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| #!/bin/sh | ||
| # | ||
| # uf-valid - Validate the sequences in an unfasta stream. | ||
| # Copyright (C) 2016 Marco van Zwetselaar <[email protected]> | ||
| # | ||
| # 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/>. | ||
| # | ||
| # Created on 2016-01-25 | ||
|
|
||
| # ALPHABETS taken from http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml | ||
|
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| # Nucleic Acids | ||
| # A adenosine C cytidine G guanine | ||
| # T thymidine N A/G/C/T (any) U uridine | ||
| # K G/T (keto) S G/C (strong) Y T/C (pyrimidine) | ||
| # M A/C (amino) W A/T (weak) R G/A (purine) | ||
| # B G/T/C D G/A/T H A/C/T | ||
| # V G/C/A - gap of indeterminate length (EXCLUDED) | ||
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| DNA_ALPHABET="ACGTN" | ||
| RNA_ALPHABET="ACGUN" | ||
| NUCL_ALPHABET="ACGTNUKSYMWRBDHV" | ||
|
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| # Amino Acids | ||
| # A alanine P proline | ||
| # B aspartate/asparagine Q glutamine | ||
| # C cystine R arginine | ||
| # D aspartate S serine | ||
| # E glutamate T threonine | ||
| # F phenylalanine U* selenocysteine (EXCLUDED) | ||
| # G glycine V valine | ||
| # H histidine W tryptophan | ||
| # I isoleucine Y tyrosine | ||
| # K lysine Z glutamate/glutamine | ||
| # L leucine X any | ||
| # M methionine * translation stop (EXCLUDED) | ||
| # N asparagine - gap of indeterminate length (EXCLUDED) | ||
|
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| AMINO_ALPHABET="ABCDEFGHIKLMNPQRSTVXWYZ" | ||
|
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| # Function to exit this script with an error message on stderr | ||
| err_exit() { | ||
| echo "$(basename "$0"): $*" >&2 | ||
| exit 1 | ||
| } | ||
|
|
||
| # Function to show usage information and exit | ||
| usage_exit() { | ||
| echo | ||
| echo "Usage: $(basename $0) [OPTIONS] [FILE] ..." | ||
| echo | ||
| echo " Validate the sequences in each FILE against the allowed alphabet. If no FILE" | ||
| echo " is present or FILE is '-', read from standard input. Only valid sequences are" | ||
| echo " copied to standard output. For invalid sequences, an error message is printed" | ||
| echo " to standard error." | ||
| echo | ||
| echo " Options" | ||
| echo " -a|--allow CHARS Validate sequences against the alphabet consisting of CHARS." | ||
| echo " May be specified in addition to the synonyms listed below." | ||
| echo " -i|--ignore-case Ignore case for allowed CHARS (default for the synonyms)." | ||
| echo " -v|--headers Also validate the syntax of the headers (default no)." | ||
| echo " -s|--stop Stop processing after the first invalid sequence." | ||
| echo " -k|--keep Do not drop invalid sequences but copy them to standard out." | ||
| echo " -q|--quiet Do not copy standard input to standard output." | ||
| echo | ||
| echo " Synonyms for the usual alphabets (mutually exclusive):" | ||
| echo " --dna Equivalent to: -i -a '$DNA_ALPHABET'" | ||
| echo " --rna Equivalent to: -i -a '$RNA_ALPHABET'" | ||
| echo " --nucl Equivalent to: -i -a '$NUCL_ALPHABET'" | ||
| echo " --amino|--prot Equivalent to: -i -a '$AMINO_ALPHABET'" | ||
| echo | ||
| echo " CAVEAT: when using --allow with symbols other than characters: the current" | ||
| echo " implementation is a simple regex search for the complement of the alphabet," | ||
| echo " so symbols which are regex meta-characters like ., ?, and * need escaping." | ||
| echo | ||
| exit ${1:-1} | ||
| } | ||
|
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| # Set defaults | ||
|
|
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| ALLOW="" | ||
| IGNORE_CASE=0 | ||
| VAL_HEADERS=0 | ||
| STOP_ON_ERR=0 | ||
| KEEP_ERRORS=0 | ||
| QUIET=0 | ||
|
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| # Parse options | ||
|
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| while [ $# -ne 0 -a "$(expr "$1" : '\(.\).*')" = "-" ]; do | ||
| case $1 in | ||
| --allow=*) | ||
| ALLOW="${ALLOW}${1#"--allow="}" | ||
| ;; | ||
| -a|--allow) | ||
| shift | ||
| ALLOW="${ALLOW}$1" | ||
| ;; | ||
| --dna) | ||
| [ -z "$ALLOW" ] || err_exit "option $1 may be followed by --allow but not otherwise combined" | ||
| ALLOW="$DNA_ALPHABET" | ||
| IGNORE_CASE=1 | ||
| ;; | ||
| --rna) | ||
| [ -z "$ALLOW" ] || err_exit "option $1 may be followed by --allow but not otherwise combined" | ||
| ALLOW="$RNA_ALPHABET" | ||
| IGNORE_CASE=1 | ||
| ;; | ||
| --nucl) | ||
| [ -z "$ALLOW" ] || err_exit "option $1 may be followed by --allow but not otherwise combined" | ||
| ALLOW="$NUCL_ALPHABET" | ||
| IGNORE_CASE=1 | ||
| ;; | ||
| --amino|--prot) | ||
| [ -z "$ALLOW" ] || err_exit "option $1 may be followed by --allow but not otherwise combined" | ||
| ALLOW="$AMINO_ALPHABET" | ||
| IGNORE_CASE=1 | ||
| ;; | ||
| -i|--ignore*) | ||
| IGNORE_CASE=1 | ||
| ;; | ||
| -v|--headers) | ||
| VAL_HEADERS=1 | ||
| ;; | ||
| -s|--stop) | ||
| STOP_ON_ERR=1 | ||
| ;; | ||
| -k|--keep-errors) | ||
| KEEP_ERRORS=1 | ||
| ;; | ||
| -q|--quiet) | ||
| QUIET=1 | ||
| ;; | ||
| --help) | ||
| usage_exit 0 | ||
| ;; | ||
| *) usage_exit | ||
| ;; | ||
| esac | ||
| shift | ||
| done | ||
|
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| # Check that at least some alphabet was selected | ||
|
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| [ -n "$ALLOW" ] || err_exit "no valid alphabet specified" | ||
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| # Do the work | ||
|
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| awk -v P="$(basename "$0")" -v WRONG="[^$ALLOW]" -v H=$VAL_HEADERS -v Q=$QUIET -v K=$KEEP_ERRORS -v S=$STOP_ON_ERR -v IGNORECASE=$IGNORE_CASE ' | ||
| { ERR = 0 | ||
| if ( H && $0 !~ /^>[[:alpha:]]+\|\w+(\|\w+)*(\s+.*)?$/ ) { | ||
| print P ": invalid header at line " NR ": " $0 > "/dev/stderr" | ||
| ERR = 1 | ||
| } | ||
| HDR = $0 | ||
| getline SEQ | ||
| #POS = SEQ ~ WRONG | ||
| POS = match (SEQ, WRONG) | ||
| if ( POS ) { | ||
| print P ": invalid character in sequence at line " NR ", pos " POS ": " substr(SEQ,POS,1) > "/dev/stderr" | ||
| ERR = 1 | ||
| } | ||
| if ( (!ERR || K) && !Q ) { | ||
| print HDR | ||
| print SEQ | ||
| } | ||
| if ( ERR && S ) { | ||
| exit 1 | ||
| } | ||
| }' "$@" | ||
|
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