make_fastq.rst

make_fastq.py

make_fastq.py -- Make FASTQ file for ERA submission from paired FASTA and QUAL files

Description:

The ERA currently requires a separate FASTQ file for each library, split by library id. This code takes the output from split_libraries.py and the corresponding QUAL files and produces ERA-compatible FASTQ files.

Usage: make_fastq.py [options]

Input Arguments:

Note

[REQUIRED]

-f, --input_fasta_fp

Path to the input fasta file

-q, --qual

Names of QUAL files, comma-delimited

[OPTIONAL]

-o, --result_fp

Path to store results [default: <input_sequences_filename>.fastq]

-s, --split

Make separate file for each library [default:False]

Output:

Matches QUAL info to FASTA entries by id, and writes FASTQ output to one file or to per-library files.

The FASTQ format for each record is as follows:

@seq_id [and optional description] seq as bases + [and optionally with repeat of seq_id and repeat line] qual scores as string of chr(33+qual)

Example:

Take input FASTA file input_fasta_filepath and QUAL file input_qual_filepath: make separate file for each library (with the -s option: assumes that the FASTA file is the output of split_libraries.py or similar script):

make_fastq.py -f $PWD/seqs.fna -q $PWD/Fasting_Example.qual -s