catfasta2phyml.pl -- Concatenate FASTA alignments to PHYML, PHYLIP, or FASTA
format
catfasta2phyml.pl [options] [files]
- -h, -?, --help
Print a brief help message and exits.
- -m, --man
Prints the manual page and exits.
- -c, --concatenate
Concatenate files even when number of taxa differ among alignments. Missing data will be filled with all gap (-) sequences.
- -i, --intersect
Concatenate sequences for sequence labels occuring in all input files (intersection).
- -f, --fasta
Print output in FASTA format (default is PHYML format).
- -p, --phylip
Print output in a strict PHYLIP format. See section "Data file format" on https://phylipweb.github.io/phylip/doc/main.html#inputfiles
Note: The current output is not entirely strict for the interleaved format. Left to do is to efficiently print sequences in blocks of 10 characters. The sequential PHYLIP format works, on the other hand (use -s in combination with -p).
- -s, --sequential
Print output in sequential format (default is interleaved).
- -b, --basename=suffix
Ensure the basename is used as partition definition. If the provided suffix (required) matches the file suffix, it will be removed from the output string.
Note: If the suffix it to be kept, one may use this format: --basename=' ' (basically providing a string that will not match the file suffix).
- -v, --verbose
Be verbose by showing some useful output. See the combination with -n.
- -n, --noprint
Do not print the concatenation, just check if all files have the same sequence lables and lengths. Program returns 1 on exit. See also the combination with -v.
-
-V, --version
Print version number and exit.
catfasta2phyml.pl will concatenate FASTA alignments to one file (interleaved PHYML or FASTA format) after checking that all sequences are aligned (of same length). If there are sequence labels that are not present in all files, a warning will be issued. Sequenced can, however, still be concatenated (and missing sequences be filled with missing data (gaps)) if the argument --concatenate is used.
In addition, only sequences with sequence labels present in all files (the intersection) can be printed using the --intersect argument.
The program prints the concatenated data to STDOUT. A table with information about partitions is printed to STDERR. Example:
file1.fas = 1-625
file2.fas = 626-1019
file3.fas = 1020-2061
file4.fas = 2062-3364
file5.fas = 3365-3796
See below for how this table can be used in other software (e.g., IQ-Tree, RAxML-ng).
To concatenate fasta files to a phyml readable format:
$ catfasta2phyml.pl file1.fas file2.fas > out.phy
$ catfasta2phyml.pl *.fas > out.phy 2> partitions.txt
$ catfasta2phyml.pl --sequential *.fas > out.phy
$ catfasta2phyml.pl --verbose *.fas > out.phy
To concatenate fasta files to fasta format:
$ catfasta2phyml.pl -f file1.fas file2.fas > out.fasta
$ catfasta2phyml.pl -f *.fas > out.fasta
To check fasta alignments:
$ catfasta2phyml.pl --noprint --verbose *.fas
$ catfasta2phyml.pl -nv *.fas
$ catfasta2phyml.pl -n *.fas
To concatenate fasta files, while filling in missing taxa:
$ catfasta2phyml.pl --concatenate --verbose *.fas
To concatenate sequences for sequence labels occuring in all files:
$ catfasta2phyml.pl --intersect *.fas
To ensure basename as name and suffix removal in partition definition:
$ catfasta2phyml.pl -b.fas dat/file1.fas dat/file2.fas > out.phy
1. "Argument list too long" error?
If we run into the issue of "Argument list too long" (where we have a command
line longer than allowed on our system (getconf ARG_MAX) - which may happen
if we try to concatenate many files), we can still do it, but in steps. For
example (here with some help of GNU
parallel):
$ catfasta2phyml.pl -c $(find . -type f -name '*.ali') > concatenated.phy 2>/dev/null
-bash: catfasta2phyml.pl: Argument list too long
Instead, start by concatenating to intermediate files using GNU parallel
$ find . -type f -name '*.ali' | \
parallel -N1000 'catfasta2phyml.pl -c -f '"{}"' > tmp.'"{#}"'.conc'
Then concatenate the intermediate files to one
$ catfasta2phyml.pl -c tmp.*.conc > concatenated.phy 2>/dev/null
$ rm tmp.*.conc
2. Prepare a RAxML-style partitions file
Catfasta2phyml does not check what data type (DNA, PROTEIN, etc) that is being
concatenated. It only checks the sequence labels and sequence lengths. When
running catfasta2phyml, a list of partition names and relative positions are
written to standard error. A partition file (for, e.g.,
IQ-Tree and
RAxML-ng does require, however, a
data type to be given in front of the partition specification. Assuming that we
are concatenating the same kind of data type, the preparation of a partitions
file is straightforward. Below is an example using sed (GNU Linux). Let us
also assume that we gave the full path to the input files (which prints the
path in the output partition table), and that the data type is "DNA":
$ catfasta2phyml.pl -c dat/*.fas > out.phy 2> partitions.txt
$ cat partitions.txt
dat/file1.fas = 1-625
dat/file2.fas = 626-1019
dat/file3.fas = 1020-2061
dat/file4.fas = 2062-3364
dat/file5.fas = 3365-3796
We can now remove the dat/ and the .fas, and add DNA, on each line:
$ sed -i -e 's#dat/##' -e 's/\.fas//' -e 's/^/DNA, /' partitions.txt
$ cat partitions.txt
DNA, file1 = 1-625
DNA, file2 = 626-1019
DNA, file3 = 1020-2061
DNA, file4 = 2062-3364
DNA, file5 = 3365-3796
3. But I want to split, not concatenate!
Facing the "opposite" situation (having a large concatenated fasta file that you want to split into individual alignments)? If you have a corresponding partitions file, you may give FastEAR a try (https://github.com/nylander/FastEAR)!
Written by Johan A. A. Nylander
Uses Perl modules Getopt::Long and Pod::Usage
Copyright (c) 2010-2024 Johan Nylander
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
https://github.com/nylander/catfasta2phyml
$ conda install -c bioconda catfasta2phyml