosen to use FabFos? I hate to leave it in an unusable state but I don't have time to make it more flexible.

Best, Connor

chklopp commented 3 years ago

We are benchmarking Fabfos and other tools used to assemble fosmids for an article.