Mgms_Double_BLASTp.sh

#!/bin/bash
rm result1_seq.txt
rm result1_stat.txt

for mgm in $(cat MGM_ID_List.txt) # for each metagenome in the list MGM_ID_List.txt (will read each object in this txt file)
do
rm temp.txt # (rm is remove, so it will remove all of these files from the last run of the loop)
rm temp2.txt
rm test.txt
rm test2.txt

curl -o temp.txt http://api.metagenomics.anl.gov/1/download/"$mgm"?file=350.1 #curl is to transfer (down/up load) a file; -o means to write an output file from whatever we download - in this case, the mgm 350 file (refer ot MGrast manual to remember what that is)
n=$(grep ">" temp.txt | wc -l | tr -d "\t") # n = # of sequences in each mgm file; calling for n will search for the carrot in the txt file, count the words by line, and delete the tabs -- making everything one file but still separating all of the sequences and knowing how many there are per mgm
n2=$(echo -e $n $mgm) # n2 = # of sequences in each file, and the mgm ID; echo -e will "echo" this information into the text file in a new line because of the -e
### -e option is used to enable echo's interpretation of additional instances of the newline character as well as the interpretation of other special characters

tr '\n' '@' < temp.txt | sed 's/@>/\n>/g' > temp2.txt # transform each new line w/ @ from temp.txt file; then stream edit (sed) + replace every @> with \n> so that each sequence is separated with the caret --> putting back in FASTA format for the BLAST

while read seq # while read seq aka sequence from temp2.txt [ if else loops are nested in the while read loop]
    do
    echo $seq | cut -d "@" -f 1 # echo sequence, then cut based on the @ delimiter from field 1
    echo $seq | tr '@' '\n' > temp3.txt
    blastp -query temp3.txt -db COx_db1_all.txt -outfmt 6 -evalue 1e-3 -out test.txt ## using a db I already made! Must make a database first depending on what you are trying to find

if [[ -s test.txt ]] ; then # -s is if file exists and is NOT empty
blastp -query temp3.txt -db COx_SuperDB_2.txt -outfmt 6 -evalue 1e-3 -out test2.txt
    if [[ -s test2.txt ]] ; then

    cat test2.txt | sed "s/^/$n2\t$n4/g" >> result1_stat.txt
    cat temp3.txt >> result1_seq.txt
    else
    echo
    fi
else
echo
fi

    done < temp2.txt

done


#| sed '/^\s*$/d' | sed 's/@/\n/g'

# to find the file types that are downloadable from MG-RAST, go here https://help.mg-rast.org/user_manual.html
# specifically the section "The downloadable files for each data set"
# 650 file : Packaged results of the blat search against all the protein databases with MD5 value of the database sequence hit followed by sequence or cluster ID, similarity information, functional annotation, organism, database name.
# 650.superblat.expand.protein file contains the following: md5 (id for database hit), feature ID for singletons or clsuter ID for query, alignment % identity, alignment length, E-value, protien function label, and species name associated with best protein hit
## Multiple types of 650 files

## For more assistance, visit this link https://angus.readthedocs.io/en/2014/howe-mgrast.html