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pepMeld-Lite

  • Simpler workflow to process Roche-NimbleGen arrays.
  • This does not complete the additional processing if the phyical coordinates of the array is present.
    • Use pepMeld for better preprocessing if the physical coordinates of the array are exposed

Summary

  • This python script will:
    • Open the data file,
      • Take the log base2 of each binding affinity value
      • Subtract the associate control with each value
      • Take the median of the repeated peptide sequences of each array, by MHC type.
    • Open a "meta data" file to
      • rename sequences to a human readable format.
      • Apply a qualitative positive/negative "Threshold" for each MHC-Type based on the distribution.
    • Open the peptide sequence to protein accession number lookup
      • Choose a unique accession number / peptide sequence
      • Join the sequences to the peptide data, for each MHC type.
    • Output a file ready to upload into iedb.org epitope databases.

Running main.py to agregate the data for IEDB.org

Creates IEDB.org ready files from Roche-NimbleGen Peptide Array datasets Arguments

argument single_character type default help required
meta_filepath m string nan filepath of the meta data t
meta_sep e string \t filepath of the meta data f
pep_seq_protein_lookup_path p string nan Filepath of the protein lookup file t
lookup_sep l string \t separator used in the pep_seq_protein_lookup file [ , \t ] f
in_dir i string nan Location of the input data files t
in_data_ext x string Mamu.txt.gz File names endswith to search for in data files of the in_dir f
in_data_sep d string \t separator used in the in_data file(s) [ , \t ] nan
sequence_lengths s string 8,9,10 comma delimited list of lengths to include [ 8,9,10 ] f
out_dir o string nan output directory t
out_prefix f string mhc_ppma prefix to use in the output files. f

Example:

python3 ~/github/pepMeld-lite/main.py \
--meta_filepath='/Volumes/mhc_dataset/mhc_meta.tsv' \
--meta_sep='\t' \
--pep_seq_protein_lookup_path=/Volumes/mhc_dataset/SIV_SHIV_PEP_QX12_correspondence_key.txt.gz \
--lookup_sep='\t' \
--in_dir='/Volumes/mhc_dataset/input_data' \
--in_data_ext='Mamu.txt.gz' \
--in_data_sep='\t' \
--sequence_lengths='8,9,10' \
--out_dir='/Volumes/mhc_dataset/output_data' \
--out_prefix='mhc_ppma'

Raw data input data format

Required columns:

Column Name Details
PROBE_SEQUENCE Peptide sequence (all caps)
REPL The corresponding Position of a Replicate (used to match control position)
SEQ_ID Either MER_REDUNDANT or _

Meta data input data format

Required columns:

Column Name Details
VENDOR_NAME Data column name from the vendor provided data table
MHC Allele Name This is the MHC Allele Name that will be uploaded to IEDB.org
CONTROL_SUBTRACT This is the column to subtract the values by Peptide_Sequence & Replicate position
EXCLUDE To exclude the column from analysis
PASSING_THRESHOLD Control Subtracted threshold that is considered passing

Peptide Sequence to Protein Accession format

Required columns:

Column Name Details
PEPTIDE_SEQUENCE Peptide sequence (all caps)
ORIGINAL_SEQ_ID Associated Virus Accession Number _ Protein Accession Number