How To Install fastaq_to_mira_xml on Ubuntu 22.04

One-liner install command

For those in a hurry, here's a one-line installation command:

sudo apt-get update && sudo apt -y install fastaq

But if you are interested in the detailed steps with descriptions, the following information is for you.

What is fastaq_to_mira_xml and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Ubuntu 22.04. This guide was written specifically with a server running Ubuntu 22.04 in mind, although it should also work on older, supported versions of the operating system.

Also, make sure you are running a regular, non-root user with sudo privileges configured on your server. When you have an account available, log in as your non-root user to begin.

There are several ways to install fastaq_to_mira_xml on Ubuntu 22.04. You can use (links are clickable):

In the following sections, we will describe each method in detail. You can choose one of them or refer to the recommended one.

Install fastaq_to_mira_xml using apt-get

First, update apt database with apt-get using the following command.

sudo apt-get update

After updating apt-get database, You can install fastaq_to_mira_xml using apt by running the following command:

sudo apt -y install fastaq

Install fastaq_to_mira_xml using apt

Because fastaq_to_mira_xml is available in Ubuntu 22.04’s default repositories, it is possible to install it from these repositories using the apt packaging system.

To begin, update apt database with apt using the following command.

sudo apt update

After updating apt database, You can install fastaq_to_mira_xml using apt by running the following command:

sudo apt -y install fastaq

Install fastaq_to_mira_xml using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu 22.04. Update apt database with aptitude using the following command.

sudo aptitude update

After updating aptitude database, You can install fastaq_to_mira_xml by running the following command:

sudo aptitude -y install fastaq

How to upgrade (update) a single package fastaq_to_mira_xml using apt-get?

First, you will need to update packages index. Run update command as usual:

sudo apt-get update

Next, to upgrade only the fastaq_to_mira_xml, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install fastaq

Note that this command will not install any new packages! If you wish to install the package if it doesn't exist you may leave out --only-upgrade part.

sudo apt-get install fastaq

How To Uninstall fastaq_to_mira_xml from Ubuntu 22.04

To uninstall only the fastaq_to_mira_xml package you can execute the following command:

sudo apt-get remove fastaq

Uninstall fastaq_to_mira_xml and all its dependencies

To uninstall fastaq_to_mira_xml and its dependencies that are no longer needed by Ubuntu 22.04, you can use the command below:

sudo apt-get -y autoremove fastaq

Remove fastaq_to_mira_xml with all configurations and data

To remove fastaq_to_mira_xml configuration and data from your system you can run the following purge command:

sudo apt-get -y purge fastaq

Remove fastaq_to_mira_xml completely (configurations, data and all of its dependencies)

And lastly, you can run the next command to remove absolutely everything related to fastaq_to_mira_xml package, e.g.: configurations, data and all of its dependencies. Just use this command:

sudo apt-get -y autoremove --purge fastaq

Extra info and code examples

A collection of scripts that perform useful and common fasta/q manipulation tasks. All scripts automatically detect whether the input is a FASTA or FASTQ file. Input and output files can be gzipped. fastaq_capillary_to_pairs - Given a fasta/q file of capillary reads, makes an interleaved file of read pairs fastaq_chunker - Splits a multi fasta/q file into separate files. Splits sequences into chunks of a fixed size. fastaq_count_sequences - Counts the number of sequences in a fasta/q file fastaq_deinterleave - Deinterleaves fasta/q file, so that reads are written alternately between two output files fastaq_enumerate_names - Renames sequences in a file, calling them 1,2,3... fastaq_expand_nucleotides - Makes all combinations of sequences in input file by using all possibilities of redundant bases. e.g. ART could be AAT or AGT. fastaq_extend_gaps - Extends the length of all gaps (and trims the start/end of sequences) in a fasta/q file. fastaq_fasta_to_fastq - Given a fasta and qual file, makes a fastq file. fastaq_filter - Filters a fasta/q file by sequence length and/or by name matching a regular expression. fastaq_get_ids - Gets IDs from each sequence in a fasta or fastq file. fastaq_get_seq_flanking_gaps - Gets the sequences either side of gaps in a fasta/q file. fastaq_insert_or_delete_bases - Deletes or inserts bases at given position(s) from a fasta/q file. fastaq_interleave - Interleaves two fasta/q files, so that reads are written alternately first/second in output file. fastaq_long_read_simulate - Simulates long reads from a fasta/q file. Can optionally make insertions into the reads, like pacbio does. fastaq_make_random_contigs - Makes a multi-fasta file of random sequences, all of the same length. Each base has equal chance of being A,C,G or T fastaq_merge - Converts multi fasta/q file to single sequence file, preserving original order of sequences. fastaq_replace_bases - Replaces all occurences of one letter with another in a fasta/q file. fastaq_reverse_complement - Reverse complements all sequences in a fasta/q file fastaq_scaffolds_to_contigs - Creates a file of contigs from a file of scaffolds - i.e. breaks at every gap in the input. fastaq_search_for_seq - Searches for an exact match on a given string and its reverese complement, in every sequences of a fasta/q file. Case insensitive. Guaranteed to find all hits. fastaq_sequence_trim - Trims sequences off the start of all sequences in a pair of fasta/q files, whenever there is a perfect match. Only keeps a read pair if both reads of the pair are at least a minimum length after any trimming. fastaq_split_by_base_count - Splits a multi fasta/q file into separate files. Does not split sequences. Puts up to max_bases into each split file. The exception is that any sequence longer than max_bases is put into its own file. fastaq_strip_illumina_suffix - Strips /1 or /2 off the end of every read name in a fasta/q file. fastaq_to_fake_qual - Makes fake quality scores file from a fasta/q file. fastaq_to_fasta - Converts sequence file to FASTA format. fastaq_to_mira_xml - Creates an xml file from a fasta/q file of reads, for use with Mira assembler. fastaq_to_orfs_gff - Writes a GFF file of open reading frames from a fasta/q file fastaq_to_perfect_reads - Makes perfect paired end fastq reads from a fasta/q file, with insert sizes sampled from a normal distribution. Read orientation is innies. Output is an interleaved fastq file. fastaq_to_quasr_primers_file - Converts a fasta/q file to QUASR primers format: just the sequence on each line and its reverse complement, tab separated. fastaq_to_random_subset - Takes a random subset of reads from a fasta/q file and optionally the corresponding read from a mates file. Ouptut is interleaved if mates file given. fastaq_to_tiling_bam - Takes a fasta/q file. Makes a BAM file containing perfect (unpaired) reads tiling the whole genome. fastaq_to_unique_by_id - Removes duplicate sequences from a fasta/q file, based on their names. If the same name is found more than once, then the longest sequence is kept. Order of sequences is preserved in output. fastaq_translate - Translates all sequences in a fasta or fastq file. Output is always fasta format fastaq_trim_ends - Trims set number of bases off each sequence in a fasta/q file fastaq_trim_Ns_at_end - Trims any Ns off each sequence in a fasta/q file. Does nothing to gaps in the middle, just trims the ends A developer API is also provided by this package. There are plenty of examples in tasks.py

Conclusion

You now have a full guide on how to install fastaq_to_mira_xml using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the fastaq_to_mira_xml from Ubuntu 22.04.

See also: