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, pulls the qual info by id, and writes everything either 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 + [optionally with repeat of seq_id and repeat line]
• qual scores as string of chr(33+qual)

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:

This script creates separate fastq files for each library.

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_fasta.py -f input_fasta_filepath -q input_qual_filepath -s