Edit MSA

A collection of scripts for editing multiple sequence alignments, usually in FASTA format. Some functionality may exist for downstream processes and may not be generally useful.

For direct correspondence, feel free to contact: Samuel S. Shepard (vfn4@cdc.gov), Centers for Disease Control and Prevention

Overview

| Script | Author | Description | Notes | | ---------------------- | ------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------- | | codonCorrect.pl | S. S. Shepard | Corrects insertions (given by the TSV) and deletions to be in-frame using the MSA stats. | Deprecated. | | codonCorrectStats.pl | S. S. Shepard | Corrects insertions (given by the TSV) and deletions to be in-frame using user-supplied statistics in Perl storable format. | Used by dais-ribosome (GitHub pending). | | displayStats.pl | S. S. Shepard | Useful for displaying the codon-weight matrix used by codonCorrectStats.pl. | Uses Perl storable format. | | storeStats.pl | S. S. Shepard | Takes an MSA and produces a codon-weight matrix in Perl storable format. | Format used by codonCorrectStats.pl | | fillSequences.pl | S. S. Shepard | Re-inserts insertions from a TSV (ID / Position / Insert) back into the MSA. | | | ordinalHeaders.pl | S. S. Shepard | Changes FASTA headers to an ordinal S#. Has various options for annotating. | | | removeGapColumns.pl | S. S. Shepard | Various options for dealing with gap columns in an MSA, including K-tons. | Overwrites in-place | | reviseTaxa.pl | S. S. Shepard | Revises annotation taxa in an MSA. | A component of the LABEL MS | | shiftAlignment.pl | S. S. Shepard | Shifts alignments to the left or right at a particular region. Useful for gaps before manual editing. || | sortFASTA.pl | S. S. Shepard | Sorts the FASTA file by the header or a designatd set of fields. | | | stripSequences.pl | S. S. Shepard | Strips unwanted characters from a FASTA file. | FASTA may be unaligned after this operation. | | treeOrderedFasta.pl | S. S. Shepard | Orders the FASTA file using a provided Newick where IDs or headers match. || | diceAlignment.pl | S. S. Shepard | Chops alignment at specified region into a de-duplicated MSA for editing and downstream splicing. | Used in tandem with spliceAlignment.pl | | spliceAlignment.pl | S. S. Shepard | Takes the manually edited miniNT or miniAA file and splices it back into a full nucleotide alignment. | Used in tandem with diceAlignment.pl |

Usage

For up-to-date usages, run perl <script.pl> with no arguments. Example usage for each script:

```bash

codonCorrect.pl

Usage: perl codonCorrect.pl [options] --insertion-table|-I Insertion table for insertion corrections. --output-table|-O Output file for the insertion table.

codonCorrectStats.pl

Usage: perl codonCorrectStats.pl [options] --stats|-S Input file for storable object. Default: none --delim|-D Delimiter for header fields. --field|-F Comma-delimited set of fields to use for group. Default: no group. --insertion-table|-I Insertion table for insertion corrections. --output-table|-O Output file for the insertion table.

diceAlignment.pl

Usage: perl diceAlignment.pl <...> -P|--prefix Prefix used for output. -B|--begin Begin coordinate. -E|--end End coordinate. -R|--shift-right Shift alignment right. -T|--translate Translate data as well. -C|--sort-by-count Sort data by their cluster counts.

displayStats.pl

Usage: perl displayStats.pl [options] --verbose|V Make display verbose.

fillSequences.pl

Usage: perl fillSequences.pl [-F|--fill-triplets]

ordinalHeaders.pl

Usage: perl ordinalHeaders.pl [-A] [-H] [-N ] [-O ]

removeGapColumns.pl

Usage: perl removeGapColumns.pl [options] -D|-display-k-tons Displays sequences where for columns with 0 < bases <= K. -T|-tab-formatted Print out tab-delimited data. -S|-show-column-support Show column support.

reviseTaxa.pl

Usage: perl reviseTaxa.pl [OPTIONS] [-M ] --confirm-prediction|-C Confirm predicted annotations. --delete-prev|-D Delete previous annotations where there are two. --delete-single|-S Delete previous annotations where there is one, filters AFTER delete-prev. --find|-F Select sequences including this annotation. --replace|-R Replace the annotation with TEXT. --add-annot|-A Add annotations based on tab delimited file (ID ANNOT). --ignore-fasta-annot|-G Ignores previous annotation on FASTA headers vs. annotation file. --fuzzy-match|-Z Searches for IDs in FASTA (-A option), matching if header contains the ID. --order-mode|-O Annotation with ordinals for truncated names. --match-files|-M Output filenames containing annotation names in the input file. --previous-infix|N Suffix and prefix only apply to a 'previous' or first of a doublet annotation. --prefix|-P Prefix for matching filenames with annotations OR adds prefix to header. --suffix|-X Suffix for matching filenames with annotations OR adds suffix to header. --in-place|-I Revise files in-place (could be dangerous). --join-to-end|-J Join annotation to end of the header (similar to add but without a file). --last-field|-L Clips the last field of the header and turns it into an annotation. Uses the specified delimiter to determine fields. --append-pipe-annot|-p Appends annotation as a header field with pipe delim.

shiftAlignment.pl

Usage: perl shiftAlignment.pl <...> -B|--begin Begin coordinate. -E|--end End coordinate. -R|--shift-right Shift alignment right.

sortFASTA.pl

Usage: perl sortFASTA.pl [FASTA ...] [OPTIONS] -C|--case-sensitive Ignore case. read if no FASTA given.

spliceAlignment.pl

Usage: perl spliceAlignment.pl [options] -F|--fill-missing Fill missing data with gaps rather than excluding. -A|--amino-acid-msa Amino acid alignment. -P|--prefix Prefix used for AAtoNT file output. -S|--splice-now Output the splice without further editing of the AAtoNT file.

storeStats.pl

Usage: perl storeStats.pl [options] --output|-O Output file for storable object. Default: STDOUT --delim|-D Delimiter for header fields. Default delim is '|'. --field|-F Comma-delimited set of fields to use for group. Default: no group.

stripSequences.pl

Usage: stripSequences.pl {-N|-L|} -N|--remove-bad-bases Removes invalid nucleotide characters from the sequence. -L|--strip-lower Removes lowercase letters from the sequence. -F|--fix-header Removes and replaces troublesome characters from the FASTA header.

treeOrderedFasta.pl

Usage: treeOrderedFasta.pl [-Q|--quoted-ids] ```

If you spot a bug in the usage, please file an issue or make a PR to this repo.

Installation

1. Install Perl 5. If you are running MacOS or Linux you likely already have it. No, you don't need a container, package manager, venv, or Conda. Perl is aggressively backwards compatible and ubiquitous.
2. Clone this repo.

Notices

Copyright is public domain but attributions to the original authors are welcomed. The software license uses ASL2.

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