Source code for the computational analyses in Ross BD, Verster AJ et al. 2019.
Most relevant data is included in this repository, excluding the file:
GCA_AllStrains_mRNA_Curated_Alt_StopFix.fasta
which was too large to host in a standard GitHub repository. To obtain this file, please contact elbo@tauex.tau.ac.il
Lib/Figure1.py
Plots the relationship between GA3 gene abundance and the Bacteroides fragilis
abundance data
--infile_counts_ei INFILE_COUNTS_EI
A dataframe of counts mapping to GA3 EI genes
--infile_seqs_ei INFILE_SEQS_EI
A fasta file of the sequences represented by
infile_counts_ei
--infile_total_reads INFILE_TOTAL_READS
A dataframe of the total number of reads in each
library
--infile_bacteroides_counts INFILE_BACTEROIDES_COUNTS
A dataframe of counts mapping to Bacteroides marker
genes
--infile_bacteroides_seqs INFILE_BACTEROIDES_SEQS
A fasta file of the sequences represented by
infile_bacteroides_counts
--indir_marker_genes INDIR_MARKER_GENES
A directory containing
markers_s__Bacteroides_XXX.fasta files
Lib/Figure2.py
Assings immunity sequences in metagenomes to their most likely species that
encodes it
--infile_counts_ei INFILE_COUNTS_EI
A dataframe of counts mapping to GA3 EI genes
--infile_seqs_ei INFILE_SEQS_EI
A fasta file of the sequences represented by
infile_counts_ei
--infile_total_reads INFILE_TOTAL_READS
A dataframe of the total number of reads in each
library
--infile_bacteroides_counts INFILE_BACTEROIDES_COUNTS
A dataframe of counts mapping to Bacteroides marker
genes
--infile_bacteroides_seqs INFILE_BACTEROIDES_SEQS
A fasta file of the sequences represented by
infile_bacteroides_counts
--indir_marker_genes INDIR_MARKER_GENES
A directory containing
markers_s__Bacteroides_XXX.fasta files
--indir_pileups INDIR_PILEUPS
A directory containing pileups that you want to build
a tree from
--infile_db INFILE_DB
A BLAST database of different bacteroides strains
genes
--infile_genome_names INFILE_GENOME_NAMES
A table with the genome names of each B. fragilis
strain