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How to delete lines like this??

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# 1  
Old 04-18-2014
How to delete lines like this??
hi, i have a very large file like this:

Code:
 <Iteration>
      <Iteration_iter-num>1073</Iteration_iter-num>
      <Iteration_query-ID>lcl|1073_0</Iteration_query-ID>
      <Iteration_query-def>contig01073  length=1  numreads=7  gene=isogroup00087  status=icl_thresh</Iteration_query-def>
      <Iteration_query-len>1</Iteration_query-len>
      <Iteration_stat>
        <Statistics>
          <Statistics_db-num>31601460</Statistics_db-num>
          <Statistics_db-len>10937649309</Statistics_db-len>
          <Statistics_hsp-len>0</Statistics_hsp-len>
          <Statistics_eff-space>0</Statistics_eff-space>
          <Statistics_kappa>0.041</Statistics_kappa>
          <Statistics_lambda>0.267</Statistics_lambda>
          <Statistics_entropy>0.14</Statistics_entropy>
        </Statistics>
      </Iteration_stat>
      <Iteration_message>No hits found</Iteration_message>
    </Iteration>
    <Iteration>
      <Iteration_iter-num>1074</Iteration_iter-num>
      <Iteration_query-ID>lcl|1074_0</Iteration_query-ID>
      <Iteration_query-def>contig01074  length=737  numreads=30  gene=isogroup00088  status=isotig</Iteration_query-def>
      <Iteration_query-len>737</Iteration_query-len>
      <Iteration_hits>
        <Hit>
          <Hit_num>1</Hit_num>
          <Hit_id>gi|222630026|gb|EEE62158.1|</Hit_id>
          <Hit_def>hypothetical protein OsJ_16945 [Oryza sativa Japonica Group]</Hit_def>
          <Hit_accession>EEE62158</Hit_accession>
          <Hit_len>89</Hit_len>
          <Hit_hsps>
            <Hsp>
              <Hsp_num>1</Hsp_num>
              <Hsp_bit-score>69.707</Hsp_bit-score>
              <Hsp_score>169</Hsp_score>
              <Hsp_evalue>1.38738e-12</Hsp_evalue>
              <Hsp_query-from>275</Hsp_query-from>
              <Hsp_query-to>457</Hsp_query-to>
              <Hsp_hit-from>30</Hsp_hit-from>
              <Hsp_hit-to>89</Hsp_hit-to>
              <Hsp_query-frame>2</Hsp_query-frame>
              <Hsp_identity>32</Hsp_identity>
              <Hsp_positive>40</Hsp_positive>
              <Hsp_align-len>61</Hsp_align-len>
              <Hsp_qseq>TPSADAVGPCAACTILHRRCTDKCYLASYFPQGVEPHNFTVVDSLFGLSNVVELLQQNSNS</Hsp_qseq>
              <Hsp_hseq>TTTTVVLSPCAACKILRRRCVDRCVLAPYFPP-TEPHKFTTAHRVFGASNIIKLLQASSYS</Hsp_hseq>
              <Hsp_midline>T +   + PCAAC IL RRC D+C LA YFP   EPH FT    +FG SN+++LLQ +S S</Hsp_midline>
            </Hsp>
          </Hit_hsps>
        </Hit>
        <Hit>
          <Hit_num>2</Hit_num>
          <Hit_id>gi|413950127|gb|AFW82776.1|</Hit_id>
          <Hit_def>putative LOB domain-containing family protein [Zea mays]</Hit_def>
          <Hit_accession>AFW82776</Hit_accession>
          <Hit_len>212</Hit_len>
          <Hit_hsps>
            <Hsp>
              <Hsp_num>1</Hsp_num>
              <Hsp_bit-score>70.4774</Hsp_bit-score>
              <Hsp_score>171</Hsp_score>
              <Hsp_evalue>1.04484e-11</Hsp_evalue>
              <Hsp_query-from>278</Hsp_query-from>
              <Hsp_query-to>445</Hsp_query-to>
              <Hsp_hit-from>29</Hsp_hit-from>
              <Hsp_hit-to>83</Hsp_hit-to>
              <Hsp_query-frame>2</Hsp_query-frame>
              <Hsp_identity>31</Hsp_identity>
              <Hsp_positive>38</Hsp_positive>
              <Hsp_align-len>56</Hsp_align-len>
              <Hsp_qseq>PSADAVGPCAACTILHRRCTDKCYLASYFPQGVEPHNFTVVDSLFGLSNVVELLQQ</Hsp_qseq>
              <Hsp_hseq>PPAPALSPCAACKILRRRCVDRCVLAPYFPP-TEPHKFATAHRVFGASNIIKLLQE</Hsp_hseq>
              <Hsp_midline>P A A+ PCAAC IL RRC D+C LA YFP   EPH F     +FG SN+++LLQ+</Hsp_midline>
            </Hsp>
          </Hit_hsps>
        </Hit>
        <Hit>
          <Hit_num>3</Hit_num>
          <Hit_id>gi|413942115|gb|AFW74764.1|</Hit_id>
          <Hit_def>putative LOB domain-containing family protein [Zea mays]</Hit_def>
          <Hit_accession>AFW74764</Hit_accession>
          <Hit_len>221</Hit_len>
          <Hit_hsps>
            <Hsp>
              <Hsp_num>1</Hsp_num>
              <Hsp_bit-score>68.9366</Hsp_bit-score>
              <Hsp_score>167</Hsp_score>
              <Hsp_evalue>4.36373e-11</Hsp_evalue>
              <Hsp_query-from>278</Hsp_query-from>
              <Hsp_query-to>445</Hsp_query-to>
              <Hsp_hit-from>34</Hsp_hit-from>

If the length <100, i wanna delete the information of that particular cotig from <Iteration> to </Iteration>..

How could i achieve??

Thanks a lot
# 2  
Old 04-19-2014
Code:
awk -F"</Iteration>" -v RS="" '{for(i=1;i<=NF;i++)if(match($i,"length="))if(substr($i,RSTART+7,3)>100)printf("%s\n</Iteration>",$i)}' test.txt

# 3  
Old 04-19-2014
To accommodate the length 100, you might want to make the test >=100.
# 4  
Old 04-22-2014
hi, itkamaraj,
Thanks for your response, but it did not work. It seems only the length=100, 100x, 100xx were deleted.

Quote:
Originally Posted by itkamaraj
Code:
awk -F"</Iteration>" -v RS="" '{for(i=1;i<=NF;i++)if(match($i,"length="))if(substr($i,RSTART+7,3)>100)printf("%s\n</Iteration>",$i)}' test.txt

# 5  
Old 04-22-2014
replace 'file' with your input filename
Code:
awk 'NR > 0 && $0 ~ /<Iteration>/{print ""}1' file | \
awk '{n=split($0, a, "[ =]");
  for(i = 1; i <= n; i++)
    {if(a[i] == "length" && a[i+1] >= 100)
      {print $0; next}}}' RS=

Last edited by SriniShoo; 04-22-2014 at 02:35 PM.. Reason: correction
# 6  
Old 04-22-2014
Quote:
Originally Posted by the_simpsons
hi, itkamaraj,
Thanks for your response, but it did not work. It seems only the length=100, 100x, 100xx were deleted.
Replace the 3 by a 9!
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