
# ---------------------------------------------------------------------------
# Library configuration for tfs-process-fastq
#
# Pass this file as the run_config argument:
#   tfs-process-fastq R1.fastq.gz R2.fastq.gz out/ library_config.yaml
#
# If you are running both tfs-simulate and tfs-process-fastq on the same
# experiment, you can pass the simulate config directly to tfs-process-fastq
# instead of maintaining a separate file — the extra keys (growth rates,
# conditions, etc.) are silently ignored by the FASTQ processor.
# ---------------------------------------------------------------------------

# Reading frame 0, 1, 2. No reverse (negative) strand allowed.
reading_frame: 0

# Amino acid residue number for the first in-frame residue of the amplicon.
first_amplicon_residue: 27

# Wildtype DNA sequence of the amplicon.
wt_seq: gccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatg

# Degenerate codon pattern for library positions.  '.' = wildtype; 'nnt' = NNT
# codon (encodes all 20 amino acids + stop with reduced synonymous redundancy).
# Must be the same length as wt_seq.
degen_sites: ......nntnnt.............................................................................................nntnnt.........................................................................................................

# tiles groups contiguous degenerate positions that were cloned together.
# '.' = wildtype; any other character defines a tile block.  Blocks must
# be contiguous (......111... ok; ....11.1... not ok).
tiles: ......111111.............................................................................................222222.........................................................................................................

# Flanking sequences immediately upstream and downstream of the amplicon.
expected_5p: cgcgtggtgaaccag
expected_3p: gtagaacgaagcggc

# Which genotype classes to include.  'single-x' = all single-mutation variants
# in tile x.  'double-x-y' = all pairwise combinations between tiles x and y.
tile_combos: ["single-1", "single-2", "double-1-2"]

# Control sequences added as spikes.  Must be the same length as wt_seq.
spiked_seqs:
- gccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctggcggcgccgtcgcaaattgtcgcggcgattctgtctcgcgccgatcaactgggtgccagcgtggtggtgtcgatg  # k84l
- gccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgattgcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattctgtctcgcgccgatcaactgggtgccagcgtggtggtgtcgatg  # m42i/k84l
