comparison visualise.py @ 13:7660519f2dc9 draft

proper layout for alignments, added some links

12:2fbdf2eb27b4

blast = objectify.parse('blast xml example1.xml').getroot()
loader = jinja2.FileSystemLoader(searchpath='.')
environment = jinja2.Environment(loader=loader, lstrip_blocks=True, trim_blocks=True, autoescape=True)

def filter(func_or_name):
    if isinstance(func_or_name, str):
        def inner(func):
            environment.filters[func_or_name] = func
            return func
        return inner

    return hit.Hit_id.text.split('|', 2)[2]

@filter
def alignment_pre(hsp):
    return (
        "Query   {:>7s}  {}  {}\n".format(hsp['Hsp_query-from'], hsp.Hsp_qseq, hsp['Hsp_query-to']) +
        "        {:7s}  {}\n".format('', hsp.Hsp_midline) +
        "Subject {:>7s}  {}  {}".format(hsp['Hsp_hit-from'], hsp.Hsp_hseq, hsp['Hsp_hit-to']))

@filter('len')
def hsplen(node):
    return int(node['Hsp_align-len'])

        cover_count = cover.count(True)
        
        def hsp_val(path):
            return (hsp[path] for hsp in hsps)
        
        yield dict(title = firsttitle(hit),
                   link_id = hit.Hit_num,
                   maxscore = "{:.1f}".format(float(max(hsp_val('Hsp_bit-score')))),
                   totalscore = "{:.1f}".format(float(sum(hsp_val('Hsp_bit-score')))),
                   cover = "{:.0%}".format(cover_count / query_length),
                   e_value = "{:.4g}".format(float(min(hsp_val('Hsp_evalue')))),

                                     queryscale=queryscale(),
                                     hit_info=hit_info(),
                                     params=params))

main()

13:7660519f2dc9

blast = objectify.parse('blast xml example1.xml').getroot()
loader = jinja2.FileSystemLoader(searchpath='.')
environment = jinja2.Environment(loader=loader, lstrip_blocks=True, trim_blocks=True, autoescape=True)

def filter(func_or_name):
    "Decorator to register a function as filter in the current jinja environment"
    if isinstance(func_or_name, str):
        def inner(func):
            environment.filters[func_or_name] = func
            return func
        return inner

    return hit.Hit_id.text.split('|', 2)[2]

@filter
def alignment_pre(hsp):
    return (
        "Query  {:>7s}  {}  {}\n".format(hsp['Hsp_query-from'], hsp.Hsp_qseq, hsp['Hsp_query-to']) +
        "       {:7s}  {}\n".format('', hsp.Hsp_midline) +
        "Subject{:>7s}  {}  {}".format(hsp['Hsp_hit-from'], hsp.Hsp_hseq, hsp['Hsp_hit-to'])
    )

@filter('len')
def hsplen(node):
    return int(node['Hsp_align-len'])

        cover_count = cover.count(True)
        
        def hsp_val(path):
            return (hsp[path] for hsp in hsps)
        
        yield dict(hit = hit,
                   title = firsttitle(hit),
                   link_id = hit.Hit_num,
                   maxscore = "{:.1f}".format(float(max(hsp_val('Hsp_bit-score')))),
                   totalscore = "{:.1f}".format(float(sum(hsp_val('Hsp_bit-score')))),
                   cover = "{:.0%}".format(cover_count / query_length),
                   e_value = "{:.4g}".format(float(min(hsp_val('Hsp_evalue')))),

                                     queryscale=queryscale(),
                                     hit_info=hit_info(),
                                     params=params))

main()

# http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nuclalign&blast_rank=1&RID=PHWP1JNZ014
# http://www.ncbi.nlm.nih.gov/nuccore/557804451?report=graph&rid=PHWP1JNZ014[557804451]&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD1,category:Sequence,annots:Sequence,ShowLabel:true][key:gene_model_track,CDSProductFeats:false][key:alignment_track,name:other%20alignments,annots:NG%20Alignments%7CRefseq%20Alignments%7CGnomon%20Alignments%7CUnnamed,shown:false]&v=752:2685&appname=ncbiblast&link_loc=fromSubj

# http://www.ncbi.nlm.nih.gov/nucleotide/557804451?report=genbank&log$=nucltop&blast_rank=1&RID=PHWP1JNZ014