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wiki:curtain_bin_vs_txt [2018/07/27 15:55]
david [Metadata and the file extension]
wiki:curtain_bin_vs_txt [2018/07/27 16:36] (current)
david [Some other binary types]
Line 87: Line 87:
 So the file extension //does// matter-- for programs that make use of it. But the data is unchanged. So the file extension //does// matter-- for programs that make use of it. But the data is unchanged.
  
-==== old ====+==== Some other binary types ====
  
 +===== Executable =====
 +<​code>​
 +$ file /bin/ls
 +/bin/ls: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.32, BuildID[sha1]=6129e7403942b90574b8c28439d128ff5515efeb,​ stripped
 +</​code>​
  
-DELETEME+You see that the command //ls// is actually a computer program that is a binary executable. ​
  
-One way to keep track of things ​is with the file extension. .txt, .sh, .bash, .c, .gff, fasta, .py are all common file extensions that a genomics user sees on a linux computer. ​They are also //all text files//. The thing that distinguishes them, from the name, is their file extension. Incorrectly labelling a filetype by its extension leads to confusion for the user down the line.+===== Binary Alignment Map ===== 
 +<​code>​ 
 +$ file AR122.bam 
 +AR122.bam: gzip compressed data, extra field 
 +</​code>​ 
 + 
 + 
 +A genomics data file format BAM ([[https://​www.biorxiv.org/​content/​early/​2015/​05/​29/​020024|binary format based on samtools Sequence Alignment Map]]) ​is recognized as having gzip compressed data, but the command doesn'​t know the full data type. 
 + 
 +==== Text-based Genomics filetypes ==== 
 + 
 +8-) 
 + 
 +As with binary data, text data can have a more specific format. The extensions: //.txt, .sh, .bash, .c, .gff, fasta, .py// are all common file extensions that a genomics user sees on a linux computer. ​ 
 + 
 +It is up to the genomicist and the programs he or she uses to produce/​validate files with the given formats.
  
 Examples of text formats in genomics. Examples of text formats in genomics.
  
-Non-text binary files can be data or a program. Data usual has a file extension, such as .bamor .gzwhereas binary programs have no extension (in linux), but have the executable permission bit set+^ Filetype ^ description ^ extension ​^ format definition ^ 
 +| Fasta | DNA/​RNA/​Protein sequence with header | .fasta, .fa | [[http://​genetics.bwh.harvard.edu/​pph/​FASTA.html|link]] | 
 +| Fastq | DNA/​RNA/​Protein sequence with header + quality information | .fastq, .fq | [[http://​maq.sourceforge.net/​fastq.shtml|link]] | 
 +| GFF   | Gene Feature Format | .gff | [[https://​genome.ucsc.edu/​FAQ/​FAQformat.html#​format3|link]] |  
 +| BED   | Browser Extensible Data | .bed | [[https://​genome.ucsc.edu/​FAQ/​FAQformat.html#​format1|link]] | 
 +| SAM   | Sequence Alignment Map | .sam | [[http://​www.htslib.org/​doc/​sam.html|link]] |
  
  
  
wiki/curtain_bin_vs_txt.1532728537.txt.gz · Last modified: 2018/07/27 15:55 by david