#!/usr/bin/env python
"""Convert a BLAST XML file to 12 column tabular output

Takes three command line options, input BLAST XML filename, output tabular
BLAST filename, output format (std for standard 12 columns, or ext for the
extended 25 columns offered in the BLAST+ wrappers).

The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart
qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which
mean:
   
====== ========= ============================================
Column NCBI name Description
------ --------- --------------------------------------------
     1 qseqid    Query Seq-id (ID of your sequence)
     2 sseqid    Subject Seq-id (ID of the database hit)
     3 pident    Percentage of identical matches
     4 length    Alignment length
     5 mismatch  Number of mismatches
     6 gapopen   Number of gap openings
     7 qstart    Start of alignment in query
     8 qend      End of alignment in query
     9 sstart    Start of alignment in subject (database hit)
    10 send      End of alignment in subject (database hit)
    11 evalue    Expectation value (E-value)
    12 bitscore  Bit score
====== ========= ============================================

The additional columns offered in the Galaxy BLAST+ wrappers are:

====== ============= ===========================================
Column NCBI name     Description
------ ------------- -------------------------------------------
    13 sallseqid     All subject Seq-id(s), separated by a ';'
    14 score         Raw score
    15 nident        Number of identical matches
    16 positive      Number of positive-scoring matches
    17 gaps          Total number of gaps
    18 ppos          Percentage of positive-scoring matches
    19 qframe        Query frame
    20 sframe        Subject frame
    21 qseq          Aligned part of query sequence
    22 sseq          Aligned part of subject sequence
    23 qlen          Query sequence length
    24 slen          Subject sequence length
    25 salltitles    All subject titles, separated by '<>'
====== ============= ===========================================

Most of these fields are given explicitly in the XML file, others some like
the percentage identity and the number of gap openings must be calculated.

Be aware that the sequence in the extended tabular output or XML direct from
BLAST+ may or may not use XXXX masking on regions of low complexity. This
can throw the off the calculation of percentage identity and gap openings.
[In fact, both BLAST 2.2.24+ and 2.2.25+ have a subtle bug in this regard,
with these numbers changing depending on whether or not the low complexity
filter is used.]

This script attempts to produce identical output to what BLAST+ would have done.
However, check this with "diff -b ..." since BLAST+ sometimes includes an extra
space character (probably a bug).
"""
import sys
import re
import os
from optparse import OptionParser

if "-v" in sys.argv or "--version" in sys.argv:
    print "v1.0.0"
    sys.exit(0)

if sys.version_info[:2] >= ( 2, 5 ):
    try:
        from xml.etree import cElementTree as ElementTree
    except ImportError:
        from xml.etree import ElementTree as ElementTree
else:
    from galaxy import eggs
    import pkg_resources; pkg_resources.require( "elementtree" )
    from elementtree import ElementTree

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

usage = "usage: %prog [options] blastxml[,...]"
parser = OptionParser(usage=usage)
parser.add_option('-o','--output', dest='output', default = None, help='output file path', metavar="FILE")
parser.add_option("-c", "--columns", dest="columns", default='std', help="[std|ext|colname[,colname,...]] std: 12 column, ext: 25 column, or user specified columns")
parser.add_option("-a", "--allqueries", action="store_true", dest="allqueries", default=False, help="ouptut row for each query, including those with no hits")
parser.add_option("-d", "--qdef", action="store_true", dest="qdef", default=False, help="use Iteration_query-def for qseqid")
parser.add_option('-u', '--unmatched', dest='unmatched', default = None, help='unmatched queries file path',  metavar="FILE")
parser.add_option('-m', '--maxhits', dest='maxhits', type="int", default = 1, help='maximum number of HITs for output for a Query')
parser.add_option('-p', '--maxhsps', dest='maxhsps', type="int", default = 1, help='maximum number of HSPs for output for a Hit')
(options, args) = parser.parse_args()

colnames = 'qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles'.split(',')

if len(args) < 1:
    parser.error("no BLASTXML input files")

if options.columns == "std":
    out_fmt = 'std'
    extended = False
    columns = colnames[0:12]
elif options.columns == "x22":
    stop_err("Format argument x22 has been replaced with ext (extended 25 columns)")
elif options.columns == "ext":
    out_fmt = 'ext'
    extended = True
    columns = colnames[0:25]
else: 
    out_fmt = 'cols'
    extended = True
    sel_cols = options.columns.split(',')
    columns = []
    for col in sel_cols:
        if col in colnames:
            columns.append(col)

for in_file in args:
    if not os.path.isfile(in_file):
        stop_err("Input BLAST XML file not found: %s" % in_file)

unhitfile = open(options.unmatched,'w') if options.unmatched else None

re_default_query_id = re.compile("^Query_\d+$")
assert re_default_query_id.match("Query_101")
assert not re_default_query_id.match("Query_101a")
assert not re_default_query_id.match("MyQuery_101")
re_default_subject_id = re.compile("^Subject_\d+$")
assert re_default_subject_id.match("Subject_1")
assert not re_default_subject_id.match("Subject_")
assert not re_default_subject_id.match("Subject_12a")
assert not re_default_subject_id.match("TheSubject_1")
    
header = "#%s\n" % "\t".join(columns)
outfile = open(options.output, 'w') if options.output else sys.stdout
outfile.write(header)

def handle_event(event, elem):
    blast_program = None
    if event == "end" and elem.tag == "BlastOutput_program":
        blast_program = elem.text
    # for every <Iteration> tag
    if event == "end" and elem.tag == "Iteration":
        #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA
        # <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
        # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
        # <Iteration_query-len>406</Iteration_query-len>
        # <Iteration_hits></Iteration_hits>
        #
        #Or, from BLAST 2.2.24+ run online
        # <Iteration_query-ID>Query_1</Iteration_query-ID>
        # <Iteration_query-def>Sample</Iteration_query-def>
        # <Iteration_query-len>516</Iteration_query-len>
        # <Iteration_hits>...
        qseqid = elem.findtext("Iteration_query-ID")
        if options.qdef or re_default_query_id.match(qseqid):
            #Place holder ID, take the first word of the query definition
            qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
        qlen = int(elem.findtext("Iteration_query-len"))
        # If no hits in this iteration
        if not elem.find("Iteration_hits/Hit"):
            if unhitfile:
                unhitfile.write("%s\n" % qseqid)
            if options.allqueries:
                if columns and len(columns) > 0:
                    v = []
                    for name in columns:
                        if name == 'qseqid':
                            v.append(qseqid)
                        elif name == 'qlen':
                            v.append(str(qlen))
                        else:
                            v.append('')
                    outfile.write("\t".join(v) + "\n")
        # for every <Hit> within <Iteration>
        for hitn, hit in enumerate(elem.findall("Iteration_hits/Hit")):
            if hitn >= options.maxhits:
                break
            #Expecting either this,
            # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>
            # <Hit_def>RecName: Full=Rhodopsin</Hit_def>
            # <Hit_accession>P56514</Hit_accession>
            #or,
            # <Hit_id>Subject_1</Hit_id>
            # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def>
            # <Hit_accession>Subject_1</Hit_accession>
            #
            #apparently depending on the parse_deflines switch
            #
            #Or, with a local database not using -parse_seqids can get this,
            # <Hit_id>gnl|BL_ORD_ID|2</Hit_id>
            # <Hit_def>chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence</Hit_def>
            # <Hit_accession>2</Hit_accession>
            sseqid = hit.findtext("Hit_id").split(None,1)[0]
            hit_def = sseqid + " " + hit.findtext("Hit_def")
            if re_default_subject_id.match(sseqid) \
            and sseqid == hit.findtext("Hit_accession"):
                #Place holder ID, take the first word of the subject definition
                hit_def = hit.findtext("Hit_def")
                sseqid = hit_def.split(None,1)[0]
            # for every <Hsp> within <Hit>
            for hspn,hsp in enumerate(hit.findall("Hit_hsps/Hsp")):
                if hspn >= options.maxhsps:
                    break
                nident = hsp.findtext("Hsp_identity")
                length = hsp.findtext("Hsp_align-len")
                pident = "%0.2f" % (100*float(nident)/float(length))

                q_seq = hsp.findtext("Hsp_qseq")
                h_seq = hsp.findtext("Hsp_hseq")
                m_seq = hsp.findtext("Hsp_midline")
                assert len(q_seq) == len(h_seq) == len(m_seq) == int(length)
                gapopen = str(len(q_seq.replace('-', ' ').split())-1  + \
                              len(h_seq.replace('-', ' ').split())-1)

                mismatch = m_seq.count(' ') + m_seq.count('+') \
                         - q_seq.count('-') - h_seq.count('-')
                #TODO - Remove this alternative mismatch calculation and test
                #once satisifed there are no problems
                expected_mismatch = len(q_seq) \
                                  - sum(1 for q,h in zip(q_seq, h_seq) \
                                        if q == h or q == "-" or h == "-")
                xx = sum(1 for q,h in zip(q_seq, h_seq) if q=="X" and h=="X")
                if not (expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch + xx):
                    stop_err("%s vs %s mismatches, expected %i <= %i <= %i" \
                             % (qseqid, sseqid, expected_mismatch - q_seq.count("X"),
                                int(mismatch), expected_mismatch))

                #TODO - Remove this alternative identity calculation and test
                #once satisifed there are no problems
                expected_identity = sum(1 for q,h in zip(q_seq, h_seq) if q == h)
                if not (expected_identity - xx <= int(nident) <= expected_identity + q_seq.count("X")):
                    stop_err("%s vs %s identities, expected %i <= %i <= %i" \
                             % (qseqid, sseqid, expected_identity, int(nident),
                                expected_identity + q_seq.count("X")))
                

                evalue = hsp.findtext("Hsp_evalue")
                if evalue == "0":
                    evalue = "0.0"
                else:
                    evalue = "%0.0e" % float(evalue)
                
                bitscore = float(hsp.findtext("Hsp_bit-score"))
                if bitscore < 100:
                    #Seems to show one decimal place for lower scores
                    bitscore = "%0.1f" % bitscore
                else:
                    #Note BLAST does not round to nearest int, it truncates
                    bitscore = "%i" % bitscore

                values = [qseqid,
                          sseqid,
                          pident,
                          length, #hsp.findtext("Hsp_align-len")
                          str(mismatch),
                          gapopen,
                          hsp.findtext("Hsp_query-from"), #qstart,
                          hsp.findtext("Hsp_query-to"), #qend,
                          hsp.findtext("Hsp_hit-from"), #sstart,
                          hsp.findtext("Hsp_hit-to"), #send,
                          evalue, #hsp.findtext("Hsp_evalue") in scientific notation
                          bitscore, #hsp.findtext("Hsp_bit-score") rounded
                          ]

                if extended:
                    sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(">"))
                    salltitles = "<>".join(name.split(None,1)[1] for name in hit_def.split(" >"))
                    #print hit_def, "-->", sallseqid
                    positive = hsp.findtext("Hsp_positive")
                    ppos = "%0.2f" % (100*float(positive)/float(length))
                    qframe = hsp.findtext("Hsp_query-frame")
                    sframe = hsp.findtext("Hsp_hit-frame")
                    if blast_program == "blastp":
                        #Probably a bug in BLASTP that they use 0 or 1 depending on format
                        if qframe == "0": qframe = "1"
                        if sframe == "0": sframe = "1"
                    slen = int(hit.findtext("Hit_len"))
                    values.extend([sallseqid,
                                   hsp.findtext("Hsp_score"), #score,
                                   nident,
                                   positive,
                                   hsp.findtext("Hsp_gaps"), #gaps,
                                   ppos,
                                   qframe,
                                   sframe,
                                   #NOTE - for blastp, XML shows original seq, tabular uses XXX masking
                                   q_seq,
                                   h_seq,
                                   str(qlen),
                                   str(slen),
                                   salltitles,
                                   ])
                if out_fmt == 'cols':
                    if columns and len(columns) > 0:
                        v = []
                        for name in columns:
                            v.append(values[colnames.index(name)])
                        values = v
                #print "\t".join(values) 
                outfile.write("\t".join(values) + "\n")
        # prevents ElementTree from growing large datastructure
        root.clear()
        elem.clear()


for in_file in args:
    # get an iterable
    try: 
        context = ElementTree.iterparse(in_file, events=("start", "end"))
    except:
        stop_err("Invalid data format.")
    # turn it into an iterator
    context = iter(context)
    # get the root element
    try:
        event, root = context.next()
    except:
        stop_err( "Invalid data format." )
    for event, elem in context:
        handle_event(event, elem)

if unhitfile:
    unhitfile.close()
if options.output:
    outfile.close()