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faq [2018/12/19 10:14] flackfaq [2018/12/21 14:00] – [Can I get a Mcule database SDF file in smaller chunks?] flack
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 If you have access to a unix based system and awk you can use the below commands to split large, gzipped SDF files into smaller chunks. If you have access to a unix based system and awk you can use the below commands to split large, gzipped SDF files into smaller chunks.
  
-To split an sdf.gz file into multiple uncompressed chunks, use a command like this:+To split an sdf.gz file into multiple **uncompressed chunks**, use a command like this:
 <code> <code>
 gzip -dc your.sdf.gz | awk -v name=<chunk_name> -v ext=sdf -v size=<size> 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 > file1}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close(file1);file1=file2}}}}' gzip -dc your.sdf.gz | awk -v name=<chunk_name> -v ext=sdf -v size=<size> 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 > file1}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close(file1);file1=file2}}}}'
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 Just replace your.sdf.gz with your filename, <chunk_name> with the name of the files you want and <size> with the intended chunk size. Just replace your.sdf.gz with your filename, <chunk_name> with the name of the files you want and <size> with the intended chunk size.
  
-For example to split the Mcule Purchasable (Full) sdf.gz file into 1M uncompressed chunks use:+For example to split the Mcule Purchasable (Full) sdf.gz file into 1M **uncompressed chunks** use:
 <code> <code>
 gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf -v size=1000000 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 > file1}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close(file1);file1=file2}}}}' gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf -v size=1000000 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 > file1}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close(file1);file1=file2}}}}'
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-To split an sdf.gz file into multiple gzip compressed chunks, use a command like this:+To split an sdf.gz file into multiple **gzip compressed chunks**, use a command like this:
 <code> <code>
 gzip -dc your.sdf.gz | awk -v name=<chunk_name> -v ext=sdf.gz -v size=<size> 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 | "gzip -9 > "file1""}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close("gzip -9 > "file1"");file1=file2}}}}' gzip -dc your.sdf.gz | awk -v name=<chunk_name> -v ext=sdf.gz -v size=<size> 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 | "gzip -9 > "file1""}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close("gzip -9 > "file1"");file1=file2}}}}'
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 Just replace your.sdf.gz with your filename, <chunk_name> with the name of the files you want and <size> with the intended chunk size. Just replace your.sdf.gz with your filename, <chunk_name> with the name of the files you want and <size> with the intended chunk size.
  
-For example to split the Mcule Purchasable (Full) sdf.gz file into 1M gzip compressed chunks use:+For example to split the Mcule Purchasable (Full) sdf.gz file into 1M **gzip compressed chunks** use:
 <code> <code>
 gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf.gz -v size=1000000 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 | "gzip -9 > "file1""}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close("gzip -9 > "file1"");file1=file2}}}}' gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf.gz -v size=1000000 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 | "gzip -9 > "file1""}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close("gzip -9 > "file1"");file1=file2}}}}'
faq.txt · Last modified: 2022/06/29 14:56 by flack