seqconverter 2.5.1

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. The executable can be installed from PyPI: https://pypi.org/project/seqconverter/

Installation

python3 -m pip install seqconverter

Dependencies

seqconverter relies on the sequencelib library and the NumPy package, which are automatically included when using pip to install.

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
  • Stockholm (so far only read)
  • 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
• Also accepts input on stdin
• 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, columns corresponding to insert states in output from HMMer's hmmalign method)
• 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, write sequences using 70 characters per line (Note: output is written to the terminal so you need to use redirection to store in a file):

seqconverter -I fasta -O nexus --width 70 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

---

Remove those columns in input (which is in Stockholm format) that correspond to insert states from HMMer's hmmalign method (these will have "." for "gaps" and/or lowercase residue symbols):

seqconverter -I stockholm -O nexus --remhmminsertcols myalignment.sto > mainstates.nexus

---

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] [--width WIDTH] [--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] [--remhmminsertcols]
                       [--paste] [--overlap] [--minoverlap N] [--multifile] [--charset]
                       [--mbpartblock] [--revcomp] [--translate] [--num] [--len] [--com]
                       [--seqcom] [--ignoregaps] [--nam] [--div] [--sit] [--debug]
                       [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, stockholm,
                        genbank, tab, raw, how [default: auto]
  -O FORMAT             Output format: fasta, nexus, nexusgap, phylip, clustal, tab, raw,
                        how [default: fasta]
  --width WIDTH         Print sequences with WIDTH characters per line [default: 60]

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
  --remhmminsertcols    When reading Stockholm format file from HMMer's hmmalign: remove
                        columns corresponding to insert states

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:
  No sequences are printed when these options are used

  --num                 Print number of sequences
  --len                 Print summary of sequence lengths
  --com                 Print overall sequence composition
  --seqcom              Print composition for each individual sequence. Output is one
                        line per residue-type per sequence: seqname, residue-type, freq,
                        count, seqlength
  --ignoregaps          When reporting composition: do not count gap symbols
  --nam                 Print names of sequences
  --div                 (For alignments) Print nucleotide diversity (=average pairwise
                        sequence difference): mean and std
  --sit                 (For alignments) Print site summary: number of columns that are
                        variable (not conserved), number of columns that contain gaps,
                        and number of columns that contain IUPAC ambiguity symbols