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@@ -722,8 +722,7 @@ function convert_tsv2gff3($blast_tsv,$blast_gff){
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continue;
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continue;
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}
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}
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- // Assign the important parts of the time to readable variables.
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- // Each line has the following Fields:
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+ // Each line has the following parts:
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// 0: query id,
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// 0: query id,
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// 1: subject id,
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// 1: subject id,
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// 2: % identity,
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// 2: % identity,
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@@ -736,10 +735,14 @@ function convert_tsv2gff3($blast_tsv,$blast_gff){
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// 9: s. end,
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// 9: s. end,
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// 10: evalue,
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// 10: evalue,
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// 11: bit score
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// 11: bit score
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+ $parts = preg_split('/\t/', $line);
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+
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+ // Assign the important parts of the time to readable variables.
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$hitname = $parts[1];
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$hitname = $parts[1];
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$hspInfo = "$parts[0],$parts[8],$parts[9],$parts[6],$parts[7]";
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$hspInfo = "$parts[0],$parts[8],$parts[9],$parts[6],$parts[7]";
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$eval = $parts[10];
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$eval = $parts[10];
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$results[$hitname][$hspInfo] = $eval;
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$results[$hitname][$hspInfo] = $eval;
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+
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$IDs = array();
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$IDs = array();
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$count = 0;
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$count = 0;
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$last_q = NULL;
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$last_q = NULL;
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@@ -779,7 +782,7 @@ function convert_tsv2gff3($blast_tsv,$blast_gff){
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$last_q = $q;
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$last_q = $q;
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}
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}
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}
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}
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- }//end of tsv file while
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+ }
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// Now can print a parent gff line and all the children.
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// Now can print a parent gff line and all the children.
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// Note: the evalues seem to be sorted properly without actually sorting them.
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// Note: the evalues seem to be sorted properly without actually sorting them.
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Lacey Sanderson