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.. _make_fastq:
.. index:: make_fastq.py
*make_fastq.py* -- Make FASTQ file for ERA submission from paired FASTA and QUAL files
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**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 <./split_libraries.html>`_ and the corresponding QUAL files and produces ERA-compatible FASTQ files.
**Usage:** :file:`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 <./split_libraries.html>`_ or similar script):
::
make_fastq.py -f $PWD/seqs.fna -q $PWD/Fasting_Example.qual -s
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