view blast2go/blast2go.py @ 17:015aef74b75c draft

Uploaded v0.0.8 preview 12, edit the default configuration file to use the August 2012 database.

#!/usr/bin/env python
"""Galaxy wrapper for Blast2GO for pipelines, b2g4pipe v2.5.

This script takes exactly three command line arguments:
 * Input BLAST XML filename
 * Blast2GO properties filename (settings file)
 * Output tabular filename

The properties filename can be a fully qualified path, but if not
this will look next to the blast2go.jar file.

Sadly b2g4pipe (at least v2.3.5 to v2.5.0) cannot cope with current
style large BLAST XML files (e.g. from BLAST 2.2.25+), so we reformat
these to avoid it crashing with a Java heap space OutOfMemoryError.

As part of this reformatting, we check for BLASTP or BLASTX output
(otherwise raise an error), and print the query count.

It then calls the Java command line tool, and moves the output file to
the location Galaxy is expecting, and removes the tempory XML file.
"""
import sys
import os
import subprocess

#You may need to edit this to match your local setup,
blast2go_dir = os.environ.get("B2G4PIPE", "/opt/b2g4pipe_v2.5/")
blast2go_jar = os.path.join(blast2go_dir, "blast2go.jar")

def stop_err(msg, error_level=1):
    """Print error message to stdout and quit with given error level."""
    sys.stderr.write("%s\n" % msg)
    sys.exit(error_level)

if len(sys.argv) != 4:
    stop_err("Require three arguments: XML filename, properties filename, output tabular filename")

xml_file, prop_file, tabular_file = sys.argv[1:]

#We should have write access here:
tmp_xml_file = tabular_file + ".tmp.xml"

if not os.path.isfile(blast2go_jar):
    stop_err("Blast2GO JAR file not found: %s" % blast2go_jar)

if not os.path.isfile(xml_file):
    stop_err("Input BLAST XML file not found: %s" % xml_file)

if not os.path.isfile(prop_file):
    tmp = os.path.join(os.path.split(blast2go_jar)[0], prop_file)
    if os.path.isfile(tmp):
        #The properties file seems to have been given relative to the JAR
        prop_file = tmp
    else:
        stop_err("Blast2GO configuration file not found: %s" % prop_file)
    del tmp

def prepare_xml(original_xml, mangled_xml):
    """Reformat BLAST XML to suit Blast2GO.

    Blast2GO can't cope with 1000s of <Iteration> tags within a
    single <BlastResult> tag, so instead split this into one
    full XML record per interation (i.e. per query). This gives
    a concatenated XML file mimicing old versions of BLAST.

    This also checks for BLASTP or BLASTX output, and outputs
    the number of queries. Galaxy will show this as "info".
    """
    in_handle = open(original_xml)
    footer = "  </BlastOutput_iterations>\n</BlastOutput>\n"
    header = ""
    while True:
        line = in_handle.readline()
        if not line:
            #No hits?
            stop_err("Problem with XML file?")
        if line.strip() == "<Iteration>":
            break
        header += line

    if "<BlastOutput_program>blastx</BlastOutput_program>" in header:
        print "BLASTX output identified"
    elif "<BlastOutput_program>blastp</BlastOutput_program>" in header:
        print "BLASTP output identified"
    else:
        in_handle.close()
        stop_err("Expect BLASTP or BLASTX output")

    out_handle = open(mangled_xml, "w")
    out_handle.write(header)
    out_handle.write(line)
    count = 1
    while True:
        line = in_handle.readline()
        if not line:
            break
        elif line.strip() == "<Iteration>":
           #Insert footer/header
           out_handle.write(footer)
           out_handle.write(header)
           count += 1
        out_handle.write(line)

    out_handle.close()
    in_handle.close()
    print "Input has %i queries" % count


def run(cmd):
    #Avoid using shell=True when we call subprocess to ensure if the Python
    #script is killed, so too is the child process.
    try:
        child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    except Exception, err:
        stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
    #Use .communicate as can get deadlocks with .wait(),
    stdout, stderr = child.communicate()
    return_code = child.returncode

    #keep stdout minimal as shown prominently in Galaxy
    #Record it in case a silent error needs diagnosis
    if stdout:
        sys.stderr.write("Standard out:\n%s\n\n" % stdout)
    if stderr:
        sys.stderr.write("Standard error:\n%s\n\n" % stderr)

    error_msg = None
    if return_code:
        cmd_str = " ".join(cmd)
        error_msg = "Return code %i from command:\n%s" % (return_code, cmd_str)
    elif "Database or network connection (timeout) error" in stdout+stderr:
        error_msg = "Database or network connection (timeout) error"
    elif "Annotation of 0 seqs with 0 annots finished." in stdout+stderr:
        error_msg = "No sequences processed!"

    if error_msg:
        print error_msg
        stop_err(error_msg)


blast2go_classpath = os.path.split(blast2go_jar)[0]
assert os.path.isdir(blast2go_classpath)
blast2go_classpath = "%s/*:%s/ext/*:" % (blast2go_classpath, blast2go_classpath)

prepare_xml(xml_file, tmp_xml_file)
#print "XML file prepared for Blast2GO"

#We will have write access wherever the output should be,
#so we'll ask Blast2GO to use that as the stem for its output
#(it will append .annot to the filename)
cmd = ["java", "-cp", blast2go_classpath, "es.blast2go.prog.B2GAnnotPipe",
       "-in", tmp_xml_file,
       "-prop", prop_file,
       "-out", tabular_file, #Used as base name for output files
       "-annot", # Generate *.annot tabular file
       #NOTE: For v2.3.5 must use -a, for v2.5 must use -annot instead
       #"-img", # Generate images, feature not in v2.3.5
       ]
#print " ".join(cmd)
run(cmd)

#Remove the temp XML file
os.remove(tmp_xml_file)

out_file = tabular_file + ".annot"
if not os.path.isfile(out_file):
    stop_err("ERROR - No output annotation file from Blast2GO")

#Move the output file where Galaxy expects it to be:
os.rename(out_file, tabular_file)

print "Done"