uf-map

#!/bin/sh
#
#  uf-map - Apply an operation to all sequences in an unfasta stream.
#  Copyright (C) 2016  Marco van Zwetselaar <io@zwets.it>
#
#  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/>.
#
#  This utility is part of http://io.zwets.it/unfasta

# 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 "
Usage: $(basename $0) [OPTIONS] OPERATION [FILE ...]

  Feed every sequence in FILE to OPERATION's standard input.  When no FILE
  is  present or FILE is '-', read from standard input.  Write to standard
  output the output of OPERATION applied to each sequence, interspersed
  with every header from the input.  With option -t apply OPERATION to the
  sequence titles instead, passing the sequence data straight through.

  OPTIONS
   -t, --titles  map OPERATION over the sequence headers instead of of data
   -h, --help    this help

  Note that OPERATION is started once, not invoked separately for each line.
  It must process every line coming in on its standard input separately.

  Example
  \$ uf-map 'tr [:upper:] [:lower:]'  # convert all seqs to lower case
  \$ uf-map 'sed -re s,^.{12},,'      # drop initial 12 elements from each
" >&2
    exit ${1:-1}
}

# Parse options

unset TITLES
while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
    case $1 in
    -t|--title*) TITLES=1 ;;
    -h|--help)   usage_exit 0 ;;
    *) usage_exit ;;
    esac
    shift || usage_exit
done

# Parse arguments

[ $# -ge 1 ] || usage_exit
OPERATION="$1"
shift

# Making this work produced two nice false starts: a race and a deadlock

# FAIL 1: using pipe inside gawk
# Fails because of race: external OPERATION is buffering its output,
# so lines do not come out in the right order, not even with flush.
# gawk -bO -v OPER="sh -c '$OPERATION'" '
#    NR%2==1 { print }
#    NR%2==0 { print | OPER }
#    { fflush() }' "$@"

# FAIL 2: using a FIFO between uf-bare and uf-dress
# Fails because of deadlock: uf-bare blocks on FIFO until uf-dress consumes,
# but uf-dress is waiting for standard input before consuming from FIFO.
# FIFO="/tmp/$(basename "$0").$$" && mkfifo "$FIFO" 
# ./uf-bare -f -w "$FIFO" | ./uf-dress -r "$FIFO"

# ATTEMPT 3: using paste to merge OPERATION output and FIFO

# Set pipefail to have the errorcode of the rightmost failing filter (OPERATION)
[ -z "$BASH" ] || set +o pipefail

# Make a FIFO to hold the straight-through lines, from which paste will merge them with OPERATION output
FIFO="/tmp/$(basename "$0").$$"
mkfifo "$FIFO" 

# The pipeline splits the lines between FIFO and OPERATION, then paste merges hem
if [ -z "$TITLES" ]; then LHS="$FIFO"; RHS="-"; else LHS="-"; RHS="$FIFO"; fi

gawk -bO -v FIFO="$FIFO" -v ONE="${TITLES:-0}" '
        (NR+ONE)%2==1 { print > FIFO }; 
        (NR+ONE)%2==0' "$@" \
    | $OPERATION \
    | paste -d '\n' "$LHS" "$RHS"

# Hold on to RETVAL as rm will reset exit status
RETVAL=$?
rm -f $FIFO

exit $RETVAL

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