run

#!/bin/bash
function usage(){
echo -e 'run -h -s [file]
	-h help
	-s seqence_file (the same file that was used on searching genes pages:
			http://genome.crg.es/geneid.html
			http://genes.mit.edu/GENSCAN.html
			http://exon.biology.gatech.edu/GeneMark/hmmchoice.html )


	All result from sites listed above shoud be placed in the "files" folder (see "files/example").

	Result files are:
	-resut.csv: contains columns (separator is tab):
		WHICH_METHOD	+\-	WHERE_IS_START	WHERE_IS_STOP	Matching_in_other_methods

	-if some genes was found by all methods then in folder "result" you will find files generated by using blastx (nr database) on input seqence_file. 

	

	AUTHOR & OWNER: ALEKSANDER MUĆK


	Plans for the future: 
		-to add automatic method_result_file dowload from sites listed above.' 

        exit


}

while getopts "hs:" opt; do
  case $opt in
    h)
      usage 
      ;;
    s)
      seq=$OPTARG
      ;;
    \?) 
      usage	
      ;;
  esac
done

if [ $OPTIND -eq 1 ]; 
then 
	echo "Seqence_file is necessary!"
	usage
fi


rm -rf result && mkdir result
rm -rf temp && mkdir temp
mkdir temp/clear
mkdir temp/result

#Cleaning method_result_file to a readable form for python.
while read genefile;
do
    if [ $genefile == "example" ] ; then 
		:
	elif grep -iq geneid files/$genefile ; then
   		cut -f4,5,7 files/$genefile| grep .| python edit_genedit.py > temp/clear/Geneid
	elif grep -iq genscan files/$genefile; then
   		sed 's/^ \+//g' files/$genefile| grep '^[0-9]' | sed 's/ \+/\t/g' | cut -f1,3,4,5| sed 's/\.[0-9]\+//g'  > temp/clear/Genescan
	else 
   		sed 's/^ \+//g' files/$genefile| grep '^[0-9]' | sed 's/ \+/\t/g' | cut -f1,3,5,6   > temp/clear/Genmark
	fi

done < <(ls files)


python final.py $seq


#web_blast dowloaded from
#https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo 
while read resultfile;
do
	echo "Searching for match in NCBI..."
	perl web_blast blastx nr temp/result/$resultfile > result/NCBI_$resultfile.txt
	echo "DONE" 
done < <(ls temp/result)

echo "OK"