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Posted by Bloguero_Connor on Wed 2 Apr 12:17
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  1. from Bio.Blast import NCBIXML
  2.  
  3. f_in='/mnt/hda2/bio/blast-2.2.18/bin/m3x-218.xml'
  4.  
  5. fr=NCBIXML.parse(open(f_in)).next()
  6.  
  7. print '''<HTML>
  8. <TITLE>BLAST Search Results</TITLE>
  9. <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
  10. <PRE>'''
  11. print '<b>%s</b>' %(fr.application+' '+fr.version+' '+fr.date)
  12. print '\n<b><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=9254694&dopt=Citation">Reference</a>:</b>'+\
  13.               fr.reference.replace('~',' ')
  14. for rec in NCBIXML.parse(open(f_in)):
  15.     print '<b>Query=</b> %s' %(rec.query)
  16.     print '         (%s letters)' %(rec.query_letters)
  17.     print '<b>Database:</b> %s' %(rec.database)
  18.     if fr.num_letters_in_database!=[]:
  19.         #This test is for a bug in Biopython 1.45
  20.         print '         %s sequences; %s total letters' \
  21.         %(fr.num_sequences_in_database,
  22.           fr.num_letters_in_database)
  23.     #except AttributeError:
  24.     else:
  25.         # For Biopython > 1.45
  26.         print '         %s sequences; %s total letters' \
  27.         %(fr.num_sequences_in_database,
  28.           fr._num_letters_in_database)
  29.        
  30.     print '''Searching..................................................done
  32. <PRE>
  35.                                                                  Score    E
  36. Sequences producing significant alignments:                      (bits) Value
  38. '''
  39.     for d in fr.descriptions:
  40.         k=d.accession
  41.         desc=d.title
  42.         bs=d.score
  43.         sc=d.e
  44.         if 'gi|' in k:
  45.             m=k.index('gi|')+3
  46.             gi=k[m:k[m:].index('|')+3]
  47.             print '<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?\
  48. cmd=Retrieve&db=Nucleotide&list_uids=%s&dopt=GenBank" >\
  49. %s</a> %s <a href = #%s> %s</a>   %s' \
  50. %(gi,k.replace('gi|'+gi+'|',''),desc[:36]+'...',gi,bs,sc)
  51.         else:
  52.             print '%s <a href = #%s> %s</a>   %s' \
  53.             %(desc[:40]+'...',k,bs,sc)
  54.     print '</PRE>\n'
  55.     for alig in fr.alignments:
  56.         print '<PRE>\n'
  57.         k=alig.hit_id
  58.         desc=alig.hit_def
  59.         if 'gi|' in k:
  60.             m=k.index('gi|')+3
  61.             gi=k[m:k[m:].index('|')+3]
  62.             print '><a name=%s></a><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?\
  63. cmd=Retrieve&db=Nucleotide&list_uids=%s&dopt=GenBank" >\
  64. %s</a> %s ' \
  65. %(gi,gi,k.replace('gi|'+gi+'|',''),desc)
  66.         else:
  67.             print '><a name=%s></a>%s' %(k[k.index('|')+1:],desc)
  68.         print ' Length = %s\n' %(alig.length)
  69.         # Walk over all the hsps
  70.         for hsp in alig.hsps:
  71.             bs=hsp.bits
  72.             hsc=hsp.score
  73.             sc=hsp.expect
  74.             h_id=hsp.identities
  75.             h_pos=hsp.positives
  76.             q_frame=hsp.frame[0]
  77.             h_frame=hsp.frame[1]
  78.             q_from=str(hsp.query_start)
  79.             q_to=str(hsp.query_end)
  80.             h_from=str(hsp.sbjct_start)
  81.             h_to=str(hsp.sbjct_end)
  82.             qseq=hsp.query
  83.             hseq=hsp.sbjct
  84.             medio=hsp.match
  85.             if q_frame==1:
  86.                 qf='Plus'
  87.             else:
  88.                 qf='Minus'
  89.             if h_frame==1:
  90.                 hf='Plus'
  91.             else:
  92.                 hf='Minus'
  93.             print 'Score = %s bits (%s), Expect = %s' %(bs,hsc,sc)
  94.             print 'Identities = %s/%s (%.0f%%)' %(h_id,
  95.                                 h_pos,float(int(h_id))/int(h_pos)*100)
  96.             print 'Strand = %s/%s\n\n' %(qf,hf)
  97.             if h_frame=='1':
  98.                 mx=max(len(q_from),len(h_from))
  99.                 print 'Query: %s %s %s' %(q_from.ljust(mx),qseq,q_to)
  100.                 print '       '+' '*mx+' '+medio
  101.                 print 'Sbjct: %s %s %s\n' %(h_from.ljust(mx),hseq,h_to)
  102.             else:
  103.                 mx=max(len(q_from),len(h_to))
  104.                 print 'Query: %s %s %s' %(q_from.ljust(mx),qseq,q_to)
  105.                 print '       '+' '*mx+' '+medio
  106.                 print 'Sbjct: %s %s %s\n' %(h_to.ljust(mx),hseq,h_from)
  107.             print '</PRE>'
  108. if fr.num_letters_in_database!=[]:
  109.     print '''<PRE>
  110.   Database: %s
  111.   Number of letters in database: %s
  112.   Number of sequences in database:  %s
  114. Lambda     K      H
  115.     %.2f    %.3f     %.2f
  117. Matrix: %s matrix:%s %s
  118. Gap Penalties: Existence: %s, Extension: %s
  119. Number of Sequences: %s
  120. Length of database: %s
  121. </PRE>
  122. </BODY>
  123. </HTML>''' %(rec.database,fr.num_letters_in_database,
  124.              fr.num_sequences_in_database,
  125.              fr.ka_params[0],fr.ka_params[1],
  126.              fr.ka_params[2],fr.application,
  127.              fr.sc_match,fr.sc_mismatch,
  128.              fr.gap_penalties[0],fr.gap_penalties[1],
  129.              fr.num_sequences_in_database,
  130.              fr._num_letters_in_database)
  131. else:
  132.     # Hack for Biopython 1.45 or earlier.
  133.     print '''<PRE>
  134.   Database: %s
  135.   Number of letters in database: %s
  136.   Number of sequences in database:  %s
  138. Lambda     K      H
  139.     %.2f    %.3f     %.2f
  141. Matrix: %s matrix:%s %s
  142. Gap Penalties: Existence: %s, Extension: %s
  143. Number of Sequences: %s
  144. Length of database: %s
  145. </PRE>
  146. </BODY>
  147. </HTML>''' %(rec.database,fr._num_letters_in_database,
  148.              fr.num_sequences_in_database,
  149.              fr.ka_params[0],fr.ka_params[1],
  150.              fr.ka_params[2],fr.application,
  151.              fr.sc_match,fr.sc_mismatch,
  152.              fr.gap_penalties[0],fr.gap_penalties[1],
  153.              fr.num_sequences_in_database,
  154.              fr._num_letters_in_database)

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