seqconverter 2.1.2

Reads and writes sequence files in various formats. Performs manipulations on sequences

seqconverter: command line program for reading, writing, and manipulating sequence files

The command-line program seqconverter can read and write text files containing aligned or unaligned DNA or protein sequences. The program understands most standard and some non-standard formats (fasta, Nexus, Phylip, Clustal, tab, raw, Genbank, How). The program can perform various manipulations on the sequences.

Availability

The seqconverter source code is available on GitHub: https://github.com/agormp/seqconverter and can be installed from PyPI: https://pypi.org/project/seqconverter/

Installation

python3 -m pip install seqconverter

Highlights

• Can be used to convert between sequence file formats but also does other things
• Read and write aligned sequences in the following formats:
  • fasta
  • Nexus
  • Phylip
  • Clustal
  • tab
  • raw
• Read and write unaligned sequences in the following formats:
  • fasta
  • tab
  • raw
  • Genbank
  • How
• Writes to stdout, so output can be used in pipes or redirected to file
• Extract subsequence (specified columns) from alignment
• Extract all overlapping windows of specified size
• Extract named sequences from set of sequences
• Randomly sample from set of sequence
• Remove columns from alignment based on one of several criteria (all gaps, some gaps, more than fraction gaps, conserved, specified indices)
• Rename sequences automatically or using file with pairs of "oldname newname"
• Generate partitioned Nexus file with charset specification automatically from separate files containing identically named sequences (sequences are concatenated end to end in same order as files).
• More...
• Underlying library has been optimized for high speed and low memory consumption
• Really has too many options, but does useful stuff (and has been created based on what I needed for own projects)

Usage examples

Get help:

seqconverter -h

---

Convert aligned sequences in fasta format to nexus (Note: output is written to the terminal so you need to use redirection to store in a file):

seqconverter -I fasta -O nexus myalignment.fasta > myalignment.nexus

---

Extract columns 50-150 (inclusive, with numbering starting at 1) from alignment in Clustal format, write output in fasta format to file (using redirection):

seqconverter -I clustal -O fasta --subseq 50,150 myalignment.aln > aligment_50_150.fasta

---

Extract all sequences containing a Lysine at position 484 and a Tyrosine at position 501 from set of amino acid sequences:

seqconverter -I clustal -O fasta --filterpos 484K,501Y myalignment.aln > voc.fasta

---

Remove columns where one or more residues are gaps from alignment:

seqconverter -I fasta -O fasta --remgapcols myalignment.fasta > gapfree.fasta

---

Concatenate identically named sequences from separate input files:

seqconverter -I fasta -O fasta --paste alignm1.fasta alignm2.fasta alignm3.fasta > concat.fasta

---

Concatenate identically named sequences from separate input files, creating partitioned Nexus file with charset specification. This can be used for phylogenetic analyses in BEAST or MrBayes where different genomic regions (e.g., genes) have different substitution models. Note: sequences in each file need to have identical names (e.g. name of species) and sequences in each file needs to be already aligned.

seqconverter -I fasta -O nexus --paste --charset gene1.fasta gene2.fasta gene3.fasta > partitioned.nexus

Usage

usage: seqconverter.py [-h] [-I FORMAT] [-O FORMAT] [--nocomments] [--rename OLD,NEW]
                       [--renamenumber BASENAME] [--appendnumber] [--renameregexp "REGEXP"]
                       [--regdupfix] [--savenames FILE] [--restorenames FILE]
                       [--gbname FIELD1[,FIELD2,FIELD3,...]] [--subsample N] [--subset NAMEFILE]
                       [--remseqs NAMEFILE] [--filterpos VARIANT[,VARIANT,...]] [--filterdupseq]
                       [--filterdupname] [--subseq START,STOP] [--subseqrename] [--windows WSIZE]
                       [--degap] [--remcols INDEX LIST] [--remambigcols] [--remgapcols]
                       [--remallgapcols] [--remfracgapcols FRAC] [--remconscols] [--paste] [--overlap]
                       [--minoverlap N] [--multifile] [--charset] [--mbpartblock] [--revcomp]
                       [--translate] [--summary] [--names] [--debug]
                       SEQFILE [SEQFILE ...]

positional arguments:
  SEQFILE               One or more sequence files

optional arguments:
  -h, --help            show this help message and exit
  --debug               Print longer error messages

File formats:
  -I FORMAT             Input format: auto, fasta, nexus, phylip, clustal, genbank, tab, raw, how
                        [default: auto]
  -O FORMAT             Output format: fasta, nexus, nexusgap, phylip, clustal, tab, raw, how
                        [default: fasta]
  --nocomments          Do not include comments in output (only print seqnames)

Renaming sequences:
  --rename OLD,NEW      Rename single sequence from OLD to NEW
  --renamenumber BASENAME
                        Rename all sequences to this form: BASENAME_001, ...
  --appendnumber        Append numbering at end of existing sequence names (SeqA_001, SeqXYZ_002, ...
  --renameregexp "REGEXP"
                        Rename sequences by deleting parts of names matching regular expression in
                        REGEXP
  --regdupfix           Fix duplicate names, created by regexp, by appending numbers to duplicates
                        (seqA, seqA_2, ...)
  --savenames FILE      Save renaming information in FILE for later use
  --restorenames FILE   Restore original names using info previously saved in FILE
  --gbname FIELD1[,FIELD2,FIELD3,...]
                        For Genbank input: construct sequence names from the list of named fields, in
                        the specified order

Retrieve subset of sequences:
  --subsample N         Randomly extract N sequences from sequence set
  --subset NAMEFILE     Retrieve sequences listed in NAMEFILE
  --remseqs NAMEFILE    Discard sequences listed in NAMEFILE
  --filterpos VARIANT[,VARIANT,...]
                        Retrieve sequences containing specific residues on specific positions. Syntax
                        is: <POS><RESIDUE>, possibly in a comma-separated list. Example: 484K,501Y
  --filterdupseq        Remove duplicate sequences (keeping one of each); print names of removed
                        sequences on stderr.
  --filterdupname       Remove sequences with duplicate names (keeping one of each). If this option is
                        not set (default): stop execution on duplicate names.

Extracting or removing parts of sequences:
  --subseq START,STOP   Extract subsequence, positions START to STOP, from alignment
  --subseqrename        When extracting sub-sequences: add '_START_STOP' to seqnames
  --windows WSIZE       Extract all overlapping sequence windows of size WSIZE
  --degap               Remove all gap characters from sequences
  --remcols INDEX LIST  Remove listed columns from alignment. Columns can be indicated as comma-
                        separated list of indices, and as ranges. Example: --remcols=10,15,22-40,57
  --remambigcols        Remove columns where one or more residues are ambiguity symbols (e.g., N for
                        nucleotides)
  --remgapcols          Remove columns where one or more residues are gaps
  --remallgapcols       Remove columns that are all-gaps
  --remfracgapcols FRAC
                        Remove columns that contain > FRAC fraction gaps
  --remconscols         Remove conserved columns from alignment

Combining multiple sequence files:
  --paste               Concatenate identically named sequences from separate input files. Sequences
                        are pasted end to end in the same order as the input files. All input files
                        must contain same number of sequences, and sequences in different files must
                        have same name.(To see partitions choose nexus output, or output to multiple
                        partition files).
  --overlap             Similar to --paste, but for input alignments that overlap partly. Overlap is
                        discovered automatically and partition boundaries are then set such that each
                        partition is covered by a unique set of genes. (To see partitions choose nexus
                        output, or output to multiple partition files).
  --minoverlap N        Minimum overlap required for merging input alignments (default: set
                        automatically based on seq lengths)
  --multifile           Outputs to multiple files (one per partition) instead of stdout. Partitions
                        are generated automatically based on other options.
  --charset             Appends Nexus form charset block listing partitions in data (forces output in
                        Nexus format). Charsets and partitions are generated automatically based on
                        other options.
  --mbpartblock         Appends MrBayes block with commands for running partitioned analysis (forces
                        output in Nexus format). Charsets and partitions are generated automatically
                        based on other options.

DNA manipulations:
  --revcomp             Return reverse complement of sequence(s). Requires sequences to be DNA.
  --translate           Translate DNA into amino acid sequences (requires sequences to be DNA, in
                        frame, and length multiple of 3)

Summaries:
  --summary             Print summary of data set (names, number, lengths, composition, etc.). No
                        sequences are output.
  --names               Print names of sequences in data set.