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<p><font size="2" face="sans-serif">Hello Gentlemen,</font><br>
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<font size="2" face="sans-serif">I am using BioPerl to a parse a blast output file but have run into some difficulties. I've pin pointed the problem and have pasted an example below. If you look at query position 223-224 you will see a large insertion 65ish nucleotides. Since the insertion spans the entire line there are no nucleotide position numbers at the end or beginning of the line nor any nucleotides within the line (dashes only). </font><br>
<font size="2" face="sans-serif">When the SearchIO parser encounters this record it dies with the error</font><br>
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<font size="2" face="sans-serif">------------- EXCEPTION: Bio::Root::Exception -------------</font><br>
<font size="2" face="sans-serif">MSG: no data for midline Query ------------------------------------------------------------</font><br>
<font size="2" face="sans-serif">STACK: Error::throw</font><br>
<font size="2" face="sans-serif">STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368</font><br>
<font size="2" face="sans-serif">STACK: Bio::SearchIO::blast::next_result /usr/local/share/perl5/Bio/SearchIO/blast.pm:1805</font><br>
<font size="2" face="sans-serif">STACK: BlastParseNucleotideForDBTopHitCONTIGSQUERY.pl:24</font><br>
<font size="2" face="sans-serif">-----------------------------------------------------------</font><br>
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<font size="2" face="sans-serif">Has anyone encountered this problem before? Am I doing something wrong?</font><br>
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<font size="2" face="sans-serif">Thanks</font><br>
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<font size="2" face="sans-serif">Jeff Kittrell<br>
Department of Genetics, Cell Biology & Anatomy<br>
University of Nebraska Medical Center<br>
985805 Nebraska Medical Center<br>
Omaha, NE 68198-5805</font><br>
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<font size="2" face="Courier New">Query= 78065535</font><br>
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<font size="2" face="Courier New">Length=523</font><br>
<font size="2" face="Courier New"> Score E</font><br>
<font size="2" face="Courier New">Sequences producing significant alignments: (Bits) Value</font><br>
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<font size="2" face="Courier New"> gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled... 576 1e-163</font><br>
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<font size="2" face="Courier New">> gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled </font><br>
<font size="2" face="Courier New">receptor 123 (GPR123), mRNA</font><br>
<font size="2" face="Courier New">Length=4298</font><br>
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<font size="2" face="Courier New"> Score = 576 bits (638), Expect = 1e-163</font><br>
<font size="2" face="Courier New"> Identities = 466/583 (80%), Gaps = 82/583 (14%)</font><br>
<font size="2" face="Courier New"> Strand=Plus/Minus</font><br>
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<font size="2" face="Courier New">Query 1 CAGGACTCCGTGG-----ATGGCATCTCGGGCAGGGCCACGCTGGGGTCTGGGTGGGTCC 55</font><br>
<font size="2" face="Courier New"> ||||||||||||| | ||||||||||||||||||| |||||||||| ||||||||</font><br>
<font size="2" face="Courier New">Sbjct 2537 CAGGACTCCGTGGGCAGCAGGGCATCTCGGGCAGGGCCATGCTGGGGTCTCAGTGGGTCC 2478</font><br>
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<font size="2" face="Courier New">Query 56 TTTGATGGAAGCCCCTGCTCTGCCTCTGGGGCGCCCCAGGACTGGAGGCCACAGGACAGA 115</font><br>
<font size="2" face="Courier New"> |||||||||| |||||||||||||||| ||| ||||||||||||||| ||||||||||||</font><br>
<font size="2" face="Courier New">Sbjct 2477 TTTGATGGAATCCCCTGCTCTGCCTCTAGGGTGCCCCAGGACTGGAGACCACAGGACAGA 2418</font><br>
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<font size="2" face="Courier New">Query 116 AACCAGATGACCTTGTGCAGGGACGAGCACGTGGAACTGGGATAAAAGGAGTGGGCGTGG 175</font><br>
<font size="2" face="Courier New"> |||| ||||||| ||||| ||||| |||||| |||| |||||||| |||||||||||||</font><br>
<font size="2" face="Courier New">Sbjct 2417 AACCGGATGACCGTGTGC-GGGACCAGCACGCGGAATTGGGATAAGGGGAGTGGGCGTGG 2359</font><br>
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<font size="2" face="Courier New">Query 176 CCCAGAGCTTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGT------------ 223</font><br>
<font size="2" face="Courier New"> ||| |||| ||||||||||||||||||||||||||||||||||||||| </font><br>
<font size="2" face="Courier New">Sbjct 2358 CCCGGAGCGTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGTGTGATCACAAGG 2299</font><br>
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<font size="2" face="Courier New">Query ------------------------------------------------------------ </font><br>
<font size="2" face="Courier New"> </font><br>
<font size="2" face="Courier New">Sbjct 2298 AAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGG 2239</font><br>
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<font size="2" face="Courier New">Query 224 ---GTGAACTGCTTCCGAAAGGTGGGGTCACTTTGGTGCCCCCAGTGACCTCATGTGGCA 280</font><br>
<font size="2" face="Courier New"> |||||| ||||| |||||| |||||||||| ||| ||||||||||||||||||||||</font><br>
<font size="2" face="Courier New">Sbjct 2238 GGTGTGAACGGCTTCTGAAAGGCGGGGTCACTTCGGTACCCCCAGTGACCTCATGTGGCA 2179</font><br>
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<font size="2" face="Courier New">Query 281 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACTGTGTCCCCTG-CTCCGCC 339</font><br>
<font size="2" face="Courier New"> ||||||||||||||||||||||||||||||||||||||||| |||||| ||| | || |</font><br>
<font size="2" face="Courier New">Sbjct 2178 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACCGTGTCCTCTGCCCCCATC 2119</font><br>
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<font size="2" face="Courier New">Query 340 TACACAGTAGTTTCATTTTTCCAGGGTCCTGTTCGGATGTTGCCGGTCCCATCGGTGCCA 399</font><br>
<font size="2" face="Courier New"> |||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||||</font><br>
<font size="2" face="Courier New">Sbjct 2118 TACACAGTAGTTTCGTTTTTCCAGGGTCCCGTTCGGATGTTGCCGGTCCCGTCGGTGCCA 2059</font><br>
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<font size="2" face="Courier New">Query 400 AACGGCAGGTCTTCTAGCAAGTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 459</font><br>
<font size="2" face="Courier New"> ||||||||| |||||||||| |||||||||||||||||||||||||||||||||||||||</font><br>
<font size="2" face="Courier New">Sbjct 2058 AACGGCAGGCCTTCTAGCAATTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 1999</font><br>
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<font size="2" face="Courier New">Query 460 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAGGTGACCAGGCC 502</font><br>
<font size="2" face="Courier New"> ||||||||||||||||||||||||||||||| ||| || ||||</font><br>
<font size="2" face="Courier New">Sbjct 1998 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAAGTGGCCGGGCC 1956</font><br>
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<font size="2" face="Courier New">Lambda K H</font><br>
<font size="2" face="Courier New"> 0.634 0.408 0.912 </font><br>
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<font size="2" face="Courier New">Gapped</font><br>
<font size="2" face="Courier New">Lambda K H</font><br>
<font size="2" face="Courier New"> 0.625 0.410 0.780 </font><br>
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<font size="2" face="Courier New">Effective search space used: 47712920310</font><br>
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