Development manual for vsearch 2.32.0, built from the dev branch: it describes changes that are not released yet. The manual for the current release is published separately.

NAME

vsearch --cut — use a restriction pattern to cut fasta sequences

SYNOPSIS

vsearch --cut fastafile --cut_pattern pattern (--fastaout | --fastaout_rev | --fastaout_discarded | --fastaout_discarded_rev) outputfile [options]

DESCRIPTION

The vsearch command --cut uses a restriction pattern to cut input fasta sequences. Input sequences are cut into fragments at each restriction site matching the pattern given with the option --cut_pattern. Restriction patterns are only searched on the forward (or normal) strand, not on the reverse strand.

Fragments on the forward strand are written to the file specified with the --fastaout file, and the reverse-complement of fragments are written to the file specified with the --fastaout_rev option. Fragments receive the name of their parent sequence. Input sequences with not match are written to the file specified with the option --fastaout_discarded, and their reverse-complement are also written to the file specified with the --fastaout_discarded_rev option.

A typical restriction pattern is “G^AATT_C”, representing the EcoRI restriction site. The nucleotide symbols represent the sequence to be matched. Lowercase or uppercase nucleotides, as well as ambiguous nucleotides (IUPAC) are accepted. See vsearch-nucleotides(7) for details. The special character ‘^’ (circumflex) indicates the cutting position on the forward strand, while ‘_’ (underscore) indicates the cutting position on the reverse strand. Forward and reverse cutting positions can be the same (for example “GG^_AA”), but exactly one cutting position on each strand must be indicated (one ‘^’ and one ‘_’).

As noted above, restriction patterns are only searched on the forward (or normal) strand, not on the reverse strand. For palindromic patterns such as EcoRI, this is not an issue. A palindromic pattern is identical to its reverse-complement (same sequence and same cutting positions), so there are no copies on the reverse strand that do not have a counterpart on the forward strand.

forward 5' A...G^AATT_C...G 3'
reverse 3' T...C_TTAA^G...C 5'

fragments: A...G, AATTC...G, but also C...G and AATTC...T

All copies are detected.

For asymetrical or non-palindromic patterns, if the pattern appears on the reverse strand, it will not be detected. For example, the pattern “GG^_C” is detected when present on the forward strand:

forward 5' A...GG^C...G 3'
reverse 3' T...CC G...C 5'

fragments: A...GG, C...G

but is not detected when present on the reverse strand:

forward 5' A...G CC...G 3'
reverse 3' T...C_GG...C 5'  <- present but not detected

To detect asymetrical or non-palindromic patterns on the reverse strand, it is necessary to run the --cut command on the reverse-complemented input sequences. See vsearch-fastx_revcomp(1) for more details.

Finally, pattern occurrences can overlap. For example, the pattern “G^_G” will be detected three times in the sequence “GGGG”.

OPTIONS

mandatory options

--cut_pattern pattern: Specify the restriction site pattern (case insensitive IUPAC characters) and cutting positions (‘^’ and ’_’). For example, “G^AATT_C”. See the PATTERN EXAMPLES section for more details.

At least one of --fastaout, --fastaout_rev, --fastaout_discarded, or --fastaout_discarded_rev must also be specified.

core options

--fastaout filename: Write the forward strand fragments to filename, in fasta format.
--fastaout_rev filename: Write the reverse strand fragments to filename, in fasta format.
--fastaout_discarded filename: Write the non-matching sequences to filename, in fasta format.
--fastaout_discarded_rev filename: Write the reverse-complemented non-matching sequences to filename, in fasta format.

secondary options

--bzip2_decompress: Specify that the input pipe is streaming data compressed using Huffman coding. See bzip2(1) for more details. This option is required when compressed data arrives on standard input through a pipe (‘-’), where the format cannot be detected without consuming the stream. It is not needed when reading from a regular file compressed with bzip2, nor when such a file is redirected to standard input: compression is then detected automatically, and a contradicting option is ignored (with a warning when the input is standard input). Pipes other than standard input, such as shell process substitutions and named FIFOs, are always read as uncompressed data; compressed data must arrive on standard input or as a named file.
--fasta_width positive integer: Set the maximal width of sequences when writing fasta files. Longer sequences are folded and written on several lines. Default width is 80 nucleotides. Set to zero (0) to suppress folding.
--gzip_decompress: Specify that the input pipe is streaming data compressed using Lempel-Ziv coding. See gzip(1) for more details. This option is required when compressed data arrives on standard input through a pipe (‘-’), where the format cannot be detected without consuming the stream. It is not needed when reading from a regular file compressed with gzip, nor when such a file is redirected to standard input: compression is then detected automatically, and a contradicting option is ignored (with a warning when the input is standard input). Pipes other than standard input, such as shell process substitutions and named FIFOs, are always read as uncompressed data; compressed data must arrive on standard input or as a named file.
--label_suffix string: Add the suffix string to sequence headers when writing fasta or fastq files. For example, with --label_suffix ";status=healthy", sequence header ‘>seq1’ becomes ‘>seq1;status=healthy’.
--lengthout: Add a sequence length annotation (;length=integer) to each sequence header when writing fasta or fastq files.
--log filename: Write messages to filename. Messages include program version, start and finish times, elapsed time, amount of memory available, maximum amount of memory consumed, number of cores and command line options, and if need be, command-specific informational messages, warnings, and errors. Messages are written in addition to the standard error, not instead of it; use --quiet to silence the standard error copy (see the --quiet entry for what it spares).
--no_progress: Suppress the gradually increasing progress indicator normally written to the standard error stderr(3).
--notrunclabels: Retain whole sequence headers in output files. By default, vsearch truncates sequence headers at first space or tabulation. This option suppresses truncation.
--quiet: Suppress messages to the standard output stdout(3) and standard error stderr(3), except for warnings and error messages.
--relabel string: Replace sequence headers with the prefix string and a ticker (1, 2, 3, etc.). For example, with --relabel "cluster:", the first sequence header becomes ‘>cluster:1’, the second sequence header becomes ‘>cluster:2’, and so on. To retain annotations, use their corresponding options (--lengthout, --eeout, and --sizeout). Use --relabel_keep to also retain old sequence identifiers.
--relabel_keep: Retain old sequence identifiers by including them at the end of the new headers, after a space.
--relabel_md5: Replace each sequence header with the MD5 digest derived from the sequence itself. The sequence is converted to upper case, and each ‘U’ is replaced with a ‘T’ before computation of the digest. The MD5 digest is a 128-bit value (16 bytes), represented using a string of 32 ASCII characters. Each pair of characters encodes an hexadecimal value, ranging from x00 to xff. See md5(3) for more details, and --relabel_sha1 for an alternative hashing algorithm. To retain annotations, use their corresponding options (--lengthout, --eeout, and --sizeout). Use --relabel_keep to also retain old sequence identifiers.
--relabel_self: Replace each sequence header with the sequence itself. To retain annotations, use their corresponding options (--lengthout, --eeout, and --sizeout). Use --relabel_keep to also retain old sequence identifiers.
--relabel_sha1: Replace each sequence header with the SHA1 digest derived from the sequence itself. The sequence is converted to upper case, and each ‘U’ is replaced with a ‘T’ before computation of the digest. The SHA1 digest is a 160-bit value (20 bytes), represented using a string of 40 ASCII characters. Each pair of characters encodes an hexadecimal value, ranging from x00 to xff. See sha1(3) for more details, and --relabel_md5 for an alternative hashing algorithm. To retain annotations, use their corresponding options (--lengthout, --eeout, and --sizeout). Use --relabel_keep to also retain old sequence identifiers.
--sample string: Add the given sample identifier string to sequence headers when writing fasta or fastq files. For instance, if string is ‘ABC’, the text ;sample=ABC will be added to the headers. string is silently truncated at the first ‘;’ or whitespace character (space, tab, newline, carriage return, vertical tab or form feed), so such characters should not be used in string. Other characters (alphabetical, numerical and punctuations) are accepted. When nothing is left after truncation — an empty string, or one starting with ‘;’ or a blank character — vsearch issues a warning and writes a bare ;sample= annotation.
--sizein: Use the abundance annotations present in sequence headers when reading fasta or fastq file. Search for the pattern [>@;]size=integer[;]. Entries without abundance annotations are silently assumed to be of size=1.
--sizeout: Add abundance annotations to sequence headers when writing fasta or fastq files. Add the pattern ;size=integer. Existing ;size= annotations are reported unchanged; entries without one receive ;size=1. For this command --sizein is not needed: abundance annotations are always parsed from the input headers.
--xee: Strip expected error (ee) annotations from sequence headers when writing fasta or fastq files. Search for the pattern [>@;]ee=float[;]. Expected error annotations are added by the synonymous options --fastq_eeout and --eeout described in vsearch-fastx_filter(1).
--xlength: Strip sequence length annotations from sequence headers when writing fasta or fastq files. Search for the pattern [>@;]length=integer[;]. Sequence length annotations are added by the --lengthout option.
--xsize: Strip abundance annotations from sequence headers when writing fasta or fastq files. Search for the pattern [>@;]size=integer[;]. Abundance annotations are added by the --sizeout option.

ignored options

--threads positive non-null integer: Command is not multithreaded, option has no effect (a warning is printed when more than one thread is requested).

EXAMPLES

Cut the sequences in query.fasta, using the restriction pattern “G^AATT_C” (--cut_pattern). Write the fragments found on the reverse strand to query_fragments.fasta, in fasta format (--fastaout_rev):

vsearch \
    --cut query.fasta \
    --cut_pattern "G^AATT_C" \
    --fastaout_rev query_fragments.fasta

PATTERN EXAMPLES

(the symbol ‘|’ is used to represent a cut on either strand)

EcoRI: use the palindromic pattern “G^AATT_C” to represent the following restriction:

5' G|AATT-C 3'
3' C-TTAA|G 5'

EcoRII: use the palindromic pattern “^CCWGG_” to represent the following restriction:

5' |CCWGG- 3'
3' -GGWCC| 5'

EcoRV: use the palindromic pattern “GAT^_ATC” to represent the following restriction:

5' GAT|ATC 3'
3' CTA|TAG 5'

Fok1: use the non-palindromic pattern “N_NNNNNNNNNNNNGGATGNNNNNNNN^N” to represent the following restriction, with a cut 9 nucleotides downstream of the motif on the forward strand, and 13 nucleotides downstream of the motif on the reverse strand:

5' -NNNNNNNNNNNNGGATGNNNNNNNN| 3'
3' |NNNNNNNNNNNNCCTACNNNNNNNN- 5'

HindIII: use the palindromic pattern “A^AGCT_T” to represent the following restriction:

5' A|AGCT-T 3'
3' T-TCGA|A 5'

NspI: use the asymetric pattern “RCATG^_Y” to represent the following restriction:

5' RCATG|Y 3'
3' YGTAC-R 5'

CITATION

Rognes T, Flouri T, Nichols B, Quince C, Mahé F. (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584 doi: 10.7717/peerj.2584

REPORTING BUGS

Submit suggestions and bug-reports at https://github.com/torognes/vsearch/issues, send a pull request on https://github.com/torognes/vsearch, or compose a friendly or curmudgeont e-mail to Torbjørn Rognes (torognes@ifi.uio.no).

AVAILABILITY

Source code and binaries are available at https://github.com/torognes/vsearch.

These manual pages are also published online at https://torognes.github.io/vsearch/.

COPYRIGHT

Contact: Torbjørn Rognes torognes@ifi.uio.no, Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316 Oslo, Norway

This software is dual-licensed and available under a choice of one of two licenses, either under the terms of the GNU General Public License version 3 or the BSD 2-Clause License.

GNU General Public License version 3

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

The BSD 2-Clause License

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

ACKNOWLEDGMENTS

We would like to thank the authors of the following projects for making their source code available:

vsearch includes code from Google’s CityHash project by Geoff Pike and Jyrki Alakuijala, providing some excellent hash functions available under a MIT license.
vsearch includes code derived from Tatusov and Lipman’s DUST program that is in the public domain.
vsearch includes public domain code written by Alexander Peslyak for the MD5 message digest algorithm.
vsearch includes public domain code written by Steve Reid and others for the SHA1 message digest algorithm.
vsearch binaries may include code from the zlib library, copyright Jean-Loup Gailly and Mark Adler.
vsearch binaries may include code from the bzip2 library, copyright Julian R. Seward.