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doc/build/_man/man1/obigrep.man
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.\" Automatically generated by Pandoc 2.19.2
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.TH "obigrep" "1" "" "" ""
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.hy
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.SH NAME
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.PP
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obigrep \[en] filters sequence files according to numerous conditions
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.SH SYNOPSIS
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.PP
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\f[B]obigrep\f[R] [\f[B]--attribute\f[R] | \f[B]-a\f[R]
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\f[I]KEY=VALUE\f[R]]\&...
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[\f[B]--compress\f[R] | \f[B]-Z\f[R]] [\f[B]--debug\f[R]]
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[\f[B]--definition\f[R]|\f[B]-D\f[R] \f[I]PATTERN\f[R]]\&...
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.PD 0
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.P
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.PD
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[\f[B]--ecopcr\f[R]] [\f[B]--embl\f[R]] [\f[B]--fasta-output\f[R]]
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[\f[B]--fastq-output\f[R]] [\f[B]--genbank\f[R]]
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[\f[B]--has-attribute\f[R] | \f[B]-A\f[R] \f[I]KEY\f[R]]\&...
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[\f[B]--help\f[R] | \f[B]-h\f[R] | \f[B]-?\f[R]] [\f[B]--id-list\f[R]
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\f[I]FILENAME\f[R]] [\f[B]--identifier\f[R] | \f[B]-I\f[R]
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\f[I]PATTERN\f[R]]\&...
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[\f[B]--ignore-taxon\f[R] | \f[B]-i\f[R] \f[I]TAXID\f[R]]\&...
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[\f[B]--input-OBI-header\f[R]] [\f[B]--input-json-header\f[R]]
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[\f[B]--inverse-match\f[R] | \f[B]-v\f[R]]
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[\f[B]--max-count\f[R]|\f[B]-C\f[R] \f[I]COUNT\f[R]]
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[\f[B]--max-cpu\f[R] \f[I]INT\f[R]] [\f[B]--max-length\f[R] |
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\f[B]-L\f[R] \f[I]LENGTH\f[R]] [\f[B]--min-count\f[R] | \f[B]-c\f[R]
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\f[I]COUNT\f[R]] [\f[B]--min-length\f[R] | \f[B]-l\f[R]
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\f[I]LENGTH\f[R]] [\f[B]--no-order\f[R]] [\f[B]--no-progressbar\f[R]]
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[\f[B]--out\f[R] | \f[B]-o\f[R] \f[I]FILENAME\f[R]]
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[\f[B]--output-OBI-header\f[R] | \f[B]-O\f[R]]
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[\f[B]--output-json-header\f[R]] [\f[B]--paired-mode\f[R]
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\f[I]forward|reverse|and|or|andnot|xor\f[R]] [\f[B]--paired-with\f[R]
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\f[I]FILENAME\f[R]] [\f[B]--predicate\f[R]|\f[B]-p\f[R]
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\f[I]EXPRESSION\f[R]]\&...
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[\f[B]--require-rank\f[R] \f[I]RANK_NAME\f[R]]\&...
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[\f[B]--restrict-to-taxon\f[R] | \f[B]-r\f[R] \f[I]TAXID\f[R]]\&...
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[\f[B]--save-discarded\f[R] \f[I]FILENAME\f[R]]
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[\f[B]--sequence\f[R]|\f[B]-s\f[R] \f[I]PATTERN\f[R]]\&...
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[\f[B]--solexa\f[R]] [\f[B]--taxdump\f[R] | \f[B]-t\f[R]
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\f[I]DIRECTORY\f[R]] [\f[B]--workers\f[R] | \f[B]-w\f[R] \f[I]INT\f[R]]
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[\f[I]FILENAMES\f[R]]
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.SH DESCRIPTION
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.PP
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The \f[V]obigrep\f[R] command is somewhat analogous to the standard Unix
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\f[V]grep\f[R] command.
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It selects a subset of sequence records from a sequence file.
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A sequence record is a complex object consisting of an identifier, a set
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of attributes (a key, defined by its name, associated with a value), a
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definition, and the sequence itself.
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Instead of working text line by text line like the standard Unix tool,
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\f[V]obigrep\f[R] selection is done sequence record by sequence record.
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A large number of options allow you to refine the selection on any
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element of the sequence.
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\f[V]obigrep\f[R] allows you to specify multiple conditions
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simultaneously (which take on the value \f[V]TRUE\f[R] or
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\f[V]FALSE\f[R]) and only those sequence records which meet all
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conditions (all conditions are \f[V]TRUE\f[R]) are selected.
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\f[V]obigrep\f[R] is able to work on two paired read files.
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The selection criteria apply to one or the other of the readings in each
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pair depending on the mode chosen (\f[B]--paired-mode\f[R] option).
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In all cases the selection is applied in the same way to both files,
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thus maintaining their consistency.
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.SH OPTIONS
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.SS General options
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.PP
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\f[B]Helpful options\f[R]
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.TP
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\f[B]--help\f[R], \f[B]-h\f[R]
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Display a friendly help message.
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.PP
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\f[B]--no-progressbar\f[R]
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.PP
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\f[B]Managing parallel execution\f[R]
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.TP
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\f[B]--max-cpu\f[R]
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OBITools V4 are able to run in parallel on all the CPU cores available
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on the computer.
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It is sometime required to limit the computation to a smaller number of
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cores.
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That option specify the maximum number of cores that the OBITools
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command can use.
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This behaviour can also be set up using the \f[V]OBIMAXCPU\f[R]
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environment variable.
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.PP
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\f[B]--workers\f[R], \f[B]-w\f[R]
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.PP
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\f[B]OBITools debuging related options\f[R]
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.PP
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\f[B]--debug\f[R]
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.SS Input format options
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.PP
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The OBITools are centered around the [FASTA]
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(https://en.wikipedia.org/wiki/FASTA_format) and [FASTQ]
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(https://en.wikipedia.org/wiki/FASTQ_format) formats.
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These formats are automaticaly recognized when data are read both from
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files, and from standard input (\f[V]stdin\f[R]).
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Other formats (genbank, EMBL, ecopcr) are also automatically identified
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when data are read from files, but for stdin input, input format must be
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indicated using one of the following options.
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.SS Output format options
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.PP
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\f[B]--fasta-output\f[R]
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.PP
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\f[B]--fastq-output\f[R]
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.PP
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\f[B]--output-OBI-header\f[R], \f[B]-O\f[R]
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.PP
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\f[B]--output-json-header\f[R]
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.TP
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\f[B]--out\f[R] \f[I]FILENAME\f[R], \f[B]-o\f[R]
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OBITools, as all standard UNIX tools, print their results to the
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standard output (\f[V]stdout\f[R]).
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To save them, stdout must be redirected to a file.
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That option allows to specify explicitely an output file to the command.
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This is especially useful when OBITools are processing paired files.
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In that later case, the indicated output file names is modified by
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adding to it the \f[I]_R1\f[R] (forward file) and \f[I]_R2\f[R] (reverse
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file) suffix just before the extensions (\f[I]e.g.\f[R] sequence.fasta
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becomes sequence_R1.fasta and sequence_R2.fasta).
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If that option is not specified and paired files are processed only the
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forward data are ouputed to the \f[I]stdout\f[R].
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.TP
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\f[B]--compress\f[R], \f[B]-Z\f[R]
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The ouput is compressed following the
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gzip (https://en.wikipedia.org/wiki/Gzip) format.
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.SS Paired reads options
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.PP
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\f[B]--paired-with\f[R] \f[I]FILENAME\f[R]
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.PP
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\f[B]--paired-mode\f[R] \f[I]forward|reverse|and|or|andnot|xor\f[R]
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.SS Taxonomy related options
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.PP
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\f[B]--taxdump\f[R] | \f[B]-t\f[R] \f[I]DIRECTORY\f[R]
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.PP
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\f[B]--ignore-taxon\f[R] | \f[B]-i\f[R] \f[I]TAXID\f[R]
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.PP
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\f[B]--require-rank\f[R] \f[I]RANK_NAME\f[R]
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.PP
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\f[B]--restrict-to-taxon\f[R] | \f[B]-r\f[R] \f[I]TAXID\f[R]
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.SS Filtering options
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.PP
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\f[B]--has-attribute\f[R] | \f[B]-A\f[R] \f[I]KEY\f[R]\&...
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.PP
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\f[B]--id-list\f[R] \f[I]FILENAME\f[R]
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.PP
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\f[B]--identifier\f[R] | \f[B]-I\f[R] \f[I]PATTERN\f[R]
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.TP
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\f[B]--max-count\f[R] | \f[B]-C\f[R] \f[I]COUNT\f[R]
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only sequences reprensenting no more than \f[I]COUNT\f[R] reads will be
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selected.
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That option rely on the \f[V]count\f[R] attribute.
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If the \f[V]count\f[R] attribute is not defined for a sequence record,
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it is assumed equal to 1.
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.TP
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\f[B]--min-count\f[R] | \f[B]-c\f[R] \f[I]COUNT\f[R]
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only sequences reprensenting at least \f[I]COUNT\f[R] reads will be
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selected.
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That option rely on the \f[V]count\f[R] attribute.
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If the \f[V]count\f[R] attribute is not defined for a sequence record,
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it is assumed equal to 1.
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.PP
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\f[B]--max-length\f[R] | \f[B]-L\f[R] \f[I]LENGTH\f[R]
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.PP
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\f[B]--min-length\f[R] | \f[B]-l\f[R] \f[I]LENGTH\f[R]
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.PP
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\f[B]--predicate\f[R]|\f[B]-p\f[R] \f[I]EXPRESSION\f[R]
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.PP
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\f[B]--sequence\f[R]|\f[B]-s\f[R] \f[I]PATTERN\f[R]
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.PP
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\f[B]--inverse-match\f[R] | \f[B]-v\f[R]
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.PP
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\f[B]--save-discarded\f[R] \f[I]FILENAME\f[R]
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.SH ENVIRONMENT
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.PP
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\f[B]OBICPUMAX\f[R]
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.SH EXAMPLES
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.IP \[bu] 2
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Filtering sequence file to keep only barcodes between 8 and 130 bp.
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.RS 2
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.IP
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.nf
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\f[C]
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obigrep -l 8 -L 130 data_SPER01.fasta > data_goodLength_SPER01.fasta
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\f[R]
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.fi
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.RE
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.IP \[bu] 2
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Filtering reads without anbiguity base code in its sequence.
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.RS 2
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.IP
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.nf
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\f[C]
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obigrep -s \[aq]\[ha][acgt]+$\[aq] data_SPER01.fasta > data_onlyACGT_SPER01.fasta
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\f[R]
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.fi
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.RE
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.IP \[bu] 2
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Filtering paired files for keeping only pairs of read without ambiguity.
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.RS 2
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.IP
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.nf
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\f[C]
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obigrep -s \[aq]\[ha][acgt]+$\[aq] \[rs]
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--paired-mode and --paired-with wolf_R.fastq.gz \[rs]
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--out wolf_good.fastq \[rs]
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wolf_F.fastq.gz
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\f[R]
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.fi
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.PP
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That command produces two files \f[V]wolf_good_R1.fastq\f[R] and
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\f[V]wolf_good_R1.fastq\f[R] containing respectively the filtered
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forward and reverse reads.
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.RE
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.SH SEE ALSO
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.PP
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\f[V]obiannotate\f[R]
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.SH HISTORY
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.SH BUGS
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.PP
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Submit bug reports online at:
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https://git.metabarcoding.org/obitools/obitools4/obitools4/-/issues
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.SH AUTHORS
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Eric Coissac <eric.coissac@metabarcoding.org>.
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