Hello,

I have the blast output in .xml form and I want to retrieve few attributes like <hit_def>. I found the parser on biophython.

CODE:

from Bio.Blast import NCBIXML
blast = NCBIXML.parse(open('output.xml', 'rU'))
for record in blast:
    for align in record.alignments:
        for hsp in align.hsps:
            print hsp.score, align.hit_def

Q1: Above code is just printing the out put on the terminal. Could anyone help me how to store the output file in .csv format.

Specifically, I need output.csv with these attribute <Iteration_query-def>, <Hit_def>, <Hsp_score>, <Hsp_evalue> as columns, in a .csv format.

Q2: How can I to get the result just for the best hit of each query? While running blastp setting -max_target_seqs to 1 will do the same?

Following is a segment of my input xml

      <Iteration_iter-num>1</Iteration_iter-num>
      <Iteration_query-ID>Query_1</Iteration_query-ID>
      <Iteration_query-def>comp552019_c3_seq6_V2</Iteration_query-def>
      <Iteration_query-len>227</Iteration_query-len>
      <Iteration_hits>
        <Hit>
          <Hit_num>1</Hit_num>
          <Hit_id>gi|148727288|ref|NP_002327.2|</Hit_id>
          <Hit_def>low-density lipoprotein receptor-related protein 6 precursor [Homo sapiens] &gt;gi|578822872|ref|XP_006719141.1| PREDICTED: low-density lipoprotein receptor-related protein 6 isoform X1 [Homo sapiens]</Hit_def>
          <Hit_accession>NP_002327</Hit_accession>
          <Hit_len>1613</Hit_len>
          <Hit_hsps>
            <Hsp>
              <Hsp_num>1</Hsp_num>
              <Hsp_bit-score>43.5133894476967</Hsp_bit-score>
              <Hsp_score>101</Hsp_score>
              <Hsp_evalue>0.000198686946331968</Hsp_evalue>
              <Hsp_query-from>43</Hsp_query-from>
              <Hsp_query-to>223</Hsp_query-to>
              <Hsp_hit-from>589</Hsp_hit-from>
              <Hsp_hit-to>767</Hsp_hit-to>
              <Hsp_query-frame>0</Hsp_query-frame>
              <Hsp_hit-frame>0</Hsp_hit-frame>
              <Hsp_identity>53</Hsp_identity>
              <Hsp_positive>79</Hsp_positive>
              <Hsp_gaps>24</Hsp_gaps>
              <Hsp_align-len>192</Hsp_align-len>
              <Hsp_qseq>TNEC--HDSKCEHICLARDAGGFVCKCSPGFTLVSGYK-CVSDSVTDDYILVADLGQKRLFQLPIRKST-----RNVGDLVAIDLDDVTDDRIYAASVIKKTGGLAWFDISAREIV--WGSKRLSRDDAVLSITTGCCNKKVYWTTQTGIYSWDGVSSTPDKLYSVSFFSDA-QIRQVVVDCKANLLYWIEY</Hsp_qseq>
              <Hsp_hseq>SNPCAEENGGCSHLCLYRPQG-LRCACPIGFELISDMKTCI---VPEAFLLFSRRADIRRISLETNNNNVAIPLTGVKEASALDFD-VTDNRIYWTDISLKTISRAFMNGSALEHVVEFGL------DYPEGMAVDWLGKNLYW-ADTGTNRIE-VSKLDGQHRQVLVWKDLDSPRALALDPAEGFMYWTEW</Hsp_hseq>
              <Hsp_midline>+N C   +  C H+CL R  G   C C  GF L+S  K C+   V + ++L +     R   L    +        V +  A+D D VTD+RIY   +  KT   A+ + SA E V  +G       D    +      K +YW   TG    + VS    +   V  + D    R + +D     +YW E+</Hsp_midline>
            </Hsp>
            <Hsp>
              <Hsp_num>2</Hsp_num>
              <Hsp_bit-score>39.6613936885231</Hsp_bit-score>
              <Hsp_score>91</Hsp_score>
              <Hsp_evalue>0.00402563881724524</Hsp_evalue>
              <Hsp_query-from>44</Hsp_query-from>
              <Hsp_query-to>128</Hsp_query-to>
              <Hsp_hit-from>891</Hsp_hit-from>
              <Hsp_hit-to>980</Hsp_hit-to>
              <Hsp_query-frame>0</Hsp_query-frame>
              <Hsp_hit-frame>0</Hsp_hit-frame>
              <Hsp_identity>34</Hsp_identity>
              <Hsp_positive>43</Hsp_positive>
              <Hsp_gaps>15</Hsp_gaps>
              <Hsp_align-len>95</Hsp_align-len>
              <Hsp_qseq>NECHDSK--CEHICLARDAGGFVCKCSPGFTLVSGYKCVSDSVTDDYI--------LVADLGQKRLFQLPIRKSTRNVGDLVAIDLDDVTDDRIY</Hsp_qseq>
              <Hsp_hseq>NECASSNGHCSHLCLAVPVGGFVCGCPAHYSLNADNRTCSAPTTFLLFSQKSAINRMVIDEQQSPDIILPIH-SLRNV---RAIDYDPL-DKQLY</Hsp_hseq>
              <Hsp_midline>NEC  S   C H+CLA   GGFVC C   ++L +  +  S   T            +V D  Q     LPI  S RNV    AID D + D ++Y</Hsp_midline>
            </Hsp>
          </Hit_hsps>

I would really appreciate your help.

Thanks