Comments on: Parsing blast xml output https://www.polarmicrobes.org/parsing-blast-xml-output/ Marine Microbial Ecology Wed, 30 Aug 2023 06:31:01 +0000 hourly 1 https://wordpress.org/?v=6.9 By: Ben https://www.polarmicrobes.org/parsing-blast-xml-output/#comment-486 Wed, 30 Aug 2023 06:31:01 +0000 http://www.polarmicrobes.org/?p=753#comment-486 Since I am reading this today, some might be tempted to use this in 2023: be careful when using .strip(foo) and .rstrip(bar)

They do not remove the foo and bar prefixes/suffixes, they would remove from the ends of the string (or only the tail when using rstrip) every character belonging in the set ‘foo’ or ‘bar’.

Example :
”’
>>> s = “id_seed”
>>> s.strip(“”).strip(“</")
'seed'
'''

…and the "id_" is lost!

]]> By: Jeff https://www.polarmicrobes.org/parsing-blast-xml-output/#comment-137 Fri, 19 Apr 2013 18:45:21 +0000 http://www.polarmicrobes.org/?p=753#comment-137 I just learned a great trick that makes this a whole lot easier. Python has a module (gzip) that allows gzipped files to be read as text files, e.g.

import gzip
with gzip.open('really_big_file.xml.gz', 'rb') as xml:
   for line in xml:
      do some stuff

This allows massive blast output files to stay compressed at about 1/5 their inflated size. I’ve placed an updated script here. The updated script also very niftily creates a fasta of hits, as aa seqs if blastx was used.

]]>