#!/bin/sh

# Given one DNA sequence file as input,
# this shell script runs several commands.
# It BLASTs the sequence against RefSeq human, rat and mouse protein databases.
# For each gene, it prints the number of species with a BLAST match.


######## 1. Check to make sure you get one argument (sequence file)

if [ -z "$1" ]
then
    echo "
    Usage:
          $0 seq"
    exit
fi

######## 2. Check to make sure the sequence file really exists

if [ ! -r "$1" ]
then
    echo "Sequence file $1 doesn't appear to exist."
    exit 1
fi

####### 3. Place the three blast commands from step 7 of exercise 1 here

echo "BLASTing $1 against RefSeq databases...."





echo 'BLAST results are hs_blast.txt, rn_blast.txt, and mm_blast.txt.'

####### 4. Place the first three commands from step 10 of exercise 1 (listing the query sequences mapped to RefSeq proteins) here





####### 5. Place the command from step 11 of exercise 1, *AND* redirect the output to a file named mapped_genes_summary.txt





echo  'For each transcript with a BLAST hit, see mapped_genes_summary.txt for the number of species with alignable proteins.'

echo 'All Done.'