Mercurial > repos > peterjc > blast2go

comparison tools/ncbi_blast_plus/blast2go.py @ 3:a5594772282c draft

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Uploaded v0.0.4 with explicit dependency on 'blast_datatypes' for 'blastxml' format definition. No functional changes.
author peterjc
date Fri, 08 Feb 2013 10:33:50 -0500
parents 0f159cf346c8
children
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2:e88a3246520e 3:a5594772282c
4 This script takes exactly three command line arguments: 4 This script takes exactly three command line arguments:
5 * Input BLAST XML filename 5 * Input BLAST XML filename
6 * Blast2GO properties filename (settings file) 6 * Blast2GO properties filename (settings file)
7 * Output tabular filename 7 * Output tabular filename
8 8
9 Sadly b2g4pipe v2.3.5 cannot cope with current style large BLAST XML 9 Sadly b2g4pipe (at least v2.3.5 to v2.5.0) cannot cope with current
10 files (e.g. from BLAST 2.2.25+), so we have to reformat these to 10 style large BLAST XML files (e.g. from BLAST 2.2.25+), so we reformat
11 avoid it crashing with a Java heap space OutOfMemoryError. 11 these to avoid it crashing with a Java heap space OutOfMemoryError.
12 12
13 As part of this reformatting, we check for BLASTP or BLASTX output 13 As part of this reformatting, we check for BLASTP or BLASTX output
14 (otherwise raise an error), and print the query count. 14 (otherwise raise an error), and print the query count.
15 15
16 It then calls the Java command line tool, and moves the output file to 16 It then calls the Java command line tool, and moves the output file to