Case studies

Here is a collection of mine and contributed awk scripts.

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General topic

• Awk and Jmol
  awk is using input data to write java script code to plot vectors in Jmol
• Multiple input files - first approach
  awk collects and assembles data from multiple files in memory
• Multiple input files - second approach
  awk collects data from multiple files but picks only the necessary data to save on memory
• Multiple output files
  MUST KNOW feature - covered during the workshop
• Color output with custom keywords
  use simple awk script to highlight keywords in your output

Bioinformatics oriented

• bioawk
  Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
• Fasta file format tips
  worth to know if working often with files in multi-fasta format
• Multiline fasta to single line fasta
  single cryptic-looking line that will decyphered during the workshop
• Sequence clustering with awk
  application of the multiple files approach - contribution by Martín González Buitrón
• Substitute scientific with common species names in a phylogenetic tree file
• Statistics on very large columns of values
• Manipulating and getting statistics for .vcf and .gff files

Math oriented

• Discrete histogram
  very handy discrete histogram awk code
• Gaussian smearing
  trivial task done with awk - example how to use functions
• Linear interpolation
  use linear interpolation to resample your data on different grid

Physics oriented

• Dipole moment example
  simple calculations should not be difficult to code - here is an example
• Multiple files - VASP CHGCAR difference
  an simplified example on how to read multiple files (bzip-ed) line-by-line simultaneously to save memory
• POSCAR: reorder atom types
  simple task creates programming nightmare

Primarily used as reference

• Awk and Gnuplot
  outdated problem but shows hot to send data to another program and read back the results
• Awk writes Python
  collecting your data might be so tedious to program, that you might wamt to use awk to write python instead
• Gaussian - extract geometry from output .log file
  example
• ProLiant Status check
  simple check on some values, collected and mailed
• Awk and Networking
  awk have some advance network protocol capabilities...