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8-2.evaluating_NOVOPlasty_animal_mitogenomes.sh
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8-2.evaluating_NOVOPlasty_animal_mitogenomes.sh
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mkdir NOVOPlasty-animal-mitogenome-eval
# NOVOPlasty is poorly designed to generate different sequences with identical names
echo "import sys; context = open(sys.argv[1]).readlines(); open(sys.argv[1], 'w').writelines([l.strip() + '__' + str(go) + '\n' if l.startswith('>') else l for go, l in enumerate(context)]) " > standardize_fas_names.py
# generate label tabel, cat all generated output
cat NOVOPlasty-animal-mitogenome/K39/SRR5620467-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR5620467-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR5620467-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR5620467-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR5620467-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR5620467 ; rm NOVOPlasty-animal-mitogenome/K39/SRR5620467-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/ERR1856354-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/ERR1856354-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/ERR1856354-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/ERR1856354-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/ERR1856354-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base ERR1856354 ; rm NOVOPlasty-animal-mitogenome/K39/ERR1856354-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR5056303-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR5056303-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR5056303-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR5056303-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR5056303-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR5056303 ; rm NOVOPlasty-animal-mitogenome/K39/SRR5056303-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR3879971-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR3879971-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR3879971-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR3879971-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR3879971-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR3879971 ; rm NOVOPlasty-animal-mitogenome/K39/SRR3879971-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR2179962-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR2179962-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR2179962-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR2179962-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR2179962-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR2179962 ; rm NOVOPlasty-animal-mitogenome/K39/SRR2179962-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR1041081-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR1041081-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR1041081-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR1041081-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR1041081-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR1041081 ; rm NOVOPlasty-animal-mitogenome/K39/SRR1041081-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR1581065-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR1581065-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR1581065-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR1581065-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR1581065-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR1581065 ; rm NOVOPlasty-animal-mitogenome/K39/SRR1581065-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR5769010-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR5769010-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR5769010-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR5769010-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR5769010-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR5769010 ; rm NOVOPlasty-animal-mitogenome/K39/SRR5769010-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/.DS_Store-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/.DS_Store-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/.DS_Store-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/.DS_Store-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/.DS_Store-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base .DS_Store ; rm NOVOPlasty-animal-mitogenome/K39/.DS_Store-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR4340274-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR4340274-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR4340274-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR4340274-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR4340274-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR4340274 ; rm NOVOPlasty-animal-mitogenome/K39/SRR4340274-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR1743021-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR1743021-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR1743021-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR1743021-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR1743021-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR1743021 ; rm NOVOPlasty-animal-mitogenome/K39/SRR1743021-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR4782254-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR4782254-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR4782254-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR4782254-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR4782254-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR4782254 ; rm NOVOPlasty-animal-mitogenome/K39/SRR4782254-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR5132384-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR5132384-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR5132384-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR5132384-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR5132384-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR5132384 ; rm NOVOPlasty-animal-mitogenome/K39/SRR5132384-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR611174-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR611174-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR611174-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR611174-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR611174-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR611174 ; rm NOVOPlasty-animal-mitogenome/K39/SRR611174-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR2132981-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR2132981-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR2132981-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR2132981-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR2132981-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR2132981 ; rm NOVOPlasty-animal-mitogenome/K39/SRR2132981-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR5201683-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR5201683-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR5201683-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR5201683-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR5201683-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR5201683 ; rm NOVOPlasty-animal-mitogenome/K39/SRR5201683-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR305235-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR305235-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR305235-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR305235-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR305235-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR305235 ; rm NOVOPlasty-animal-mitogenome/K39/SRR305235-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR1950515-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR1950515-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR1950515-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR1950515-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR1950515-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR1950515 ; rm NOVOPlasty-animal-mitogenome/K39/SRR1950515-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR2318706-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR2318706-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR2318706-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR2318706-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR2318706-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR2318706 ; rm NOVOPlasty-animal-mitogenome/K39/SRR2318706-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR941879-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR941879-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR941879-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR941879-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR941879-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR941879 ; rm NOVOPlasty-animal-mitogenome/K39/SRR941879-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR2730309-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR2730309-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR2730309-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR2730309-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR2730309-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR2730309 ; rm NOVOPlasty-animal-mitogenome/K39/SRR2730309-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR3953043-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR3953043-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR3953043-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR3953043-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR3953043-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR3953043 ; rm NOVOPlasty-animal-mitogenome/K39/SRR3953043-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR955308-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR955308-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR955308-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR955308-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR955308-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR955308 ; rm NOVOPlasty-animal-mitogenome/K39/SRR955308-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR5875655-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR5875655-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR5875655-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR5875655-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR5875655-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR5875655 ; rm NOVOPlasty-animal-mitogenome/K39/SRR5875655-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR5878339-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR5878339-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR5878339-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR5878339-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR5878339-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR5878339 ; rm NOVOPlasty-animal-mitogenome/K39/SRR5878339-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR4095109-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR4095109-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR4095109-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR4095109-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR4095109-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR4095109 ; rm NOVOPlasty-animal-mitogenome/K39/SRR4095109-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR847379-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR847379-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR847379-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR847379-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR847379-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR847379 ; rm NOVOPlasty-animal-mitogenome/K39/SRR847379-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR329682-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR329682-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR329682-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR329682-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR329682-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR329682 ; rm NOVOPlasty-animal-mitogenome/K39/SRR329682-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR1284940-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR1284940-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR1284940-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR1284940-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR1284940-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR1284940 ; rm NOVOPlasty-animal-mitogenome/K39/SRR1284940-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/DRR014695-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/DRR014695-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/DRR014695-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/DRR014695-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/DRR014695-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base DRR014695 ; rm NOVOPlasty-animal-mitogenome/K39/DRR014695-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR5527082-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR5527082-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR5527082-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR5527082-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR5527082-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR5527082 ; rm NOVOPlasty-animal-mitogenome/K39/SRR5527082-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/ERR1952738-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/ERR1952738-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/ERR1952738-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/ERR1952738-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/ERR1952738-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base ERR1952738 ; rm NOVOPlasty-animal-mitogenome/K39/ERR1952738-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR2737540-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR2737540-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR2737540-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR2737540-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR2737540-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR2737540 ; rm NOVOPlasty-animal-mitogenome/K39/SRR2737540-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR940268-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR940268-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR940268-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR940268-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR940268-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR940268 ; rm NOVOPlasty-animal-mitogenome/K39/SRR940268-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR5860573-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR5860573-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR5860573-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR5860573-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR5860573-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR5860573 ; rm NOVOPlasty-animal-mitogenome/K39/SRR5860573-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR3041429-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR3041429-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR3041429-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR3041429-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR3041429-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR3041429 ; rm NOVOPlasty-animal-mitogenome/K39/SRR3041429-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR4339879-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR4339879-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR4339879-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR4339879-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR4339879-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR4339879 ; rm NOVOPlasty-animal-mitogenome/K39/SRR4339879-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR836315-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR836315-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR836315-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR836315-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR836315-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR836315 ; rm NOVOPlasty-animal-mitogenome/K39/SRR836315-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR2717571-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR2717571-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR2717571-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR2717571-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR2717571-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR2717571 ; rm NOVOPlasty-animal-mitogenome/K39/SRR2717571-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR5863004-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR5863004-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR5863004-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR5863004-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR5863004-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR5863004 ; rm NOVOPlasty-animal-mitogenome/K39/SRR5863004-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR3098386-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR3098386-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR3098386-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR3098386-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR3098386-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR3098386 ; rm NOVOPlasty-animal-mitogenome/K39/SRR3098386-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR039541-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR039541-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR039541-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR039541-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR039541-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR039541 ; rm NOVOPlasty-animal-mitogenome/K39/SRR039541-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/DRR095708-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/DRR095708-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/DRR095708-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/DRR095708-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/DRR095708-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base DRR095708 ; rm NOVOPlasty-animal-mitogenome/K39/DRR095708-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR1946581-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR1946581-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR1946581-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR1946581-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR1946581-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR1946581 ; rm NOVOPlasty-animal-mitogenome/K39/SRR1946581-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR136494-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR136494-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR136494-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR136494-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR136494-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR136494 ; rm NOVOPlasty-animal-mitogenome/K39/SRR136494-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR1298377-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR1298377-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR1298377-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR1298377-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR1298377-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR1298377 ; rm NOVOPlasty-animal-mitogenome/K39/SRR1298377-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR1566160-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR1566160-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR1566160-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR1566160-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR1566160-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR1566160 ; rm NOVOPlasty-animal-mitogenome/K39/SRR1566160-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/ERR466754-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/ERR466754-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/ERR466754-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/ERR466754-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/ERR466754-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base ERR466754 ; rm NOVOPlasty-animal-mitogenome/K39/ERR466754-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR1200276-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR1200276-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR1200276-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR1200276-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR1200276-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR1200276 ; rm NOVOPlasty-animal-mitogenome/K39/SRR1200276-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR1300141-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR1300141-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR1300141-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR1300141-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR1300141-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR1300141 ; rm NOVOPlasty-animal-mitogenome/K39/SRR1300141-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR748049-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR748049-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR748049-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR748049-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR748049-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR748049 ; rm NOVOPlasty-animal-mitogenome/K39/SRR748049-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR5495100-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR5495100-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR5495100-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR5495100-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR5495100-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR5495100 ; rm NOVOPlasty-animal-mitogenome/K39/SRR5495100-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR1657027-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR1657027-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR1657027-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR1657027-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR1657027-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR1657027 ; rm NOVOPlasty-animal-mitogenome/K39/SRR1657027-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR1055280-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR1055280-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR1055280-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR1055280-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR1055280-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR1055280 ; rm NOVOPlasty-animal-mitogenome/K39/SRR1055280-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR1822107-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR1822107-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR1822107-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR1822107-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR1822107-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR1822107 ; rm NOVOPlasty-animal-mitogenome/K39/SRR1822107-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR747928-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR747928-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR747928-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR747928-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR747928-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR747928 ; rm NOVOPlasty-animal-mitogenome/K39/SRR747928-animal-mitogenome/temp.fa ; fi;
cat NOVOPlasty-animal-mitogenome/K39/SRR620242-animal-mitogenome/*fasta > NOVOPlasty-animal-mitogenome/K39/SRR620242-animal-mitogenome/temp.fa ; if [ -n "`ls NOVOPlasty-animal-mitogenome/K39/SRR620242-animal-mitogenome/temp.fa`" ]; then python standardize_fas_names.py NOVOPlasty-animal-mitogenome/K39/SRR620242-animal-mitogenome/temp.fa ; slim_fastg.py -F animal_mt `ls NOVOPlasty-animal-mitogenome/K39/SRR620242-animal-mitogenome/temp.fa | head -n1` --out-dir NOVOPlasty-animal-mitogenome-eval --out-base SRR620242 ; rm NOVOPlasty-animal-mitogenome/K39/SRR620242-animal-mitogenome/temp.fa ; fi;
# only keep the label files
rm NOVOPlasty-animal-mitogenome-eval/*.fa
rm standardize_fas_names.py
# summary
python << END
import os
samples = [x for x in os.listdir("NOVOPlasty-animal-mitogenome-eval") if x.endswith(".csv")]
with open("NOVOPlasty-animal-mitogenome-eval/summary.tab", "w") as output_h:
for s in samples:
with open(os.path.join("NOVOPlasty-animal-mitogenome-eval", s)) as input_h:
head = input_h.readline()
genes = []
for line in input_h:
if line.strip():
genes.extend(line.split("\t")[2].split(","))
genes = sorted(set(genes))
output_h.write(s.replace(".csv", "") + "\t" + str(len(genes)) + "\t" + ",".join(genes) + "\n")
END