comparison blast_report.py @ 0:a61ee7b075c0 draft default tip

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit b9c92df78fd78bf5881ab0cc5f5692d2bc71f5f6"

0:a61ee7b075c0

#!/usr/bin/env python

from __future__ import print_function

import argparse
import re
import sys

from Cheetah.Template import Template


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


class BLASTBin:
    def __init__(self, label, file):
        self.label = label
        self.dict = {}

        file_in = open(file)
        for line in file_in:
            self.dict[line.rstrip().split('.')[0]] = ''
        file_in.close()

    def __str__(self):
        return "label: %s    dict: %s" % (self.label, str(self.dict))


class BLASTQuery:
    def __init__(self, query_id):
        self.query_id = query_id
        self.matches = []
        self.match_accessions = {}
        self.bins = {}  # {bin(label):[match indexes]}
        self.pident_filtered = 0
        self.kw_filtered = 0
        self.kw_filtered_breakdown = {}  # {kw:count}

    def __str__(self):
        format_string = "\t".join([
            "query_id: %s",
            "len(matches): %s",
            "bins (labels only): %s",
            "pident_filtered: %s",
            "kw_filtered: %s",
            "kw_filtered_breakdown: %s"
        ])
        return format_string \
            % (self.query_id,
               str(len(self.matches)),
               str([bin.label for bin in bins]),
               str(self.pident_filtered),
               str(self.kw_filtered),
               str(self.kw_filtered_breakdown))


class BLASTMatch:
    def __init__(self, subject_acc, subject_descr, score, p_cov, p_ident, subject_bins):
        self.subject_acc = subject_acc
        self.subject_descr = subject_descr
        self.score = score
        self.p_cov = p_cov
        self.p_ident = p_ident
        self.bins = subject_bins

    def __str__(self):
        return "subject_acc: %s    subject_descr: %s    score: %s    p-cov: %s    p-ident: %s" \
            % (self.subject_acc,
               self.subject_descr,
               str(self.score),
               str(round(self.p_cov, 2)),
               str(round(self.p_ident, 2)))


# PARSE OPTIONS AND ARGUMENTS
parser = argparse.ArgumentParser()

parser.add_argument('-f', '--filter-keywords',
                    dest='filter_keywords',
                    )
parser.add_argument('-i', '--min-identity',
                    dest='min_identity',
                    )
parser.add_argument('-b', '--bins',
                    dest='bins',
                    action='append',
                    nargs='+'
                    )
parser.add_argument('-r', '--discard-redundant',
                    dest='discard_redundant',
                    default=False,
                    action='store_true'
                    )
parser.add_argument('input_tab')
parser.add_argument('cheetah_tmpl')
parser.add_argument('output_html')
parser.add_argument('output_tab')

args = parser.parse_args()

# BINS
bins = []
if args.bins is not None:
    for bin in args.bins:
        bins.append(BLASTBin(bin[0], bin[1]))

print('database bins: %s' % str([bin.label for bin in bins]))

# FILTERS
filter_pident = 0
filter_kws = []
if args.filter_keywords:
    filter_kws = args.filter_keywords.split(',')
print('minimum percent identity: %s    filter_kws: %s' % (str(args.min_identity), str(filter_kws)))

if args.discard_redundant:
    print('Throwing out redundant hits...')


PIDENT_COL = 2
DESCR_COL = 24
SUBJ_ID_COL = 12
SCORE_COL = 11
PCOV_COL = 25
queries = []
current_query = ''
output_tab = open(args.output_tab, 'w')

with open(args.input_tab) as input_tab:
    for line in input_tab:
        cols = line.split('\t')
        if cols[0] != current_query:
            current_query = cols[0]
            queries.append(BLASTQuery(current_query))

        try:
            accs = cols[SUBJ_ID_COL].split('|')[1::2][1::2]
        except IndexError as e:
            stop_err("Problem with splitting:" + cols[SUBJ_ID_COL])

        # keep best (first) hit only for each query and accession id.
        if args.discard_redundant:
            if accs[0] in queries[-1].match_accessions:
                continue  # don't save the result and skip to the next
            else:
                queries[-1].match_accessions[accs[0]] = ''

        p_ident = float(cols[PIDENT_COL])
        # FILTER BY PIDENT
        if p_ident < filter_pident:  # if we are not filtering, filter_pident == 0 and this will never evaluate to True
            queries[-1].pident_filtered += 1
            continue

        descrs = cols[DESCR_COL]
        # FILTER BY KEY WORDS
        filter_by_kw = False
        for kw in filter_kws:
            kw = kw.strip()
            if kw != '' and re.search(kw, descrs, re.IGNORECASE):
                filter_by_kw = True
                try:
                    queries[-1].kw_filtered_breakdown[kw] += 1
                except Exception as e:
                    queries[-1].kw_filtered_breakdown[kw] = 1
        if filter_by_kw:  # if we are not filtering, for loop will not be entered and this will never be True
            queries[-1].kw_filtered += 1
            continue
        descr = descrs.split(';')[0]

        # ATTEMPT BIN
        subj_bins = []
        for bin in bins:  # if we are not binning, bins = [] so for loop not entered
            for acc in accs:
                if acc.split('.')[0] in bin.dict:
                    try:
                        queries[-1].bins[bin.label].append(len(queries[-1].matches))
                    except Exception as e:
                        queries[-1].bins[bin.label] = [len(queries[-1].matches)]
                    subj_bins.append(bin.label)
                    break  # this result has been binned to this bin so break
        acc = accs[0]

        score = int(float(cols[SCORE_COL]))
        p_cov = float(cols[PCOV_COL])

        # SAVE RESULT
        queries[-1].matches.append(
            BLASTMatch(acc, descr, score, p_cov, p_ident, subj_bins)
        )
        output_tab.write(line)
input_tab.close()
output_tab.close()

'''
for query in queries:
    print(query)
    for match in query.matches:
        print('    %s' % str(match))
    for bin in query.bins:
        print('    bin: %s' % bin)
        for x in query.bins[bin]:
            print('        %s' % str(query.matches[x]))
'''

namespace = {'queries': queries}
html = Template(file=args.cheetah_tmpl, searchList=[namespace])
out_html = open(args.output_html, 'w')
out_html.write(str(html))
out_html.close()