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POHow to extract the first hit elements from an XML NCBI BLAST file?
 

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  1. POHow to extract the first hit elements from an XML NCBI BLAST file?
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    <p>Im trying to extract only the first hit from an NCBI xml BLAST file. next I would like to get only the first HSP. at the final stage I would like to get these based on best score. to make things clear here a sample of the xml file:</p> <pre><code>&lt;?xml version="1.0"?&gt; &lt;!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"&gt; &lt;BlastOutput&gt; &lt;BlastOutput_program&gt;blastx&lt;/BlastOutput_program&gt; &lt;BlastOutput_version&gt;blastx 2.2.22 [Sep-27-2009]&lt;/BlastOutput_version&gt; &lt;BlastOutput_reference&gt;~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~&amp;quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs&amp;quot;, Nucleic Acids Res. 25:3389-3402.&lt;/BlastOutput_reference&gt; &lt;BlastOutput_db&gt;/Applications/blast/db/viral1.protein.faa&lt;/BlastOutput_db&gt; &lt;BlastOutput_query-ID&gt;lcl|1_0&lt;/BlastOutput_query-ID&gt; &lt;BlastOutput_query-def&gt;DSAD-090629_plate11A01a.g1 CHROMAT_FILE: DSAD-090629_plate11A01a.g1 PHD_FILE: DSAD-090629_plate11A01a.g1.phd.1 CHEM: term DYE: big TIME: Thu Sep 17 15:33:59 2009 TEMPLATE: DSAD-090629_plate11A01a DIRECTION: rev&lt;/BlastOutput_query-def&gt; &lt;BlastOutput_query-len&gt;1024&lt;/BlastOutput_query-len&gt; &lt;BlastOutput_param&gt; &lt;Parameters&gt; &lt;Parameters_matrix&gt;BLOSUM62&lt;/Parameters_matrix&gt; &lt;Parameters_expect&gt;1e-05&lt;/Parameters_expect&gt; &lt;Parameters_gap-open&gt;11&lt;/Parameters_gap-open&gt; &lt;Parameters_gap-extend&gt;1&lt;/Parameters_gap-extend&gt; &lt;Parameters_filter&gt;F&lt;/Parameters_filter&gt; &lt;/Parameters&gt; &lt;/BlastOutput_param&gt; &lt;BlastOutput_iterations&gt; &lt;Iteration&gt; &lt;Iteration_iter-num&gt;1&lt;/Iteration_iter-num&gt; &lt;Iteration_query-ID&gt;lcl|1_0&lt;/Iteration_query-ID&gt; &lt;Iteration_query-def&gt;DSAD-090629_plate11A01a.g1 CHROMAT_FILE: DSAD-090629_plate11A01a.g1 PHD_FILE: DSAD-090629_plate11A01a.g1.phd.1 CHEM: term DYE: big TIME: Thu Sep 17 15:33:59 2009 TEMPLATE: DSAD-090629_plate11A01a DIRECTION: rev&lt;/Iteration_query-def&gt; &lt;Iteration_query-len&gt;1024&lt;/Iteration_query-len&gt; &lt;Iteration_stat&gt; &lt;Statistics&gt; &lt;Statistics_db-num&gt;68007&lt;/Statistics_db-num&gt; &lt;Statistics_db-len&gt;19518578&lt;/Statistics_db-len&gt; &lt;Statistics_hsp-len&gt;0&lt;/Statistics_hsp-len&gt; &lt;Statistics_eff-space&gt;0&lt;/Statistics_eff-space&gt; &lt;Statistics_kappa&gt;0.041&lt;/Statistics_kappa&gt; &lt;Statistics_lambda&gt;0.267&lt;/Statistics_lambda&gt; &lt;Statistics_entropy&gt;0.14&lt;/Statistics_entropy&gt; &lt;/Statistics&gt; &lt;/Iteration_stat&gt; &lt;Iteration_message&gt;No hits found&lt;/Iteration_message&gt; &lt;/Iteration&gt; &lt;Iteration&gt; &lt;Iteration&gt; &lt;Iteration_iter-num&gt;6&lt;/Iteration_iter-num&gt; &lt;Iteration_query-ID&gt;lcl|6_0&lt;/Iteration_query-ID&gt; &lt;Iteration_query-def&gt;DSAD-090629_plate11A05a.g1 CHROMAT_FILE: DSAD-090629_plate11A05a.g1 PHD_FILE: DSAD-090629_plate11A05a.g1.phd.1 CHEM: term DYE: big TIME: Thu Sep 17 15:33:59 2009 TEMPLATE: DSAD-090629_plate11A05a DIRECTION: rev&lt;/Iteration_query-def&gt; &lt;Iteration_query-len&gt;1068&lt;/Iteration_query-len&gt; &lt;Iteration_hits&gt; &lt;Hit&gt; &lt;Hit_num&gt;1&lt;/Hit_num&gt; &lt;Hit_id&gt;gnl|BL_ORD_ID|23609&lt;/Hit_id&gt; &lt;Hit_def&gt;gi|38707884|ref|NP_945016.1| Putative ribose-phosphate pyrophosphokinase [Enterobacteria phage Felix 01]&lt;/Hit_def&gt; &lt;Hit_accession&gt;23609&lt;/Hit_accession&gt; &lt;Hit_len&gt;293&lt;/Hit_len&gt; &lt;Hit_hsps&gt; &lt;Hsp&gt; &lt;Hsp_num&gt;1&lt;/Hsp_num&gt; &lt;Hsp_bit-score&gt;49.2914&lt;/Hsp_bit-score&gt; &lt;Hsp_score&gt;116&lt;/Hsp_score&gt; &lt;Hsp_evalue&gt;5.15408e-06&lt;/Hsp_evalue&gt; &lt;Hsp_query-from&gt;580&lt;/Hsp_query-from&gt; &lt;Hsp_query-to&gt;792&lt;/Hsp_query-to&gt; &lt;Hsp_hit-from&gt;202&lt;/Hsp_hit-from&gt; &lt;Hsp_hit-to&gt;273&lt;/Hsp_hit-to&gt; &lt;Hsp_query-frame&gt;-1&lt;/Hsp_query-frame&gt; &lt;Hsp_identity&gt;26&lt;/Hsp_identity&gt; &lt;Hsp_positive&gt;45&lt;/Hsp_positive&gt; &lt;Hsp_gaps&gt;2&lt;/Hsp_gaps&gt; &lt;Hsp_align-len&gt;73&lt;/Hsp_align-len&gt; &lt;Hsp_qseq&gt;MHIIGDVE--GRTCILVDDMVDTAGTLCHAAKALKERGAAKVYAYCTHPVLSGRAIENIENSVLDELVVTNTI&lt;/Hsp_qseq&gt; &lt;Hsp_hseq&gt;MRILDDVDLTDKTVMILDDICDGGRTFVEAAKHLREAGAKRVELYVTHGIFS-KDVENLLDNGIDHIYTTNSL&lt;/Hsp_hseq&gt; &lt;Hsp_midline&gt;M I+ DV+ +T +++DD+ D T AAK L+E GA +V Y TH + S + +EN+ ++ +D + TN++&lt;/Hsp_midline&gt; &lt;/Hsp&gt; &lt;/Hit_hsps&gt; &lt;/Hit&gt; &lt;Hit&gt; &lt;Hit_num&gt;2&lt;/Hit_num&gt; &lt;Hit_id&gt;gnl|BL_ORD_ID|2466&lt;/Hit_id&gt; &lt;Hit_def&gt;gi|51557505|ref|YP_068339.1| large tegument protein [Suid herpesvirus 1]&lt;/Hit_def&gt; &lt;Hit_accession&gt;2466&lt;/Hit_accession&gt; &lt;Hit_len&gt;3084&lt;/Hit_len&gt; &lt;Hit_hsps&gt; &lt;Hsp&gt; &lt;Hsp_num&gt;1&lt;/Hsp_num&gt; &lt;Hsp_bit-score&gt;48.9062&lt;/Hsp_bit-score&gt; &lt;Hsp_score&gt;115&lt;/Hsp_score&gt; &lt;Hsp_evalue&gt;6.70494e-06&lt;/Hsp_evalue&gt; &lt;Hsp_query-from&gt;369&lt;/Hsp_query-from&gt; &lt;Hsp_query-to&gt;875&lt;/Hsp_query-to&gt; &lt;Hsp_hit-from&gt;2312&lt;/Hsp_hit-from&gt; &lt;Hsp_hit-to&gt;2465&lt;/Hsp_hit-to&gt; &lt;Hsp_query-frame&gt;-2&lt;/Hsp_query-frame&gt; &lt;Hsp_identity&gt;52&lt;/Hsp_identity&gt; &lt;Hsp_positive&gt;70&lt;/Hsp_positive&gt; &lt;Hsp_gaps&gt;4&lt;/Hsp_gaps&gt; &lt;Hsp_align-len&gt;173&lt;/Hsp_align-len&gt; &lt;Hsp_qseq&gt;APESQEPGASTWRSSTSVVKKGQPSQK*CTSSVTSKAVPASWSTTWSTLPAPCATPPKR*KSAAPPRSTPTAPTRCCPAAPSRTSRIPSWTSWWSPTPSRCPLRRSPARVFASSTSPR-SSPKRSAASATKNRSAP---CSAKRNWPDHTAPPRAGLFALPPEAGRKPQGGLV&lt;/Hsp_qseq&gt; &lt;Hsp_hseq&gt;APPAQKPPAQPATAAATTAPKATPQTQPPTRAQTQTAPPPPSAAT-----AAAQVPPQ------PPSSQPAAKPRGAPPAPPAPP--PPSAQTTLPRPAAPPAPPPPS---AQTTLPRPAPPPPSAPAATPTPPAPGPAPSAKKSDGDRIVEPKAG---APPDVRDAKFGGKV&lt;/Hsp_hseq&gt; &lt;Hsp_midline&gt;AP +Q+P A ++ + K P + T + T A P + T A PP+ PP S P A R P AP P P P+ P P+ A +T PR + P SA +AT AP SAK++ D P+AG PP+ GG V&lt;/Hsp_midline&gt; &lt;/Hsp&gt; &lt;/Hit_hsps&gt; &lt;/Hit&gt; &lt;/Iteration_hits&gt; &lt;Iteration_stat&gt; &lt;Statistics&gt; &lt;Statistics_db-num&gt;68007&lt;/Statistics_db-num&gt; &lt;Statistics_db-len&gt;19518578&lt;/Statistics_db-len&gt; &lt;Statistics_hsp-len&gt;0&lt;/Statistics_hsp-len&gt; &lt;Statistics_eff-space&gt;0&lt;/Statistics_eff-space&gt; &lt;Statistics_kappa&gt;0.041&lt;/Statistics_kappa&gt; &lt;Statistics_lambda&gt;0.267&lt;/Statistics_lambda&gt; &lt;Statistics_entropy&gt;0.14&lt;/Statistics_entropy&gt; &lt;/Statistics&gt; &lt;/Iteration_stat&gt; &lt;/Iteration&gt; </code></pre> <p>basically each query search creates an Iteration element. each iteration can have multiple hit which in turn can have multiple HSPs. I would like to get only the first hit and it's first HSP from each iteration. if the BLAST found no hits I would like to ignore the iteration. I worked up this simple code:</p> <pre><code>#!/usr/bin/env python from elementtree.ElementTree import parse from elementtree import ElementTree as ET file = open("/Applications/blast/blanes_viral_nr_results.xml", "r") save_file = open("/Applications/blast/Blast_parse_ET.txt", 'w') tree = parse(file) elem = tree.getroot() print elem Per_ID = () save_file.write('&gt;%s\t%s\t%s\t%s\t%s\t%s\t\n\n\n\n' % ("It_Num\t", "It_ID\t", "Hit_Def\t", "Num\t", "ID\t", "ACC\t")) iteration = tree.findall('BlastOutput_iterations/Iteration') for iteration in iteration: for hit in iteration.findall('Iteration_hits/Hit'): It_Num = iteration.findtext('Iteration_iter-num') It_ID = iteration.findtext('Iteration_query-def') Hit_Def = hit.findtext('Hit_def') Num = hit.findtext('Hit_num') ID = hit.findtext('Hit_id') DEF = hit.findtext('Hit_def') ACC = hit.findtext('Hit_accession') save_file.write('&gt;%s\t%s\t%s\t%s\t%s\t%s\t' % (It_Num, It_ID[12:26], Hit_Def[1:10], Num, ID, ACC,)) for hsp in hit.findall('Hit_hsps'): HSPN = hsp.findtext('Hsp/Hsp_num') identities = hsp.findtext('Hsp/Hsp_identity') #print 'id: ', identities.rjust(4), length = hsp.findtext('Hsp/Hsp_align-len') #print 'len:', length.rjust(4), Per_ID = int(identities) * 100.0 / int(length) #print hsp.findtext('Hsp/Hsp_qseq')[:50] #print hsp.findtext('Hsp/Hsp_midline')[:50] #print hsp.findtext('Hsp/Hsp_hseq')[:50] save_file.write('%s\t%s\t%s\%st\n' % ('***', '%', HSPN, Per_ID)) save_file.write('n\n' % ()) </code></pre> <p>any help would be greatly appriciated!</p>
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