9/6/12&

1&

2012&(&BMMB&597D:&Analyzing&Next&Genera=on&Sequencing&Data&

&&Week&2,&Lecture&4 &

István'Albert''

Biochemistry&and&Molecular&Biology&&and&Bioinforma=cs&Consul=ng&Center&

&Penn&State&

Shell&scripts&

Collect&mul=ple&commands&into&a&single&program&

•  Run&the&same&commands&again&or&on&other&data&

•  Document&the&steps&and&describe&the&thought&process&

&

Crea=ng&and&refining&a&shell&script& Add&another&step &

9/6/12&

2&

Using&Shell&Variables& Single&and&double&quoted&strings&

Essen=al&detail&

•  Remember&that&you&may&be&using&dis=nct&languages&–&shell,&awk,&perl,&python&variables&may&look&the&same&but&are&interpreted&differently!&&

•  Avoid&mixing&the&context&(& i.e.&awk&program&modified&via&&bash&variables.&&Instead&write&the&awk&program&separately&and&pass&the&variables&into&it.&

Error&management&

9/6/12&

3&

Strict&error&checking& Looping&over&mul=ple&files&

Bash&has&lots&of&features&

We&will&slowly&introduce&some&features&along&the&way&

Entrez&Programming&U=li=es:&EU=ls&

•  Query&and&download&Entrez&(Genbank&and&other&databases)&via&URLS&

•  Combined&with&UNIX&tools&allow&you&to&automa=cally&download&data&&&

•  Named&as&efetch,&esearch,& &etc. &

9/6/12&

4&

Download&via&Eu=ls& Refine&our&script&

Valid&databases& Valid&return&types&and&modes&

9/6/12&

5&

Adding&more&interac=vity& Always&inves=gate&files&

XML&markup&

XML&is&a&file&markup&format&but&it&is&not&a&data&format.&

Advanced&topic:&XSLT&transforma=ons&

•  An&XML&document&can&be&transformed&by&rules&described&in&another&XML&document&&

•  XSL&Transforma=ons&

•  You&don’t&need&to&know&these,&but&are&very&handy&if&someone&can&make&one&for&you&

•  Programmers&love&to&make&these&post&it&on&&h1p:/www.stackoverflow.com'

9/6/12&

6&

Example&XSLT& Homework&4&

•  Create&a&shell&script&that&can&download&three&proteins&of&interest&to&you&from&the&protein&database.&

•  Write&a&shell&script&that&lists&the&journal&papers&that&GeneBank&references&for&your&data&