virfac

Set of python scripts for the virulence factors project

Common dependency of the scripts are: 1- Matplotlib 2- NumPy 3- SciPy 4- Pandas 5- BioPython

Some scripts may also require: MySQLdb Networkx Statsmodels

The majority of these scripts were developed to be used in a interactive session (i.e. vim-ipython) and a great part of input files are hard coded and probably really badly explained (sorry)...

If interested in something contact me! =D

Name		Name	Last commit message	Last commit date
Latest commit History 39 Commits
README.md		README.md
annotate_profiles.py		annotate_profiles.py
binary_heatmap.py		binary_heatmap.py
bipartition_agreement.py		bipartition_agreement.py
creates_fastas_from_sql.py		creates_fastas_from_sql.py
domain_assesment.py		domain_assesment.py
eval_blast.py		eval_blast.py
feed_mysql.py		feed_mysql.py
gene_distances_correlation-jaccard_filter-parallel.py		gene_distances_correlation-jaccard_filter-parallel.py
gene_distances_correlation-parallel.py		gene_distances_correlation-parallel.py
guidance.py		guidance.py
hgt_test.py		hgt_test.py
merge_groups.py		merge_groups.py
network_from_corr.py		network_from_corr.py
prepare_fastas_for_clustering.py		prepare_fastas_for_clustering.py
puzzle_2_pandas.py		puzzle_2_pandas.py
retrieve_profile_annotation.py		retrieve_profile_annotation.py
retrive_profile_annotation.py		retrive_profile_annotation.py
robinson_foulds.py		robinson_foulds.py
size_taxa-hist.py		size_taxa-hist.py
t3ss_pan_genome.py		t3ss_pan_genome.py
xargs_blast.py		xargs_blast.py
xargs_fastree.py		xargs_fastree.py
xargs_guidance.py		xargs_guidance.py
xargs_hmmbuild.py		xargs_hmmbuild.py
xargs_hmmsearch.py		xargs_hmmsearch.py
xargs_interproscan.py		xargs_interproscan.py
xargs_mafft.py		xargs_mafft.py
xargs_puzzle.py		xargs_puzzle.py

shannonmargaret/virfac

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