fasta_count

#!/bin/bash

# count records in fasta files

usage="fasta_count [-s] <fasta_file_1> ... <fasta_file_n>"

silent=0
estimated=0

while getopts "se" optname
  do
    case "$optname" in
      "s")
        silent=1
        ;;
      "e")
        estimated=1
        ;;
      "h")
        echo "$usage"
        exit
        ;;
      "?")
        echo "$usage"
        exit
        ;;
    esac
  done

# shift away the options
shift $((OPTIND-1))

big_count=0
for file in "$@"
do
   if [ $estimated -eq 1 ]; then
      count=`estimated_fastx_count $file`
   else
      # count the number of lines beginning with ">"
      count=`grep -c \> $file`
      big_count=`expr $count + $big_count`
   fi
 
   if [ $silent -eq 1 ]; then
      printf "$count\n";
   else
      printf "$file\t$count\n";
   fi
done

if [ $silent -eq 0 ]; then
   printf "total\t$big_count\n"
fi