getAlignment.sh

#!/bin/bash

prot="type protein name between quotes"
email="type email address between quotes"
accessionNum="type accession number between quotes"
eid=TypeEIDHereNoQuotesOrSpaces 

start=$SECONDS

mv ~/outputFiles/Scripts/biopython-1.73 ~/outputFiles
mv ~/outputFiles/Scripts/mafft-linux64 ~/outputFiles
mv ~/outputFiles/Scripts/getAlignment.sh ~/outputFiles
mv ~/outputFiles/Scripts/GetFASTA.py ~/outputFiles
mv ~/outputFiles/Scripts/newBlast.py ~/outputFiles
mv ~/outputFiles/Scripts/newTranspose.py ~/outputFiles
mv ~/outputFiles/Scripts/transposer.py ~/outputFiles
mv ~/outputFiles/Scripts/refSeqGetter.py ~/outputFiles


cd ~/outputFiles/

python refSeqGetter.py $email $prot $accessionNum
python newBlast.py $prot $eid

xmlFiles="2_${prot}_20000_BLAST"

for file in $xmlFiles
do
	xmltable2csv --input "$file.xml" --output "$file.csv" --tag "Hit_accession"
done

python newTranspose.py $prot

python GetFASTA.py $email $accessionNum $prot

fastaFiles="_${prot}_20000_"

echo Starting MAFFT, this will also take some time

for file in $fastaFiles
do
	echo Creating 4${file}MAFFT.fasta file
	~/outputFiles/mafft-linux64/mafft.bat "2${file}BLAST.fasta" > "4${file}MAFFT.fasta"
	echo Finished creating 4${file}MAFFT.fasta file
done

mv ~/outputFiles/biopython-1.73 ~/outputFiles/Scripts
mv ~/outputFiles/mafft-linux64 ~/outputFiles/Scripts
mv ~/outputFiles/getAlignment.sh ~/outputFiles/Scripts
mv ~/outputFiles/GetFASTA.py ~/outputFiles/Scripts
mv ~/outputFiles/newBlast.py ~/outputFiles/Scripts
mv ~/outputFiles/newTranspose.py ~/outputFiles/Scripts
mv ~/outputFiles/refSeqGetter.py ~/outputFiles/Scripts
mv ~/outputFiles/Scripts ~/

duration=$(( SECONDS - start))
echo This process took $duration seconds