partitioned 0.1.4

Determine if a series of lines is partitioned (all identical lines sequential).

The partitioned package is a simple Python script to check if a sequence of lines is partitioned (all duplicate lines are sequential).

Example of partitioned lines (where partitioned exits 0): WORLD WORLD HELLO HELLO

Note the above are not sorted, only partitioned! The partitioned tool does not detect if its input is sorted.

Example of unpartitioned lines (where partitioned exits 1): HELLO WORLD HELLO WORLD

The original motive for partitioned was for bioinformatics, specifically to determine if a .sam/.bam file was partitioned by readID, permitting a time-consuming sort by name that is usually unnecessary. An example of how it can be used for this is:

samtools view demo.bam | awk -F'\\t' '{ print \$1 }' | partitioned && echo "demo.bam is partitioned by readID" || echo "demo.bam is not partitioned by readID"

Details:

• partitioned exits 0 (success) if the file is partitioned, 1 otherwise.
• It uses a temporary SQLite3 database cache previously seen lines. This starts primarily in memory and spills to disk if necessary and is cleaned up automatically when the command terminates.
• It can also read from a file with -i (streams from stdin if unspecified).
• Pragmas can be set with --pragmas as a space-separated list.
• The number of lines read in at once is configurable with --chunk-size (default is 1 million lines).