hitac 1.1

A hierarchical taxonomy classifier for fungal ITS sequences

HiTaC

A hierarchical taxonomy classifier for fungal ITS sequences.

Installation

HiTaC can be easily installed with conda:

conda install -c bioconda hitac

Input Files

HiTaC accepts training and test files in FASTA format. However, the taxonomy in the training file must be specified in the header in TAXXI format. For example:

>DQ286276;tax=d:Fungi,p:Ascomycota,c:Sordariomycetes,o:Diaporthales,f:Diaporthaceae,g:Diaporthe,s:Diaporthe_aspalathi;
GGATCATTGCTGGAACGCGCCCCAGGCGCACCCAGAAACCCTTTGTGAACTCATACCTTACTGTTGCCTCGGCGCAGGCC
GGCCCCCCAGGGGGCCCCTCGGAGACGAGGAGCAGGCCCGCCGGCGGCCAAGCCAACTCTTGTTTTTACACCGAAACTCT
GAGCAAAAAACACAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGC
GATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGC
ATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCTGGCTTGGTGTTGGGGCACTGCCTGTAGAAGGGCAGGCCCTGAAAT
CTAGTGGCGGGCTCGCCAGGACCCCGAGCGCAGTAGTTAAACCCTCGCTCGGGAGGCCCTGGCGGTGCCCTGCCGTTAAA
CCCCCAACTTCTGAAAAT
>EU272527;tax=d:Fungi,p:Ascomycota,c:Eurotiomycetes,o:Eurotiales,f:Trichocomaceae,g:Paecilomyces,s:Paecilomyces_sinensis;
CCGAGTGAGGGTCCCACGAGGCCCAACCTCCCATCCGTGTTGAACTACACCTGTTGCTTCGGCGGGCCCGCCGTGGTTCA
CGCCCGGCCGCCGGGGGGCCTTGTGCTCCCGGGCCCGCGCCCGCCGAAGACCCCTCGAACGCTGCCCTGAAGGTTGCCGT
CTGAGTATAAAATCAATCATTAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCG
ATAAGTAATGTGAATTGCAGAATTCCGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCTGGCATTCCGGGGGGCA
TGCCTGTCCGAGCGTCATTGCTAACCCTCCAGCCCGGCTGGTGTGTTGGGTCGACGTCCCCCCCGGGGGACGGGCCCGAA
AGGCAGCGGCGGCGCCGCGTCCGATCCTCGAGCGTATGGGGCTTTGTCACGCGCTCTGGTAGGGTCGGCCGGCTGGCCAG
CCAGCGACCTCACGGTCACCTATTTTTTCTCTTAGG

Output File

The predictions are written in a TSV file, where the first column contains the identifier of the test sequence and the second column holds the predictions made by HiTaC. For example:

EF535685	d:Fungi,p:Ascomycota,c:Dothideomycetes,o:Capnodiales,f:Mycosphaerellaceae,g:Pseudocercospora,s:Pseudocercospora_basitruncata
JN943699	d:Fungi,p:Ascomycota,c:Lecanoromycetes,o:Lecanorales,f:Parmeliaceae,g:Melanohalea,s:Melanohalea_elegantula
FJ596843	d:Fungi,p:Basidiomycota,c:Agaricomycetes,o:Agaricales,f:Agaricaceae,g:Agaricus,s:Agaricus_pseudopratensis
HM017845	d:Fungi,p:Basidiomycota,c:Agaricomycetes,o:Agaricales,f:Cortinariaceae,g:Cortinarius,s:Cortinarius_biformis
AF398455	d:Fungi,p:Basidiomycota,c:Exobasidiomycetes,o:Tilletiales,f:Tilletiaceae,g:Tilletia,s:Tilletia_bromi

Running

To see the usage run hitac -h

usage: hitac.py [-h] [--kmer KMER] [--threads THREADS] train test predictions

HiTaC, a hierarchical taxonomy classifier for fungal ITS sequences

positional arguments:
  train              Input FASTA file containing the sequences for training
  test               Input FASTA file containing the sequences for taxonomy
                     prediction
  predictions        Output file to write the predictions

optional arguments:
  -h, --help         show this help message and exit
  --kmer KMER        Kmer size for feature extraction [default: 6]
  --threads THREADS  Number of threads [default: all threads available]

To test the installation, run the following commands:

wget -O train_sp_rdp_its.100.fasta https://drive5.com/taxxi/benchmark/trainfa/sp_rdp_its.100
wget -O test_sp_rdp_its.100.fasta https://drive5.com/taxxi/benchmark/testfa/sp_rdp_its.100
hitac.py --kmer 6 train_sp_rdp_its.100.fasta test_sp_rdp_its.100.fasta predictions_sp_rdp_its.100.tsv

If everything is OK, a file called predictions_sp_rdp_its.100.tsv will be created.