Changeset 247
Legend:
- Unmodified
- Added
- Removed
- Modified
- Copied
- Moved
lib/GI.pm
r244 r247 242 242 my $keepers = blastx($chunk, 243 243 $t_file, 244 undef,245 244 $the_void, 246 245 $p_safe_id.".".$piece->[0]->{b}.".".$piece->[0]->{e}, … … 272 271 my $keepers = tblastx($chunk, 273 272 $t_file, 274 undef,275 273 $the_void, 276 274 $p_safe_id.".".$piece->[0]->{b}.".".$piece->[0]->{e}, … … 1238 1236 my $cpus = $CTL_OPT->{cpus}; 1239 1237 my $formater = $CTL_OPT->{_formater}; 1238 my $softmask = $CTL_OPT->{softmask}; 1239 my $org_type = $CTL_OPT->{organism_type}; 1240 1240 1241 1241 #build names for files to use and copy … … 1285 1285 $split_hit, 1286 1286 $cpus, 1287 $CTL_OPT->{organism_type} 1287 $org_type, 1288 $softmask 1288 1289 ); 1289 1290 … … 1353 1354 my $chunk = shift; 1354 1355 my $db = shift; 1355 my $old_db = shift;1356 1356 my $the_void = shift; 1357 1357 my $seq_id = shift; 1358 1358 my $CTL_OPT = shift; 1359 my $rank = shift;1360 1359 my $LOG = shift; 1361 1360 … … 1368 1367 my $cpus = $CTL_OPT->{cpus}; 1369 1368 my $formater = $CTL_OPT->{_formater}; 1369 my $softmask = $CTL_OPT->{softmask}; 1370 my $org_type = $CTL_OPT->{organism_type}; 1370 1371 1371 1372 my ($db_n) = $db =~ /([^\/]+)$/; … … 1387 1388 $split_hit, 1388 1389 $cpus, 1389 $CTL_OPT->{organism_type} 1390 $org_type, 1391 $softmask 1390 1392 ); 1391 1393 … … 1413 1415 #----------------------------------------------------------------------------- 1414 1416 sub runBlastn { 1415 my $q_file = shift;1416 my $db = shift;1417 my $out_file = shift;1418 my $blast = shift;1417 my $q_file = shift; 1418 my $db = shift; 1419 my $out_file = shift; 1420 my $blast = shift; 1419 1421 my $eval_blast = shift; 1420 my $split_hit = shift; 1421 my $cpus = shift; 1422 my $org_type = shift; 1422 my $split_hit = shift; 1423 my $cpus = shift; 1424 my $org_type = shift; 1425 my $softmask = shift; 1423 1426 1424 1427 my $command = $blast; 1425 1428 if ($command =~ /blastn$/) { 1426 1429 $command .= " $db $q_file B=100000 V=100000 E=$eval_blast"; 1427 $command .= " wordmask=seg";1430 $command .= ($softmask) ? " wordmask=seg" : " filter=seg";; 1428 1431 $command .= " R=3"; 1429 1432 $command .= " W=15"; … … 1502 1505 my $formater = $CTL_OPT->{_formater}; 1503 1506 my $softmask = ($rflag) ? 1 : $CTL_OPT->{softmask}; #always on for repeats 1507 my $org_type = $CTL_OPT->{organism_type}; 1504 1508 1505 1509 #build names for files to use and copy … … 1549 1553 $split_hit, 1550 1554 $cpus, 1551 $ softmask,1552 $ CTL_OPT->{organism_type}1555 $org_type, 1556 $softmask 1553 1557 ); 1554 1558 … … 1618 1622 my $chunk = shift; 1619 1623 my $db = shift; 1620 my $old_db = shift;1621 1624 my $the_void = shift; 1622 1625 my $seq_id = shift; 1623 1626 my $CTL_OPT = shift; 1624 my $rank = shift;1625 1627 my $LOG = shift; 1626 1628 1627 my $rflag = 1 if($ old_db && $CTL_OPT->{repeat_protein} eq $old_db); #am I running repeat data?1629 my $rflag = 1 if($db && $CTL_OPT->{repeat_protein} eq $db); #am I running repeat data? 1628 1630 1629 1631 my $blastx = $CTL_OPT->{_blastx}; … … 1636 1638 my $formater = $CTL_OPT->{_formater}; 1637 1639 my $softmask = ($rflag) ? 1 : $CTL_OPT->{softmask}; 1640 my $org_type = $CTL_OPT->{organism_type}; 1638 1641 1639 1642 my ($db_n) = $db =~ /([^\/]+)$/; … … 1656 1659 $split_hit, 1657 1660 $cpus, 1658 $ softmask,1659 $ CTL_OPT->{organism_type}1661 $org_type, 1662 $softmask 1660 1663 ); 1661 1664 … … 1707 1710 my $split_hit = shift; 1708 1711 my $cpus = shift; 1712 my $org_type = shift; 1709 1713 my $softmask = shift; 1710 my $org_type = shift; 1714 1711 1715 1712 1716 my $command = $blast; … … 1781 1785 my $formater = $CTL_OPT->{_formater}; 1782 1786 my $softmask = $CTL_OPT->{softmask}; 1787 my $org_type = $CTL_OPT->{organism_type}; 1783 1788 1784 1789 #build names for files to use and copy … … 1828 1833 $split_hit, 1829 1834 $cpus, 1830 $ softmask,1831 $ CTL_OPT->{organism_type}1835 $org_type, 1836 $softmask 1832 1837 ); 1833 1838 … … 1897 1902 my $chunk = shift; 1898 1903 my $db = shift; 1899 my $old_db = shift;1900 1904 my $the_void = shift; 1901 1905 my $seq_id = shift; 1902 1906 my $CTL_OPT = shift; 1903 my $rank = shift;1904 1907 my $LOG = shift; 1905 1908 … … 1913 1916 my $formater = $CTL_OPT->{_formater}; 1914 1917 my $softmask = $CTL_OPT->{softmask}; 1918 my $org_type = $CTL_OPT->{organism_type}; 1915 1919 1916 1920 my ($db_n) = $db =~ /([^\/]+)$/; … … 1932 1936 $split_hit, 1933 1937 $cpus, 1934 $ softmask,1935 $ CTL_OPT->{organism_type}1938 $org_type, 1939 $softmask 1936 1940 ); 1937 1941 … … 1966 1970 my $split_hit = shift; 1967 1971 my $cpus = shift; 1972 my $org_type = shift; 1968 1973 my $softmask = shift; 1969 my $org_type = shift; 1974 1970 1975 1971 1976 my $command = $blast;
