find_combine_sort.sh

#!/bin/bash

# FUNCTION
## this script recursively searches a directory for fasta files matching a pattern
## found files are concatenated and sorted by descending sequence length

# INPUT
## first positional parameter is the directory to search
## second is the pattern to match in fasta filenames
## third is the output filename

# USAGE EXAMPLE
## ./find_combine_sort.sh . phage.fna sort.fna

find ${1} -name "*${2}*" | \
  xargs cat | \
  awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' | \
  awk -F '\t' '{printf("%d\t%s\n",length($2),$0);}' | \
  sort -k1,1nr | \
  cut -f 2- | \
  tr "\t" "\n" \
  > ${3}

Based on this Biostars post.