Mercurial > repos > peterjc > blast2go
annotate tools/blast2go/massage_xml_for_blast2go.py @ 24:05eef6b222af draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/blast2go commit 6f3c1a8da279f3b34d3bc627c97713d8dfe5f8ed
| author | peterjc |
|---|---|
| date | Fri, 15 May 2015 06:01:16 -0400 |
| parents | 31cb702eb5a8 |
| children | 242cf17c3bf9 |
| rev | line source |
|---|---|
| 23 | 1 #!/usr/bin/env python |
| 2 """Script for reformatting Blast XML to suit Blast2GO. | |
| 3 | |
| 4 This script takes exactly two command line arguments: | |
| 5 * Input BLAST XML filename | |
| 6 * Output BLAST XML filename | |
| 7 | |
| 8 Sadly b2g4pipe (at least v2.3.5 to v2.5.0) cannot cope with current | |
| 9 style large BLAST XML files (e.g. from BLAST 2.2.25+), so we reformat | |
| 10 these to avoid it crashing with a Java heap space OutOfMemoryError. | |
| 11 | |
| 12 As part of this reformatting, we check for BLASTP or BLASTX output | |
| 13 (otherwise raise an error), and print the query count. | |
| 14 | |
| 15 This script is called from my Galaxy wrapper for Blast2GO for pipelines, | |
| 16 available from the Galaxy Tool Shed here: | |
| 17 http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go | |
| 18 | |
| 19 This script is under version control here: | |
| 20 https://github.com/peterjc/galaxy_blast/tree/master/blast2go | |
| 21 """ | |
| 22 import sys | |
| 23 import os | |
| 24 | |
| 25 def stop_err(msg, error_level=1): | |
| 26 """Print error message to stdout and quit with given error level.""" | |
| 27 sys.stderr.write("%s\n" % msg) | |
| 28 sys.exit(error_level) | |
| 29 | |
| 30 def prepare_xml(original_xml, mangled_xml): | |
| 31 """Reformat BLAST XML to suit Blast2GO. | |
| 32 | |
| 33 Blast2GO can't cope with 1000s of <Iteration> tags within a | |
| 34 single <BlastResult> tag, so instead split this into one | |
| 35 full XML record per interation (i.e. per query). This gives | |
| 36 a concatenated XML file mimicing old versions of BLAST. | |
| 37 | |
| 38 This also checks for BLASTP or BLASTX output, and outputs | |
| 39 the number of queries. Galaxy will show this as "info". | |
| 40 """ | |
| 41 in_handle = open(original_xml) | |
| 42 footer = " </BlastOutput_iterations>\n</BlastOutput>\n" | |
| 43 header = "" | |
| 44 while True: | |
| 45 line = in_handle.readline() | |
| 46 if not line: | |
| 47 #No hits? | |
| 48 stop_err("Problem with XML file?") | |
| 49 if line.strip() == "<Iteration>": | |
| 50 break | |
| 51 header += line | |
| 52 | |
| 53 if "<BlastOutput_program>blastx</BlastOutput_program>" in header: | |
|
24
05eef6b222af
planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/blast2go commit 6f3c1a8da279f3b34d3bc627c97713d8dfe5f8ed
peterjc
parents:
23
diff
changeset
|
54 print("BLASTX output identified") |
| 23 | 55 elif "<BlastOutput_program>blastp</BlastOutput_program>" in header: |
|
24
05eef6b222af
planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/blast2go commit 6f3c1a8da279f3b34d3bc627c97713d8dfe5f8ed
peterjc
parents:
23
diff
changeset
|
56 print("BLASTP output identified") |
| 23 | 57 else: |
| 58 in_handle.close() | |
| 59 stop_err("Expect BLASTP or BLASTX output") | |
| 60 | |
| 61 out_handle = open(mangled_xml, "w") | |
| 62 out_handle.write(header) | |
| 63 out_handle.write(line) | |
| 64 count = 1 | |
| 65 while True: | |
| 66 line = in_handle.readline() | |
| 67 if not line: | |
| 68 break | |
| 69 elif line.strip() == "<Iteration>": | |
| 70 #Insert footer/header | |
| 71 out_handle.write(footer) | |
| 72 out_handle.write(header) | |
| 73 count += 1 | |
| 74 out_handle.write(line) | |
| 75 | |
| 76 out_handle.close() | |
| 77 in_handle.close() | |
|
24
05eef6b222af
planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/blast2go commit 6f3c1a8da279f3b34d3bc627c97713d8dfe5f8ed
peterjc
parents:
23
diff
changeset
|
78 print("Input has %i queries" % count) |
| 23 | 79 |
| 80 | |
| 81 if __name__ == "__main__": | |
| 82 # Run the conversion... | |
| 83 if len(sys.argv) != 3: | |
| 84 stop_err("Require two arguments: XML input filename, XML output filename") | |
| 85 | |
| 86 xml_file, out_xml_file = sys.argv[1:] | |
| 87 | |
| 88 if not os.path.isfile(xml_file): | |
| 89 stop_err("Input BLAST XML file not found: %s" % xml_file) | |
| 90 | |
| 91 prepare_xml(xml_file, out_xml_file) |