To run AbAnalysis on a single FASTA or FASTQ file:
python ab_analysis.py -i <input-file> -o <output-directory> -t <temp-directory>
To iteratively run AbAnalysis on all files in an input directory:
python ab_analysis.py -i <input-directory> -o <output-directory> -t <temp-directory>
-m, --merge Input directory should contain paired FASTQ (or gzipped FASTQ) files. Paired files will be merged with PANDAseq prior to processing with AbAnalysis.
-u N, --uaid N Sequences contain a unique antibody ID (uaid) of length N. The uaid will be parsed and added to the JSON output.
-s, --species Select the species from which the input sequences are derived. Supported options are 'human', 'mouse', and 'macaque'. Default is 'human'.
-n, --next_seq Use if the sequences were generated on a NextSeq sequencer. Multiple lane files from the same sample will be merged.
Two helper scripts are included:
batch_merge.py performs PANDAseq merging on a directory of paired FASTQ (or gzipped FASTQ) files.
mongoimport.py iteratively imports a directory of JSON files into a MongoDB database.
Python >= 2.7
biopython
batch_merge requires PANDAseq (https://github.com/neufeld/pandaseq)
mongoimport requries MongoDB (http://www.mongodb.org/) and pymongo