Skip to content

Latest commit

 

History

History
153 lines (117 loc) · 7.46 KB

README.md

File metadata and controls

153 lines (117 loc) · 7.46 KB
Raw

Fastaq

Manipulate FASTA and FASTQ files

Build Status
License: GPL v3

Contents

Introduction

Python3 script to manipulate FASTA and FASTQ (and other format) files, plus API for developers

Installation

There are a number of ways to install Fastaq and details are provided below. If you encounter an issue when installing Fastaq please contact your local system administrator. If you encounter a bug please log it here or email us at [email protected].

Pip install

Install from PyPi

pip3 install pyfastaq

Or pip install the latest development version directly from this repo.

pip3 install git+https://github.com/sanger-pathogens/Fastaq.git

From source

If you want to edit the codebase, clone this repo and install in editable mode.

# Clone and install from this repository:
git clone https://github.com/sanger-pathogens/Fastaq.git && cd Fastaq && pip install -e ".[tests]"

Running the tests

The test can be run from the top level directory:

pytest tests

Runtime dependencies

These must be available in your path at run time:

  • samtools 0.1.19
  • gzip
  • gunzip

Usage

The installation will put a single script called fastaq in your path. The usage is:

fastaq <command> [options]

Key points:

  • To list the available commands and brief descriptions, just run fastaq
  • Use fastaq command -h or fastaq command --help to get a longer description and the usage of that command.
  • The type of input file is automatically detected. Currently supported: FASTA, FASTQ, GFF3, EMBL, GBK, Phylip.
  • fastaq only manipulates sequences (and quality scores if present), so annotation is ignored where present in the input.
  • Input and output files can be gzipped. An input file is assumed to be gzipped if its name ends with .gz. To gzip an output file, just name it with .gz at the end.
  • You can use a minus sign for a filename to use stdin or stdout, so commands can be piped together. See the example below.

Examples

Reverse complement all sequences in a file:

fastaq reverse_complement in.fastq out.fastq

Reverse complement all sequences in a gzipped file, then translate each sequence:

fastaq reverse_complement in.fastq.gz - | fastaq translate - out.fasta

Available commands

Command Description
acgtn_only Replace every non acgtnACGTN with an N
add_indels Deletes or inserts bases at given position(s)
caf_to_fastq Converts a CAF file to FASTQ format
capillary_to_pairs Converts file of capillary reads to paired and unpaired files
chunker Splits sequences into equal sized chunks
count_sequences Counts the sequences in input file
deinterleave Splits interleaved paired file into two separate files
enumerate_names Renames sequences in a file, calling them 1,2,3... etc
expand_nucleotides Makes every combination of degenerate nucleotides
fasta_to_fastq Convert FASTA and .qual to FASTQ
filter Filter sequences to get a subset of them
get_ids Get the ID of each sequence
get_seq_flanking_gaps Gets the sequences flanking gaps
interleave Interleaves two files, output is alternating between fwd/rev reads
make_random_contigs Make contigs of random sequence
merge Converts multi sequence file to a single sequence
replace_bases Replaces all occurrences of one letter with another
reverse_complement Reverse complement all sequences
scaffolds_to_contigs Creates a file of contigs from a file of scaffolds
search_for_seq Find all exact matches to a string (and its reverse complement)
sequence_trim Trim exact matches to a given string off the start of every sequence
sort_by_name Sorts sequences in lexographical (name) order
sort_by_size Sorts sequences in length order
split_by_base_count Split multi sequence file into separate files
strip_illumina_suffix Strips /1 or /2 off the end of every read name
to_fake_qual Make fake quality scores file
to_fasta Converts a variety of input formats to nicely formatted FASTA format
to_mira_xml Create an xml file from a file of reads, for use with Mira assembler
to_orfs_gff Writes a GFF file of open reading frames
to_perfect_reads Make perfect paired reads from reference
to_random_subset Make a random sample of sequences (and optionally mates as well)
to_tiling_bam Make a BAM file of reads uniformly spread across the input reference
to_unique_by_id Remove duplicate sequences, based on their names. Keep longest seqs
translate Translate all sequences in input nucleotide sequences
trim_Ns_at_end Trims all Ns at the start/end of all sequences
trim_contigs Trims a set number of bases off the end of every contig
trim_ends Trim fixed number of bases of start and/or end of every sequence
version Print version number and exit

For developers

Here is a template for counting the sequences in a FASTA or FASTQ file:

from pyfastaq import sequences
seq_reader = sequences.file_reader(infile)
count = 0
for seq in seq_reader:
    count += 1
print(count)

Hopefully you get the idea and there are plenty of examples in tasks.py. Detection of the input file type and whether gzipped or not is automatic. See help(sequences) for the various methods already defined in the classes Fasta and Fastq.

License

Fastaq is free software, licensed under GPLv3.

Feedback/Issues

Please report any issues to the issues page or email [email protected].