From 3debe31ee75ce9707686e89bc0e0c65181f6e525 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Dra=C5=A1ko=20Tomi=C4=8D?= Date: Wed, 15 Nov 2023 15:20:51 +0100 Subject: [PATCH] 15112023 update --- VelikaVini | 5 + Vini | 6 +- cosmicTools.py | 2 +- create_SLEM_named_list | 66 ++++++---- delete_SLEM_entries_with_equal_indices | 1 - download_Cosmic_data | 2 + genes/Uniprot_ID_list | 162 ++++++++++++------------- get_gene_expression_parallel.py | 2 +- get_gene_mutation.py | 2 +- get_gene_mutation_cell_line.py | 2 +- predict_mutated_genes | 4 +- wait_until_jobs_finish | 10 +- 12 files changed, 149 insertions(+), 115 deletions(-) diff --git a/VelikaVini b/VelikaVini index 55da97b7..2c572733 100755 --- a/VelikaVini +++ b/VelikaVini @@ -88,6 +88,8 @@ then else sh $vini_dir/download_Cosmic_data + + rm -f $WORKDIR/*err $WORKDIR/*out if [ $cosmic == y ] then @@ -197,8 +199,11 @@ do let i++ done < $vini_dir/ligands/ligands_list +rm -f $WORKDIR/SLEM_values +rm -f $WORKDIR/${CANCER_PATHWAY}_results/* for (( therapy_level=1; therapy_level<$((max_therapy_level+1)); therapy_level++ )) do + sed -i '/\btherapy_level\b/d' $vini_dir/globals echo "export therapy_level=${therapy_level}" >> $vini_dir/globals sh $vini_dir/malavini done diff --git a/Vini b/Vini index fd95568d..e9f53b1e 100755 --- a/Vini +++ b/Vini @@ -14,11 +14,13 @@ else > Vini.crashlog > restartfile > globals - SEVEN=7 ; TWO=2 ; TRUE=1 ; FALSE=0 ; ONES=1 ; NULL=0 + NULL=0 ; ONES=1 ; TWO=2 ; THREE=3 ; SEVEN=7 + TRUE=1 ; FALSE=0 echo "export TRUE=$TRUE" >> $vini_dir/globals echo "export FALSE=$FALSE" >> $vini_dir/globals echo "export ONES=$ONES" >> $vini_dir/globals echo "export TWO=$TWO" >> $vini_dir/globals + echo "export THREE=$THREE" >> $vini_dir/globals echo "export SEVEN=$SEVEN" >> $vini_dir/globals echo "export NULL=$NULL" >> $vini_dir/globals echo "export state=init" >> $vini_dir/globals @@ -265,6 +267,8 @@ then touch -a -m -t 200001010101 $WORKDIR/COSMIC_token #reset time creation to 01-01-2000 sh $vini_dir/renew_COSMIC_token #update COSMIC token if older than 24 hours kit="n" + echo "export kit=$kit" >> $vini_dir/globals + else echo "export cosmic=n" >> $vini_dir/globals echo "export exp=noexp" >> $vini_dir/globals diff --git a/cosmicTools.py b/cosmicTools.py index 67b3d383..84589391 100755 --- a/cosmicTools.py +++ b/cosmicTools.py @@ -7,7 +7,7 @@ from time import sleep import random -TOKEN_NUMBER = "525119157257208421313759694701535336" +TOKEN_NUMBER = "850268004265384203146370457663115076" WORKING_DIR = os.path.join(os.path.realpath('.'), 'genes') def mapUniprotIDToCosmicID_fromList(UNIPROT_LIST): diff --git a/create_SLEM_named_list b/create_SLEM_named_list index 6a196b11..2f6c2757 100755 --- a/create_SLEM_named_list +++ b/create_SLEM_named_list @@ -1,5 +1,9 @@ source $vini_dir/globals +SLEM_FILE=$WORKDIR/${CANCER_PATHWAY}_results/SLEM_values_${cell_line}_thl${therapy_level}_${exp} +> ${SLEM_FILE}_named + + while read -r line do echo -n "." @@ -17,39 +21,59 @@ do if [[ $therapy_level == 1 ]] then - drug1=`head -"$i" $vini_dir/ligands/ligands_list | tail -1` #get drug name - drug1=`echo $drug1 | awk -F',' '{print $1}'` - printf "%s%s%s%s\n" "SLEM_" $drug1 " " $SLEM >> ${SLEM_FILE}_named + dot_count=$(echo "$word" | tr -cd '.' | wc -c) + if [ ${dot_count} == $NULL ] + then + drug1=`head -"$i" $vini_dir/ligands/ligands_list | tail -1` #get drug name + drug1=`echo $drug1 | awk -F',' '{print $1}'` + printf "%s%s%s%s\n" "SLEM_" $drug1 " " $SLEM >> ${SLEM_FILE}_named + fi else if [[ $therapy_level == 2 ]] then - drug1=`head -"$i" $vini_dir/ligands/ligands_list | tail -1` #convert "i" to name - drug1=`echo $drug1 | awk -F',' '{print $1}'` - drug2=`head -"$j" $vini_dir/ligands/ligands_list | tail -1` #convert "j" to name - drug2=`echo $drug2 | awk -F',' '{print $1}'` - printf "%s%s%s%s%s%s\n" "SLEM_" $drug1 "." $drug2 " " $SLEM >> ${SLEM_FILE}_named - else - if [[ $therapy_level == 3 ]] + word=`echo $line | awk '{print $1}'` + dot_count=$(echo "$word" | tr -cd '.' | wc -c) + if [ ${dot_count} == $ONES ] then drug1=`head -"$i" $vini_dir/ligands/ligands_list | tail -1` #convert "i" to name drug1=`echo $drug1 | awk -F',' '{print $1}'` drug2=`head -"$j" $vini_dir/ligands/ligands_list | tail -1` #convert "j" to name - drug2=`echo $drug2 | awk -F',' '{print $1}'` - drug3=`head -"$k" $vini_dir/ligands/ligands_list | tail -1` #convert "k" to name - drug3=`echo $drug3 | awk -F',' '{print $1}'` - printf "%s%s%s%s%s%s%s%s\n" "SLEM_" $drug1 "." $drug2 "." $drug3 " " $SLEM >> ${SLEM_FILE}_named - else - if [[ $therapy_level == 4 ]] + drug2=`echo $drug2 | awk -F',' '{print $1}'` + printf "%s%s%s%s%s%s\n" "SLEM_" $drug1 "." $drug2 " " $SLEM >> ${SLEM_FILE}_named + #echo "brakepoint! $dot_count" ; sleep 1000 + fi + else + if [[ $therapy_level == 3 ]] + then + word=`echo $line | awk '{print $1}'` + dot_count=$(echo "$word" | tr -cd '.' | wc -c) + if [ ${dot_count} == $TWO ] then - drug1=`head -"$i" $vini_dir/ligands/ligands_list | tail -1` #convert "i" - drug1=`echo $drug1 | awk -F',' '{print $1}'` + drug1=`head -"$i" $vini_dir/ligands/ligands_list | tail -1` #convert "i" to name + drug1=`echo $drug1 | awk -F',' '{print $1}'` drug2=`head -"$j" $vini_dir/ligands/ligands_list | tail -1` #convert "j" to name drug2=`echo $drug2 | awk -F',' '{print $1}'` drug3=`head -"$k" $vini_dir/ligands/ligands_list | tail -1` #convert "k" to name drug3=`echo $drug3 | awk -F',' '{print $1}'` - drug4=`head -"$l" $vini_dir/ligands/ligands_list | tail -1` #convert "l" to name - drug4=`echo $drug4 | awk -F',' '{print $1}'` - printf "%s%s%s%s%s%s%s%s%s%s\n" "SLEM_" $drug1 "." $drug2 "." $drug3 "." $drug4 " " $SLEM >> ${SLEM_FILE}_named + printf "%s%s%s%s%s%s%s%s\n" "SLEM_" $drug1 "." $drug2 "." $drug3 " " $SLEM >> ${SLEM_FILE}_named + fi + else + if [[ $therapy_level == 4 ]] + then + word=`echo $line | awk '{print $1}'` + dot_count=$(echo "$word" | tr -cd '.' | wc -c) + if [ ${dot_count} == $THREE ] + then + drug1=`head -"$i" $vini_dir/ligands/ligands_list | tail -1` #convert "i" + drug1=`echo $drug1 | awk -F',' '{print $1}'` + drug2=`head -"$j" $vini_dir/ligands/ligands_list | tail -1` #convert "j" to name + drug2=`echo $drug2 | awk -F',' '{print $1}'` + drug3=`head -"$k" $vini_dir/ligands/ligands_list | tail -1` #convert "k" to name + drug3=`echo $drug3 | awk -F',' '{print $1}'` + drug4=`head -"$l" $vini_dir/ligands/ligands_list | tail -1` #convert "l" to name + drug4=`echo $drug4 | awk -F',' '{print $1}'` + printf "%s%s%s%s%s%s%s%s%s%s\n" "SLEM_" $drug1 "." $drug2 "." $drug3 "." $drug4 " " $SLEM >> ${SLEM_FILE}_named + fi fi fi fi diff --git a/delete_SLEM_entries_with_equal_indices b/delete_SLEM_entries_with_equal_indices index 0b9c5955..931228c7 100755 --- a/delete_SLEM_entries_with_equal_indices +++ b/delete_SLEM_entries_with_equal_indices @@ -2,7 +2,6 @@ source $vini_dir/globals SLEM_FILE=$WORKDIR/${CANCER_PATHWAY}_results/SLEM_values_${cell_line}_thl${therapy_level}_${exp} -> ${SLEM_FILE}_named > ${SLEM_FILE}_reduced while read -r line diff --git a/download_Cosmic_data b/download_Cosmic_data index fe65366d..78bb4d56 100755 --- a/download_Cosmic_data +++ b/download_Cosmic_data @@ -1,5 +1,7 @@ module purge +source $vini_dir/globals + echo -n "Activating miniconda3 environment..." source $INSTALL/miniconda3/bin/activate conda activate env310 diff --git a/genes/Uniprot_ID_list b/genes/Uniprot_ID_list index d1c40049..68ee37bb 100644 --- a/genes/Uniprot_ID_list +++ b/genes/Uniprot_ID_list @@ -1,97 +1,97 @@ -P18848 -P01116 -O00716 +Q9NQB0 +Q04206 +P04637 +P31213 +Q9Y243 P38936 +O14920 P14616 -P09211 -P04626 -P08238 -Q9GZP0 -P04049 -P37275 -Q12778 -P16234 -Q02930 -P14780 +P01112 +P19838 +Q9UJU2 +P36402 +P07288 +O43278 +Q00987 +P01127 +O15393 +P27930 +P14625 +P00750 +Q07890 P24864 +P37275 +Q92793 +P35222 +P21802 +Q68CJ9 P55211 -P10275 -P31213 -O00459 -Q07890 -P11362 -Q02750 +P01308 P11308 -P25963 -P14625 -Q9HCS4 -P35222 -Q92934 -Q9Y243 -O43278 -P46527 -Q09472 -Q07889 +P60484 +P01133 +Q8TEY5 +O15530 P49841 -P00749 +P41161 +Q9GZP0 +O00329 +O96020 +P24941 O43889 -P16220 -P31749 -P00533 -P01133 -P10398 -P09619 Q92569 -P42338 -P31751 -Q01094 -O00329 -P07900 -P41161 -P07288 -P08069 -Q04206 -Q70SY1 -Q9NRA1 -Q9UJU2 -Q8TEY5 -Q92793 -P36402 -O14920 -P06400 -Q9NQB0 -P27361 +P18848 +Q02930 +O00459 +P09619 +P10398 Q14209 -P10415 -P01308 +Q9HCS4 +P10275 +P08238 +P04626 P15056 -P05019 -P01127 -O15393 -Q96BA8 -P36507 +Q92934 P62993 +P11362 +P36507 +P10415 +P04049 +P24385 +P07900 +P08254 +P16234 +P09211 +Q96BA8 +P01116 O15111 +Q12778 +Q09472 +P42338 +P27986 +P27361 +Q02750 +Q9Y6K9 +P25963 +O00716 +P31749 +P04085 +P16220 +P00749 +P14780 +P00533 +P01135 +Q01094 Q99801 -Q00987 -P01112 -Q68CJ9 -P24941 -P08254 -P19838 -O15530 P42345 +P31751 +Q9NRA1 +Q70SY1 +P46527 +P08069 +P42336 P01111 -P60484 -P27930 -Q9Y6K9 -P01135 -P27986 P28482 -P04637 -P42336 -P00750 -P24385 -P04085 -P21802 -O96020 +Q07889 +P05019 +P06400 diff --git a/get_gene_expression_parallel.py b/get_gene_expression_parallel.py index 557d4d85..25d545cb 100755 --- a/get_gene_expression_parallel.py +++ b/get_gene_expression_parallel.py @@ -13,7 +13,7 @@ t0 = time.time() # this token has to be manually obtained from https://cancer.sanger.ac.uk/cosmic/download -TOKEN_NUMBER = "525119157257208421313759694701535336" +TOKEN_NUMBER = "850268004265384203146370457663115076" WORKING_DIR = os.path.join(os.path.realpath('.'), 'genes', 'expressions') def mapUniprotIDtoCosmicID(UNIPROT_ID): diff --git a/get_gene_mutation.py b/get_gene_mutation.py index f7acd957..97f3176f 100755 --- a/get_gene_mutation.py +++ b/get_gene_mutation.py @@ -15,7 +15,7 @@ t0 = time.time() # this token has to be manually obtained from https://cancer.sanger.ac.uk/cosmic/download -TOKEN_NUMBER = "525119157257208421313759694701535336" +TOKEN_NUMBER = "850268004265384203146370457663115076" WORKING_DIR_MUTATIONS = os.path.join(os.path.realpath('.'), 'genes', 'mutations') WORKING_DIR_SEQUENCES = os.path.join(os.path.realpath('.'), 'genes', 'sequences') diff --git a/get_gene_mutation_cell_line.py b/get_gene_mutation_cell_line.py index fa026019..022f30a8 100755 --- a/get_gene_mutation_cell_line.py +++ b/get_gene_mutation_cell_line.py @@ -10,7 +10,7 @@ t0 = time.time() # this token has to be manually obtained from https://cancer.sanger.ac.uk/cosmic/download -TOKEN_NUMBER = "525119157257208421313759694701535336" +TOKEN_NUMBER = "850268004265384203146370457663115076" WORKING_DIR_MUTATIONS = os.path.join(os.path.realpath('.'), 'genes', 'mutations') WORKING_DIR_SEQUENCES = os.path.join(os.path.realpath('.'), 'genes', 'sequences') diff --git a/predict_mutated_genes b/predict_mutated_genes index 7fc3b693..cb3f6352 100755 --- a/predict_mutated_genes +++ b/predict_mutated_genes @@ -1,7 +1,7 @@ #Using https://web.expasy.org/translate/ tool for nucleotide to aminoacids sequence translation -#partition=`cat active_partition` #Define AlphaFold parameters -cpus=`cat ${partition}_cores` + +cpus=`cat ${active_partition}_cores` outdir=$vini_dir/genes/pdb_files SEQDIR=$vini_dir/genes/sequences/ diff --git a/wait_until_jobs_finish b/wait_until_jobs_finish index 7c8e7361..cecdc3f6 100755 --- a/wait_until_jobs_finish +++ b/wait_until_jobs_finish @@ -25,8 +25,8 @@ do then echo "Error while submitting SLURM jobs (launch failed requeued held). Exiting." >> Vini.crashlog echo "" >> Vini.crashlog - requeued_job=`squeue -u eudraskot | grep Q07889 | awk '{print $1}'` - requeued_node=`squeue -u eudraskot | grep Q07889 | awk '{print $8}'` + requeued_job=`squeue -u $USER | grep Q07889 | awk '{print $1}'` + requeued_node=`squeue -u $USER | grep Q07889 | awk '{print $8}'` ${job_cancel} ${requeued_job} $job_cancel -u $USER masterpid=`cat masterpid` @@ -42,9 +42,9 @@ do echo "You will need to re-login and then start Vini again." echo "" >> Vini.crashlog $job_cancel -u $USER - old="\/exa5\/scratch\/user\/eudraskot" - new="\/ceph\/hpc\/data\/r2022r03-224-users\/eudraskot\/WORKDIR" - sed -i -e "s/$old/$new/" $vini_dir/sourceme + old=`grep WORKDIR $vini_dir/sourceme | awk -F'=' '{print $2}'` + new=`grep INSTALL $vini_dir/sourceme | awk -F'=' '{print $2}'` + sed -i -e "s|$old|$new|" "$vini_dir/sourceme" masterpid=`cat $vini_dir/masterpid` kill -9 $masterpid fi