fastq_generator

A suite of tools to generate random or mapped fastq files. The script is compatible with python2.7 and python3.4.

Table of content

• fastq_generator
• Table of content
  • Usage
  • Generate random fasta files
  • Generate random fastq files with single-end reads
  • Generate random fastq files with paired-end reads
  • Generate fastq files SE mapping on a specified fasta reference
  • Generate fastq files PE mapping on a specified fasta reference
  • Generate reads mapping to the reverse strand
  • Authors
  • License

Table of contents generated with markdown-toc

Usage

The different functions of fastq_generator are located within one python script. One can call the script in python without argument or with '-h' to get the help message.

Generate random fasta files

generate_fasta creates a de novo fasta file of chosen name and size. The sequences are generated randomly.

usage: generate_fasta name_seq sequence_size

arguments: name_seq = name of the sequence (string) sequence_size = length of the sequence in bp (integer)

python fastq_generator.py generate_fasta Chr1 1000 > chr1.fa

cat chr1.fa

>Chr1
TGGGATCTCTAAGCACTTGTACTCGATGCATCTCCACGATTACCGTTGCCATAGCTGCGAAACGATATAAAGGGTTTGGCTGTGCATGGTGTTCTCTTCAACGCCTGTACCAAACTTTCTACAATTGTCGGTGACCTCTTCCGGAAGCTGAGAATCGCTAATGAGACAAACGGCTTACTCCCTGAGTAGTACGACGTCCAAGCGAAACTATCACCACGGACTTTTTGTGTATAACTGCGTTTATCTAAAACAAGGTCGTGAGGCCTGATTGCGCACTTACGTCTGGGCCAAGACCGTGTGGACGTCTCCAACCAACACTGCTCGATGCTGCCTTGAAGATCTCGCCATCTCGAGTCAGTAACATCCCAGTGGAACACTTGAGACAGGGAAATCAGGCGCGTCTTCACGACAGGACTCTCCCCAGAGGTCCTCACTGAAGAGGTGCTATCGGTCAACCGTTCGTGGGGCCCGTTAGGCGTCTGATCTACCCAGGTCATCTTGAGACTCCCGACACCCGCATTAATTGTACCGAAATTACAAGCCAACCAAGACATTCTCGCCAATTCGTATTTGCAGCAGGCGCAAGAACATATTAGTCAATTTGCGTTCCCGGGTATTTAAGCTCAAGCAATTCTGATGTATGTAGAGACCCGTTTAGGCGTGCGTCCACAGATGGTTCGTGAGGAACCGACCGCGGCTCGCTATGCAATCAACCTACAGGTAGTGACACGCCGCAGCGGTAAACAGTGTTGTTTCGCCTTATGTCCGACCGGGTATTGTGTAATCCTCATTGAAACCCAGAGGAGCGGTATCTTAACCCATGCACATCCCTCCCCGACCACTTTCGGGCCGACCTACGCCTCTCTTTTCGTTGACTGCAGAGGCCCACCGAGCGGTCCTGATTTCATTACTTGGATAACCCGAACCTCCGATAGACCTTAGTGCCCGGTCGAGTCAGCCGTCCGCATTTCTCGATATGTCGGAGCACCAGGTGAGTATC

Generate random fastq files with single-end reads

generate_random_fastq_SE generates random sets of single-end reads usage: generate_random_fastq_SE sequence_size nb_seq

arguments: sequence_size = length of the sequence in bp (integer)
nb_seq = number of sequences required (integer)

python fastq_generator.py generate_random_fastq_SE 100 10 > random.fastq

head random.fastq

@FAKE-SEQ:1:FAKE-FLOWCELL-ID:1:1:0:1 1:N:0:TGACCAAT
AGGCCTATATAAGCTCTGAAGGACAGTATTGAGGCGAGCTTACCCCAAATCGGGTGATCCATGACGGAAACCCTTCGCGCTCGTTTGGCTTTAGGTCTTC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@FAKE-SEQ:1:FAKE-FLOWCELL-ID:1:1:0:2 1:N:0:TGACCAAT
TCATAACCCCTAGTCCCGTCTGCTGAATTAATAAGGCAAATTACTCGCTTGAGGACCGAACAAGGGATGCCGACTTTTGGGCCCAGAGCTTGTTTAACTT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

Generate random fastq files with paired-end reads

generate_random_fastq_PE generates random sets of paired-end reads usage: generate_random_fastq_SE sequence_size nb_seq arguments: sequence_size = length of the sequence in bp (integer)
nb_seq = number of sequences required (integer)

*Note that the left reads (/1) and right reads (/2) are within the same file.

python fastq_generator.py generate_random_fastq_PE 100  10 > random.fastq

head random.fastq

@FAKE-SEQ:1:FAKE-FLOWCELL-ID:1:1:0:1#0/1
TAACACTTAGGGGGCTGCTACGCAGGGGCGCAAAGGCGGTGCCACTGATTTTGCTCGAGACATAATCACGCCATATCCACGGCAGCTTTACATGGATTAG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@FAKE-SEQ:1:FAKE-FLOWCELL-ID:1:1:0:2#0/1
GGCAGGGCGAGACATGGTAACGGAGACAGGTCTGCTGACGGTCTTTAACGAATATCACTCTTCACCGTACGGGTTTAGTCTATGAGTCCAAGACGCGTGA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@FAKE-SEQ:1:FAKE-FLOWCELL-ID:1:1:0:3#0/1
GGGTATCGTTCGCCACGGAACAGCTATGGGTTACAGCACCTCGGTATTCGCTTCTGCCAGTGGCGCTAATGTAGGAGAAAACTGATGCCGTGGATCCCAA

Generate fastq files SE mapping on a specified fasta reference

generate_mapped_fastq_SE generates sets of single-end reads from a reference fasta file usage: generate_mapped_fastq_SE ref_fasta sequence_size coverage arguments: ref_fasta = reference file in fasta format (fasta file) sequence_size = length of the sequence in bp (integer) coverage = number of reads covering each bp (integer)

python fastq_generator.py generate_mapped_fastq_SE chr1.fa 100 2 > chr1_SE.fastq

head chr1_SE.fastq

@FAKE-SEQ:1:FAKE-FLOWCELL-ID:1:1:0:1 1:N:0:ATGT
CGTTGCTCTGAATAGGCCGGGAGGACGACTAGGCCGATTCCACGAACTGCACAGCGCCTATAATTTAGAAGGCGGGCACTGGAGATCTAAGATGGTTTTG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@FAKE-SEQ:1:FAKE-FLOWCELL-ID:1:1:0:2 1:N:0:ATGT
TCTACTAAAAACCTTTCATCTTTCATGGTCTTTGCCCTAACATTATGGGCCGCGGCCGTTGCAGGAGTAGACCTGATTACTCCTCACTGTATAGTTATCA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@FAKE-SEQ:1:FAKE-FLOWCELL-ID:1:1:0:3 1:N:0:ATGT
GCCTTCTCTCAAACTGGCTTCGAATTACTTTAAGAATTTCTCTTATAAGCTACGCTGACCTACACCGCTTTCCAGGCGTGGTACGACAAAGCGGGGACCG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@FAKE-SEQ:1:FAKE-FLOWCELL-ID:1:1:0:4 1:N:0:ATGT
CCAGAGCGCGAAAGAAATGCACTACTAGGAAGTTGGGCTCTACATTGTTCACAATCGAGAGGTTCTACCTGGCTCTGCACTGTGACTCAACAGCGGCGCG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

Generate fastq files PE mapping on a specified fasta reference

generate_mapped_fastq_PE generates sets of paired-end reads from a reference fasta file usage: generate_mapped_fastq_PE ref_fasta sequence_size insertion_size coverage

arguments: ref_fasta = reference file in fasta format (fasta file) sequence_size = length of the sequence in bp (integer)
insertion_size = distance between the paired reads in bp (integer) coverage = number of reads covering each bp (integer)

python fastq_generator.py generate_mapped_fastq_PE chr1.fa 100  100 2 > chr1_PE.fastq

head chr1_PE.fastq

@FAKE-SEQ:1:FAKE-FLOWCELL-ID:1:1:0:1#0/1
GCGTTGCTCTGAATAGGCCGGGAGGACGACTAGGCCGATTCCACGAACTGCACAGCGCCTATAATTTAGAAGGCGGGCACTGGAGATCTAAGATGGTTTT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@FAKE-SEQ:1:FAKE-FLOWCELL-ID:1:1:0:2#0/1
GCCAGAGCGCGAAAGAAATGCACTACTAGGAAGTTGGGCTCTACATTGTTCACAATCGAGAGGTTCTACCTGGCTCTGCACTGTGACTCAACAGCGGCGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@FAKE-SEQ:1:FAKE-FLOWCELL-ID:1:1:0:3#0/1
TGTGGGACTAAACATAGGTCGTTTGTTGCTCCCCGCGCAACTGATCAGGATTAGGCCGTGCGGCAGAAGCACCATCTTTTGCACGCCGCTTGTTTACCTT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@FAKE-SEQ:1:FAKE-FLOWCELL-ID:1:1:0:4#0/1
GGCGTTGCTCTGAATAGGCCGGGAGGACGACTAGGCCGATTCCACGAACTGCACAGCGCCTATAATTTAGAAGGCGGGCACTGGAGATCTAAGATGGTTT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@FAKE-SEQ:1:FAKE-FLOWCELL-ID:1:1:0:5#0/1
CGCCAGAGCGCGAAAGAAATGCACTACTAGGAAGTTGGGCTCTACATTGTTCACAATCGAGAGGTTCTACCTGGCTCTGCACTGTGACTCAACAGCGGCG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

Generate reads mapping to the reverse strand

Here I show an example for SE reads but it is the same process for PE reads.

cat chr1.fa | python reverse_complement.py > chr1_reverse_complement.fa

python fastq_generator.py generate_mapped_fastq_SE chr1_reverse_complement.fa 100 2 > chr1_SE_rc.fastq

# (Optional) Merge fastq files with reads mapping to both + and - strands
cat chr1_SE.fastq chr1_SE_rc.fastq > chr1_SE_both_strands.fastq

Authors

• Johan Zicola - Initial work - johanzi

License

This project is licensed under the MIT License - see the LICENSE file for details