anvi-script-reformat-fasta

Reformat FASTA file (remove contigs based on length, or based on a given list of deflines, and/or generate an output with simpler names).

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Authors

Can consume

fasta

Can provide

contigs-fasta

Usage

This program converts a fasta file to a contigs-fasta. In other words, it reformats your FASTA formatted file to meet the conditions required of a contigs-fasta, which is able to be used by other anvi’o programs.

anvi-script-reformat-fasta fasta \ -o contigs-fasta \ --simplify-names

If you use the flag --report-file, it will also create a TAB-delimited file for you to keep track of which defline in the new file corresponds to which defline in the original file.

In addition to simplifying names, this program will allow you to do a combination of the operations that include,

  • Add a prefix to sequnce names in a FASTA file,
  • Remove sequences that are shorter than a specific length or only keep sequences that match to a specific length,
  • Remove sequences if they contain more than a number of gap characters or exceed the precentage of gap characters you permit,
  • Exclude sequences that match to a list of sequence IDs, or only keep those that match to a list of sequence IDs,
  • Enforce a sequence type to replace any character with N for nucleotide sequences that are not A, C, T, or G, or replace any character with X for amino acid sequences if the character does not match any of the single-letter amino acid characters.

Removing the short reads is important

If your FASTA file includes a lot of very short contigs, removing them may dramatically improve the performance of the generation and processing of your contigs-db. The example below runs the same command while also removing sequences that are shorter than 1,000 nts:

anvi-script-reformat-fasta fasta \ -o contigs-fasta \ -l 1000 \ --simplify-names

Example output

anvi-script-reformat-fasta contigs.fa \
                           --simplify-names \
                           --prefix YYY \
                           --min-len 1000 \
                           --seq-type NT \
                           --overwrite-input
Input ........................................: contigs.fa
Output .......................................: (anvi'o will overwrite your input file)

WHAT WAS THERE
===============================================
Total num contigs ............................: 4,189
Total num nucleotides ........................: 35,766,167

WHAT WAS ASKED
===============================================
Simplify deflines? ...........................: Yes
Add prefix to sequence names? ................: Yes, add 'YYY'
Minimum length of contigs to keep ............: 1,000
Max % gaps allowed ...........................: 100.00%
Max num gaps allowed .........................: 1,000,000
Exclude specific sequences? ..................: No
Keep specific sequences? .....................: No
Enforce sequence type? .......................: Yes, enforce 'NT'

WHAT HAPPENED
===============================================
Contigs removed ..............................: 3,156 (75.34% of all)
Nucleotides removed ..........................: 6,121,239 (17.11% of all)
Nucleotides modified .........................: 161 (0.00045% of all)
Deflines simplified ..........................: True


* The contents of your input file have changed because you used the flag
`--overwrite-input`.

Please use the flag --overwrite-input with extreme caution.

Edit this file to update this information.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.