db_reformatter

Script to reformat the EzBioCloud database to be used with mg_classifier.

The EzBioCloud database is not publicly available (although it is free for academia); you can ask for it here: http://www.ezbiocloud.net/resources/pipelines.

You´ll have to formatted to be able to used it with mg_classifier.

Usage

You have to make the script executable (chmod +x db_reformatter.sh) and then run it:

$ ./db_reformatter.sh eztaxon_qiime_full.fasta eztaxon_id_taxonomy.txt

The order of files is important, first the fasta file and then the taxonomy file.

You will get a new fasta file in the following format:

>100000:Eukarya;Viridiplantae;Streptophyta;Jungermanniopsida;Pallaviciniales;Pallaviciniaceae;Pallavicinia;Pallavicinia_lyellii
TTACCTAATTGGTGAGGCAATGGCTCACCAAGGCGACGATCACTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCTTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAGAGCCTGACGGAGCAATGCCGCGTGGAGGTACAAGGCTCACGGGTCGTAAACTCCTTTTCTCGGAGAAGATGCAATGACGGTATCCGAGGAATAAGCATCGGCTAACTCTGTGCCACCAGCCGCGGTAAGACAGAGGA
>100001:Eukarya;Viridiplantae;Streptophyta;Jungermanniopsida;Pallaviciniales;Pallaviciniaceae;Symphyogyna;Symphyogyna_circinata
GTACACATGCAAGTCGGACGGGGAGCATCCTAGTGATGTTTTCAGTGGCGGACGGGTGAGTAACGCGTAAGAACCTGCCCCTGGGAGGGGGACAACAGCTGGAAACGGTTGCTAATACCCCGTAGGCTGAGGAGCAAAAGGAGGGATCCGCCCAAGGAGGGGCTTGCGTCTGATTAGCTAGTTGGTGGGGTAATGGCTCACCAAGGCGACGATCAGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCTTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAGAGCCTGACGGAGCAATGCCGCGTGGAGGTAGAAGGCTCACGGGTCGTAAACTCCTTTTCTCGGAGAAGATGCAATGACGGTATCCGAGGAATAAGCATCGGC