comparison tools/ncbi_blast_plus/blastxml_to_tabular.py @ 14:2fe07f50a41e draft

Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.

13:623f727cdff1

import re
import os
from optparse import OptionParser

if "-v" in sys.argv or "--version" in sys.argv:
    print "v0.1.00"
    sys.exit(0)

if sys.version_info[:2] >= ( 2, 5 ):
    try:
        from xml.etree import cElementTree as ElementTree

    sys.stderr.write("%s\n" % msg)
    sys.exit(1)

if len(sys.argv) == 4 and sys.argv[3] in ["std", "x22", "ext"]:
    #False positive if user really has a BLAST XML file called 'std' or 'ext'...
    stop_err("ERROR: The script API has changed, sorry.")

usage = """usage: %prog [options] blastxml[,...]

Convert one (or more) BLAST XML files into a single tabular file.

14:2fe07f50a41e

import re
import os
from optparse import OptionParser

if "-v" in sys.argv or "--version" in sys.argv:
    print "v0.1.01"
    sys.exit(0)

if sys.version_info[:2] >= ( 2, 5 ):
    try:
        from xml.etree import cElementTree as ElementTree

    sys.stderr.write("%s\n" % msg)
    sys.exit(1)

if len(sys.argv) == 4 and sys.argv[3] in ["std", "x22", "ext"]:
    #False positive if user really has a BLAST XML file called 'std' or 'ext'...
    stop_err("""ERROR: The script API has changed, sorry.

Instead of the old style:

$ python blastxml_to_tabular.py input.xml output.tabular std

Please use:

$ python blastxml_to_tabular.py -o output.tabular -c std input.xml

For more information, use:

$ python blastxml_to_tabular.py -h
""")

usage = """usage: %prog [options] blastxml[,...]

Convert one (or more) BLAST XML files into a single tabular file.