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Elegantly converting Python list into another list with changed items

30th August 2007

I just had a small problem with my Python script:

1. I have a list of tuples, called records_cache; each tuple looks like this:
(note: for copy-pasting, click the PLAIN TEXT box headers)

1. (ensembl_transcript_id, ensembl_gene_id, chrom_start, chrom_end, utr_start, utr_end, sequence, strand)

2. I need to INSERT only some of those values into MySQL table, using the MySQLdb executemany() method. The values I need are utr_start, utr_end, ensembl_gene_id (in exactly this order).

To do this, I need to create another list of tuples, but with shorter 3-item tuples. Let us call the new list genes_update.

Here is the elegant, though probably not the most efficient, solution:

1. genes_update = [(onetuple[4],onetuple[5],onetuple[1]) for onetuple in records_cache]]

Let’s see what is happening here:

1. First, note the brackets around the r-expression. These brackets force the result to be a list.
2. Next, note the construct used, it is from the Python manual: list_element.method() for list_element in list. This construct iterates all items of the list, in our case – of the records_cache list. This construct also applies the list_element.method() to each list method.
3. Instead of applying some list_element.method(), I just use tuple indices to select the values I need, and then (using parenthesis) join those values into a tuple again.
4. So for each tuple in the records_cache list, another (shorter) tuple is returned, and those shorter tuples are joined into the new list, which is assigned to the genes_update list.

After this conversion, I can happily write that list of tuples into MySQL table, using cursor.executemany():
(note: error_log() is a small custom function for appending to script’s error.log file)

1. try:
2.     cursor.executemany("""UPDATE genes SET
3.        5utr_start = %s,
4.        5utr_end = %s
5.        WHERE ensembl_gene_id = %s""", genes_update)
6.     db.commit()
7. except MySQLdb.Error, (errno, strerror):
8.     db.rollback()
9.     error_log("Error %d: %s (%s)\n" % (errno, strerror, insertq))
10.     return False # failed to update
11. return True # updated

Comments are welcome, especially on the efficiency improvement.

This entry was posted on Thursday, August 30th, 2007 at 11:06 and is filed under Programming, Python. You can follow any responses to this entry through the RSS 2.0 feed. You can skip to the end and leave a response. Pinging is currently not allowed.

One Response to “Elegantly converting Python list into another list with changed items”

1. Wahoo Says:
   October 6th, 2007 at 4:51

   Thank you for sharing!

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