fosmid_qc

Here we describe how to use the fosmid quality control script (fosmid_qc.py).

Issues

This script requires the argparse Python package, which is not included on older versions of python, i.e., 2.5 and 2.6, which are common in the lab. Download and unzip the above and then run the following in the directory:

python setup.py install

Like most argparse scripts you can ask it for help:

python fosmid_qc.py -help

The command takes a number of arguments as input to specify which fosmid to search, the fosmid-end libraries, the vector databases, and an output directory. These are lists of files specified by the Unix glob * e.g.

python fosmid_qc.py -i workspace/melanie_fosmids/IX1407_final_assemblies/A25*fa -o workspace/melanie_fosmids_out -d data/vector_sequenceDB/UniVec.fasta -n data/GSC_fosmid_mapfile.txt -e data/EndSequenceDB/*fasta

where -i is a list of full-fosmid input files

-o which is a new folder that will be created

-d is a fasta file of the vector database

-n name mapping file between sequencing centre names and our internal fosmid end libraries

-e a list of fasta files of the actual fosmid end libraries to search