The Gut Phage Database (GPD)

Scripts used for characterizing human gut bacteriophages in the following manuscript:

Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD (2020) [Massive expansion of human gut bacteriophage diversity]

Associated data can also be found in our FTP server

classifier/classifier.py

Neural network that distinguishes phages from integrative and conjugative elements (ICEs).

<b>Requirements:</b>

• Python (tested v3.6.7)
• TensorFlow (tested v1.10)
• Keras (tested v.2.2.4)

<b>Usage:</b>

classifier.py <input_features_file.txt>

<b>Notes:</b>

• input_features_file.txt: It contains a feature vector of 1026 dimensions: fraction of hypothetical proteins (1), gene density (1), 5-kmer signature (1024) that represents a phage or an ICE (1 feature vector per line) <br />
• classifier/classifier_demo.py: It runs a demo of the classifier with 50 examples of phages and ICEs each <br />

<b>Input features generation files:</b>

getGeneDensity.py: This function takes in a GFF3 file and returns the number of genes / kb. <br /> getHypothetical.py: This function takes in a GFF3 file and returns the fraction of hypothetical proteins. <br /> getKmer.py: This function takes in a DNA sequence and counts the proportion of each of the 1024 possible 5mers. <br />

<b>Usage:</b>

getGeneDensity(<gff3_file_name>)
getHypothetical(<gff3_file_name>)
getSignature_hash(<DNA_sequence>)

Other analysis and plotting scripts

<b>figures/</b>

• 'Figure 1.py': Distribution of MIUViG scores from CheckV analysis
• 'Figure 2.py': Viral diversity patterns across gut bacteria genera and broad host range VCs
• 'Figure 3.py': Gut phageome profiling across human populations and correlation with gut bacteria enterotypes
• 'Figure 4.py': Crass-like family global distribution and host-phage network of globally distributed VCs
• 'Figure 5.py': Phylogenetic structure of the pX phage and global distribution
• 'Figure S1.py': Quality control assessment of GPD
• 'Figure S2.py': Viral diversity patterns across gut bacteria phyla and host range analysis of gut phages
• 'Figure S3.py': Correlation between sequencing depth and number of phages detected in a sample
• 'Figure S4.py': Host range analysis of globally distributed phages