trna-batch.sh

# let's assume we have two FASTA files for two samples:
#
# sample_01: fasta_01.fa
# sample_02: fasta_02.fa
#

# genrating trna profile dtabases for each sample:
trna-profile fasta_01.fa --name sample_01 -o sample_01.db
trna-profile fasta_01.fa --name sample_01 -o sample_01.db

# once profiles are generated,

# generate a three-column file from one profile:
trna-gen-anti-codon-profile sample_01.db -o trna-profile.txt

# generate a three-column file from two profiles (columns: sample_name, anti-codon, count):
trna-gen-anti-codon-profile sample_01.db sample_02.db -o trna-profile.txt

# generate a samples x anti-codon counts matrix:
trna-gen-anti-codon-profile sample_01.db sample_02.db -o trna-profile.txt --matrix-form

# generate a samples x anti-codon counts matrix using only full-length trna sequences:
trna-gen-anti-codon-profile sample_01.db sample_02.db -o trna-profile.txt --matrix-form --only-full-length-seqs

# generate a samples x anti-codon counts matrix based on some min/max values (default --min-seq-length is 10, default --max-seq-length is sys.maxint):
trna-gen-anti-codon-profile sample_01.db sample_02.db -o trna-profile.txt --matrix-form --min-seq-length 20 --max-seq-length 80

# generate a samples x anti-codon counts matrix based only on some comma-separated anti-codon names:
trna-gen-anti-codon-profile sample_01.db sample_02.db -o trna-profile.txt --matrix-form --anti-codonds X,Y,Z