Mercurial > repos > jankanis > blast2html
changeset 69:19c48f2ec775 draft
wrap alignments if they are too long
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Tue, 17 Jun 2014 18:07:02 +0200 |
| parents | e3dd39906eef |
| children | fa8a93bdefd7 |
| files | blast2html.html.jinja blast2html.py |
| diffstat | 2 files changed, 32 insertions(+), 6 deletions(-) [+] |
line wrap: on
line diff
--- a/blast2html.html.jinja Wed Jun 04 16:28:45 2014 +0200 +++ b/blast2html.html.jinja Tue Jun 17 18:07:02 2014 +0200 @@ -603,7 +603,9 @@ </tr> </table> - <pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre> + {% for alignment_line in hsp|alignment_pre %} + <pre class=alignmentgraphic>{{alignment_line}}</pre> + {% endfor %} </div> {% endfor %}
--- a/blast2html.py Wed Jun 04 16:28:45 2014 +0200 +++ b/blast2html.py Tue Jun 17 18:07:02 2014 +0200 @@ -83,11 +83,35 @@ @filter def alignment_pre(hsp): - return ( - "Query {:>7s} {} {}\n".format(hsp['Hsp_query-from'].text, hsp.Hsp_qseq, hsp['Hsp_query-to']) + - " {:7s} {}\n".format('', hsp.Hsp_midline) + - "Subject{:>7s} {} {}".format(hsp['Hsp_hit-from'].text, hsp.Hsp_hseq, hsp['Hsp_hit-to']) - ) + step = 60 + + def split(txt): + return [txt[i:i+step] for i in range(0, len(txt), step)] + + qfrom = int(hsp['Hsp_query-from']) + qto = int(hsp['Hsp_query-to']) + hfrom = int(hsp['Hsp_hit-from']) + hto = int(hsp['Hsp_hit-to']) + qseq = hsp.Hsp_qseq.text + midline = hsp.Hsp_midline.text + hseq = hsp.Hsp_hseq.text + + offset = 0 + for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), step)): + yield ( + "Query {:>7} {} {}\n".format(qfrom+offset, qs, qfrom+len(qs)-1) + + " {:7} {}\n".format('', mid) + + "Subject{:>7} {} {}".format(hfrom+offset, hs, hfrom+len(hs)-1) + ) + + if qfrom+len(qseq)-1 != qto: + warnings.warn("Error in BlastXML input: Hsp node {} qseq length mismatch: from {} to {} length {}".format( + nodeid(hsp), qfrom, qto, len(qseq))) + if hfrom+len(hseq)-1 != hto: + warnings.warn("Error in BlastXML input: Hsp node {} hseq length mismatch: from {} to {} length {}".format( + nodeid(hsp), hfrom, hto, len(hseq))) + + @filter('len') def blastxml_len(node):