# HG changeset patch # User pmac # Date 1464767843 14400 # Node ID 3ddf2607e3a2a35d5e01696b732de83f1c6c7dce Uploaded diff -r 000000000000 -r 3ddf2607e3a2 reformatPlatesTabularToLinear.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reformatPlatesTabularToLinear.pl Wed Jun 01 03:57:23 2016 -0400 @@ -0,0 +1,108 @@ +############################################################################### +# This script converts plate data from tabular to linear format. +# +# Args: +# input file: +# a text file containing a set of tabular data in vertical layout in either 384/96 well format, +# typically generated from synergy or cellomics software. +# +# Returns: +# For each input file, a linear version of tabular data is returned with +# "Well" column inserted as first column and "Table_ for all subsequent +# columns where is ordinal number of tables in file. +# +# Author: jason ellul +############################################################################### + +use strict; +use warnings; +use IO::Handle; +use File::Temp qw/ tempfile tempdir /; +my $tdir = tempdir( CLEANUP => 0 ); + +# check to make sure having correct input and output files +my $usage = "usage: reformatPlatesTabularToLinear.pl [TABULAR.in] [TABULAR.out] \n"; +die $usage unless @ARGV == 2; + +#get the input arguments +my $tabularPlateTable = $ARGV[0]; +my $linearPlateTable = $ARGV[1]; + +#open the input files +open (INPUT, "<", $tabularPlateTable) || die("Could not open file $tabularPlateTable \n"); +open (OUTPUT1, ">", $linearPlateTable) || die("Could not open file $linearPlateTable \n"); + +#variable to store the name of the R script file +my $r_script; + +# R script to implement the calcualtion of q-values based on multiple simultaneous tests p-values +# construct an R script file and save it in a temp directory +#chdir $tdir; +$r_script = "reformatPlatesTabularToLinear.r"; + +open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; +print Rcmd " + #options(show.error.messages = FALSE); + + #read the plates table + tables <- scan(\"$tabularPlateTable\", sep=\"\\n\", what=\"character\", quiet = TRUE); + + # if there any lines which when all tabs/spaces are removed amounts to an empty line then remove this line + if(length(which(gsub(\"\\t|\\\\s\", \"\", tables) == \"\")) > 0) tables <- tables[-which(gsub(\"\\t|\\\\s\", \"\", tables) == \"\")]; + + # search for occurrences of the below column header line in the tables data. + colheads <- grep(\"^\\t 1 \\t 2 \\t 3 \\t 4 \\t 5 \\t 6 \\t 7 \\t 8 \\t 9 \\t 10 \\t 11 \\t 12 \\t 13 \\t 14 \\t 15 \\t 16 \\t 17 \\t 18 \\t 19 \\t 20 \\t 21 \\t 22 \\t 23 \\t 24 \", tables); + # if not found we assume the tables are 96-well + if(length(colheads) == 0) { + platetype <- 96; + colheads <- grep(\"^\\t 1 \\t 2 \\t 3 \\t 4 \\t 5 \\t 6 \\t 7 \\t 8 \\t 9 \\t 10 \\t 11 \\t 12 \", tables); + nc <- 12; + nr <- 8; + } else { + # else dealing with 384-well + platetype <- 384; + nc <- 24; + nr <- 16; + } + # set up the structure of the output matrix + linearized.data <- matrix(NA, nrow=platetype, ncol=length(colheads)+1); + + # generate the well column + well.name <- NULL; + for(i in LETTERS[1:nr]) { + for(j in c(\"01\", \"02\", \"03\", \"04\", \"05\", \"06\", \"07\", \"08\", \"09\", 10:nc)) { + well.name <- c(well.name , paste(i, j, sep=\"\")); + } + } + + # set up the column names for the output matrix + colnames(linearized.data) <- c(\"\\\\#Well\", paste(\"Table\", 1:length(colheads), sep=\"_\")); + linearized.data[, \"\\\\#Well\"] <- well.name; + colnames(linearized.data)[1] <- sub(\"^.\", \"\", colnames(linearized.data)[1]); + + for(i in 1:length(colheads)) { + for(j in 1:nr) { + # for each row of current table split the data by tab. + tab.row <- strsplit(tables[colheads[i]+j], \"\\t\"); + # assign the current row from the current table + # the min part of code takes account for table rows which may not have the full set of values expected + linearized.data[((j-1)*nc+1):((j*nc)-(nc-min(nc+1, length(tab.row[[1]]))+1)), i+1] <- tab.row[[1]][2:min(length(tab.row[[1]]),(nc+1))]; + } + } + linearized.data <- as.data.frame(linearized.data, stringsAsFactors=FALSE); + # ensure all columns excluding first one are numeric + #for(i in 2:ncol(linearized.data)) { + # linearized.data[,i] <- as.numeric(linearized.data[,i]); + #} + + #save the linear plate data + write.table(linearized.data, file=\"$linearPlateTable\", quote=F, sep=\"\\t\", row.names=F); + #eof\n"; + +close Rcmd; + +system("R --no-restore --no-save --no-readline < $r_script > $r_script.out"); + +#close the input and output files +close(OUTPUT1); +close(INPUT); diff -r 000000000000 -r 3ddf2607e3a2 reformatPlatesTabularToLinear.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reformatPlatesTabularToLinear.xml Wed Jun 01 03:57:23 2016 -0400 @@ -0,0 +1,465 @@ + + + + reformatPlatesTabularToLinear.pl $inputFile1 $outputFile1 + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**What it does** + +This program converts a plates table from a tabular format to a linear format. + + +**Example** + +If the plates table consisted of:: + + Feature: ValidCellCount + + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 + A 1654 1719 1624 1518 1587 1517 1638 1733 1617 1722 1665 1536 1636 1691 1773 1554 1651 1670 1748 1541 1549 1550 1615 + B 1553 1588 1557 1786 1635 1679 1533 1720 1562 1577 1713 1526 1559 1706 1690 1707 1651 1687 1584 1638 1722 1562 1696 + C 1579 1568 1684 1501 1546 1718 1569 1532 1530 1572 1517 1573 1518 1585 1595 1505 1593 1735 1548 1534 1512 1577 1519 + D 1551 502 1764 1827 1587 1655 1625 1549 1798 1689 1588 1630 1620 1595 1711 1504 1511 1645 1608 1745 1525 1646 674 + E 1809 1624 1791 1556 1530 1604 1610 1620 1506 1609 1620 1531 1534 1723 1600 1480 1714 1574 1658 1634 1632 1671 1639 + F 1804 1815 1644 1618 1686 1523 1501 1587 1502 1742 1621 1638 1640 1588 1542 1720 1503 1788 1571 1547 1653 1752 1687 + G 1540 1567 1587 1564 1671 1552 1555 1571 1693 1692 1617 1590 1589 1546 1648 1583 1538 1560 1553 1598 1561 1523 1599 + H 1700 513 1615 1656 1796 1547 1563 1598 1555 1621 1644 1760 1525 1541 1635 1527 1651 1643 1593 1551 1507 1504 522 + I 1604 1591 1626 1585 1522 1546 1520 1582 1664 1589 1508 1505 1577 1657 1560 1561 1597 1505 1646 1579 1602 1621 1583 + J 1520 1577 1692 1510 1691 1747 1744 1724 1666 1645 1637 1706 1672 1522 1535 1528 1569 1592 1812 1806 1525 1675 1540 + K 1626 1513 1624 1530 1650 1610 1644 1522 1544 1532 1229 1520 1540 1630 1668 1519 1657 1509 1543 1513 1564 1660 1632 + L 1676 507 1682 1595 1557 1593 1734 1519 1550 1528 1781 1500 1573 1524 1735 1523 1503 1621 1559 1795 1667 1560 420 + M 1625 1548 1538 1731 1607 1637 1544 1703 1617 1635 1528 1532 1583 1555 1551 1580 1655 1662 1591 1758 1623 1597 1561 + N 1660 592 1595 1527 1745 1543 1529 1691 1705 1612 1769 1624 1673 1683 1637 1786 1593 1636 1614 1650 1553 1671 628 + O 1692 1701 1611 1370 1537 1538 1582 1515 1587 1582 1660 1544 1544 1603 1592 1518 1606 1565 1617 1543 1649 1710 1788 + P 1818 1611 1736 1642 1557 1606 1558 1627 1579 1733 1520 1558 1804 1630 1576 1740 1578 1544 1692 1560 1552 1790 1537 + + Feature: ValidFieldCount + + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 + A 6 8 19 6 12 8 9 7 6 8 7 9 13 8 8 12 13 7 7 7 9 8 6 + B 5 8 6 7 6 6 6 7 6 6 6 6 7 7 6 6 6 7 6 6 6 6 9 + C 6 14 8 12 22 9 11 8 11 12 12 8 21 16 17 9 10 7 8 10 6 17 19 + D 7 25 6 7 6 6 7 6 7 6 7 7 7 6 6 6 6 6 6 7 5 7 25 + E 7 8 6 17 7 10 14 11 7 15 7 19 8 7 15 25 7 9 8 7 10 8 8 + F 6 6 7 6 6 8 6 7 6 6 6 8 7 6 6 6 7 6 6 5 8 6 7 + G 6 22 7 18 9 18 7 11 7 7 11 7 16 8 8 10 17 9 6 9 16 11 13 + H 6 25 6 6 6 6 7 6 6 6 7 7 6 7 6 6 6 7 5 8 6 5 25 + I 7 9 11 11 17 9 6 9 9 10 10 23 7 12 7 12 14 13 9 15 13 12 6 + J 6 17 8 5 7 7 7 8 6 6 6 7 6 7 5 6 6 8 7 7 6 7 22 + K 6 6 7 7 11 11 11 11 14 7 25 11 9 10 8 17 8 21 7 12 7 10 6 + L 7 25 6 7 6 7 6 6 6 6 7 6 6 6 7 5 6 6 6 6 6 8 25 + M 6 19 25 7 14 7 9 9 6 8 16 6 7 8 9 15 6 7 8 8 8 6 18 + N 6 25 7 5 6 6 5 6 7 6 7 6 7 7 6 7 6 6 6 6 6 6 25 + O 6 8 10 25 10 14 8 11 6 6 10 10 8 9 12 11 6 10 6 18 7 8 7 + P 7 5 7 6 5 6 6 6 6 6 6 7 7 6 6 7 6 6 6 6 6 7 6 + +Running the program will give the following output:: + + #Well Table_1 Table_2 + A01 1654 6 + A02 1719 8 + A03 1624 19 + A04 1518 6 + A05 1587 12 + A06 1517 8 + A07 1638 9 + A08 1733 7 + A09 1617 6 + A10 1722 8 + A11 1665 7 + A12 1536 9 + A13 1636 13 + A14 1691 8 + A15 1773 8 + A16 1554 12 + A17 1651 13 + A18 1670 7 + A19 1748 7 + A20 1541 7 + A21 1549 9 + A22 1550 8 + A23 1615 6 + A24 NA NA + B01 1553 5 + B02 1588 8 + B03 1557 6 + B04 1786 7 + B05 1635 6 + B06 1679 6 + B07 1533 6 + B08 1720 7 + B09 1562 6 + B10 1577 6 + B11 1713 6 + B12 1526 6 + B13 1559 7 + B14 1706 7 + B15 1690 6 + B16 1707 6 + B17 1651 6 + B18 1687 7 + B19 1584 6 + B20 1638 6 + B21 1722 6 + B22 1562 6 + B23 1696 9 + B24 NA NA + C01 1579 6 + C02 1568 14 + C03 1684 8 + C04 1501 12 + C05 1546 22 + C06 1718 9 + C07 1569 11 + C08 1532 8 + C09 1530 11 + C10 1572 12 + C11 1517 12 + C12 1573 8 + C13 1518 21 + C14 1585 16 + C15 1595 17 + C16 1505 9 + C17 1593 10 + C18 1735 7 + C19 1548 8 + C20 1534 10 + C21 1512 6 + C22 1577 17 + C23 1519 19 + C24 NA NA + D01 1551 7 + D02 502 25 + D03 1764 6 + D04 1827 7 + D05 1587 6 + D06 1655 6 + D07 1625 7 + D08 1549 6 + D09 1798 7 + D10 1689 6 + D11 1588 7 + D12 1630 7 + D13 1620 7 + D14 1595 6 + D15 1711 6 + D16 1504 6 + D17 1511 6 + D18 1645 6 + D19 1608 6 + D20 1745 7 + D21 1525 5 + D22 1646 7 + D23 674 25 + D24 NA NA + E01 1809 7 + E02 1624 8 + E03 1791 6 + E04 1556 17 + E05 1530 7 + E06 1604 10 + E07 1610 14 + E08 1620 11 + E09 1506 7 + E10 1609 15 + E11 1620 7 + E12 1531 19 + E13 1534 8 + E14 1723 7 + E15 1600 15 + E16 1480 25 + E17 1714 7 + E18 1574 9 + E19 1658 8 + E20 1634 7 + E21 1632 10 + E22 1671 8 + E23 1639 8 + E24 NA NA + F01 1804 6 + F02 1815 6 + F03 1644 7 + F04 1618 6 + F05 1686 6 + F06 1523 8 + F07 1501 6 + F08 1587 7 + F09 1502 6 + F10 1742 6 + F11 1621 6 + F12 1638 8 + F13 1640 7 + F14 1588 6 + F15 1542 6 + F16 1720 6 + F17 1503 7 + F18 1788 6 + F19 1571 6 + F20 1547 5 + F21 1653 8 + F22 1752 6 + F23 1687 7 + F24 NA NA + G01 1540 6 + G02 1567 22 + G03 1587 7 + G04 1564 18 + G05 1671 9 + G06 1552 18 + G07 1555 7 + G08 1571 11 + G09 1693 7 + G10 1692 7 + G11 1617 11 + G12 1590 7 + G13 1589 16 + G14 1546 8 + G15 1648 8 + G16 1583 10 + G17 1538 17 + G18 1560 9 + G19 1553 6 + G20 1598 9 + G21 1561 16 + G22 1523 11 + G23 1599 13 + G24 NA NA + H01 1700 6 + H02 513 25 + H03 1615 6 + H04 1656 6 + H05 1796 6 + H06 1547 6 + H07 1563 7 + H08 1598 6 + H09 1555 6 + H10 1621 6 + H11 1644 7 + H12 1760 7 + H13 1525 6 + H14 1541 7 + H15 1635 6 + H16 1527 6 + H17 1651 6 + H18 1643 7 + H19 1593 5 + H20 1551 8 + H21 1507 6 + H22 1504 5 + H23 522 25 + H24 NA NA + I01 1604 7 + I02 1591 9 + I03 1626 11 + I04 1585 11 + I05 1522 17 + I06 1546 9 + I07 1520 6 + I08 1582 9 + I09 1664 9 + I10 1589 10 + I11 1508 10 + I12 1505 23 + I13 1577 7 + I14 1657 12 + I15 1560 7 + I16 1561 12 + I17 1597 14 + I18 1505 13 + I19 1646 9 + I20 1579 15 + I21 1602 13 + I22 1621 12 + I23 1583 6 + I24 NA NA + J01 1520 6 + J02 1577 17 + J03 1692 8 + J04 1510 5 + J05 1691 7 + J06 1747 7 + J07 1744 7 + J08 1724 8 + J09 1666 6 + J10 1645 6 + J11 1637 6 + J12 1706 7 + J13 1672 6 + J14 1522 7 + J15 1535 5 + J16 1528 6 + J17 1569 6 + J18 1592 8 + J19 1812 7 + J20 1806 7 + J21 1525 6 + J22 1675 7 + J23 1540 22 + J24 NA NA + K01 1626 6 + K02 1513 6 + K03 1624 7 + K04 1530 7 + K05 1650 11 + K06 1610 11 + K07 1644 11 + K08 1522 11 + K09 1544 14 + K10 1532 7 + K11 1229 25 + K12 1520 11 + K13 1540 9 + K14 1630 10 + K15 1668 8 + K16 1519 17 + K17 1657 8 + K18 1509 21 + K19 1543 7 + K20 1513 12 + K21 1564 7 + K22 1660 10 + K23 1632 6 + K24 NA NA + L01 1676 7 + L02 507 25 + L03 1682 6 + L04 1595 7 + L05 1557 6 + L06 1593 7 + L07 1734 6 + L08 1519 6 + L09 1550 6 + L10 1528 6 + L11 1781 7 + L12 1500 6 + L13 1573 6 + L14 1524 6 + L15 1735 7 + L16 1523 5 + L17 1503 6 + L18 1621 6 + L19 1559 6 + L20 1795 6 + L21 1667 6 + L22 1560 8 + L23 420 25 + L24 NA NA + M01 1625 6 + M02 1548 19 + M03 1538 25 + M04 1731 7 + M05 1607 14 + M06 1637 7 + M07 1544 9 + M08 1703 9 + M09 1617 6 + M10 1635 8 + M11 1528 16 + M12 1532 6 + M13 1583 7 + M14 1555 8 + M15 1551 9 + M16 1580 15 + M17 1655 6 + M18 1662 7 + M19 1591 8 + M20 1758 8 + M21 1623 8 + M22 1597 6 + M23 1561 18 + M24 NA NA + N01 1660 6 + N02 592 25 + N03 1595 7 + N04 1527 5 + N05 1745 6 + N06 1543 6 + N07 1529 5 + N08 1691 6 + N09 1705 7 + N10 1612 6 + N11 1769 7 + N12 1624 6 + N13 1673 7 + N14 1683 7 + N15 1637 6 + N16 1786 7 + N17 1593 6 + N18 1636 6 + N19 1614 6 + N20 1650 6 + N21 1553 6 + N22 1671 6 + N23 628 25 + N24 NA NA + O01 1692 6 + O02 1701 8 + O03 1611 10 + O04 1370 25 + O05 1537 10 + O06 1538 14 + O07 1582 8 + O08 1515 11 + O09 1587 6 + O10 1582 6 + O11 1660 10 + O12 1544 10 + O13 1544 8 + O14 1603 9 + O15 1592 12 + O16 1518 11 + O17 1606 6 + O18 1565 10 + O19 1617 6 + O20 1543 18 + O21 1649 7 + O22 1710 8 + O23 1788 7 + O24 NA NA + P01 1818 7 + P02 1611 5 + P03 1736 7 + P04 1642 6 + P05 1557 5 + P06 1606 6 + P07 1558 6 + P08 1627 6 + P09 1579 6 + P10 1733 6 + P11 1520 6 + P12 1558 7 + P13 1804 7 + P14 1630 6 + P15 1576 6 + P16 1740 7 + P17 1578 6 + P18 1544 6 + P19 1692 6 + P20 1560 6 + P21 1552 6 + P22 1790 7 + P23 1537 6 + P24 NA NA + + + + diff -r 000000000000 -r 3ddf2607e3a2 test-data/150615-HR-12015-01A.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/150615-HR-12015-01A.out Wed Jun 01 03:57:23 2016 -0400 @@ -0,0 +1,385 @@ +#Well Table_1 Table_2 Table_3 Table_4 Table_5 Table_6 +A01 2215 8.88 55.62 2.57 2.91 78.76 +A02 2811 8.61 57.35 1.07 2.03 63.32 +A03 2226 10.96 70.4 0.54 2.41 79.41 +A04 2528 9.35 61.59 1.66 2.14 74.9 +A05 1827 11.87 73.78 0.66 2.27 79.31 +A06 2337 8.69 58.49 1.07 1.87 62.34 +A07 2233 9.7 63.41 1.07 2.32 77.48 +A08 2462 8.48 57.39 1.06 2.07 67.32 +A09 2790 9.5 62.83 1.65 2.52 80.57 +A10 2792 9.19 60.67 1.9 2.38 73.6 +A11 2547 9.51 61.76 1.33 2.8 84.6 +A12 2629 9.47 60.94 2.09 2.42 72.34 +A13 1655 11.8 71.24 0.85 2.3 71.88 +A14 2647 8.27 52.13 2.15 2.37 72.76 +A15 2300 11.5 72.17 0.57 2.68 86.26 +A16 2030 11.71 71.63 0.74 2.66 89.03 +A17 2124 9.78 63.89 1.13 2.45 81.13 +A18 2461 9.14 59.65 1.83 2.3 77.14 +A19 2273 8.68 57.85 0.97 2.32 69.57 +A20 2281 10.62 70.58 0.7 1.98 65.3 +A21 2412 10.49 69.86 0.46 2.07 70.27 +A22 1331 10.72 69.65 0.68 1.97 61.54 +A23 2245 9.88 66.24 0.4 2.17 66.33 +A24 2037 8.13 53.26 1.42 2.06 70.05 +B01 2184 10.31 65.29 0.87 2.33 72.4 +B02 2104 9.33 57.94 3.09 2.44 79.26 +B03 1639 11.13 69.68 0.55 2.03 67.42 +B04 2467 9.84 64.33 0.77 2.03 67.95 +B05 1818 11.75 75.25 0.66 1.97 68.96 +B06 1769 9.08 57.32 2.43 2.29 69.18 +B07 1654 12.22 75.7 0.6 2.14 75.29 +B08 2199 10.04 68.58 0.73 2.43 73.55 +B09 2043 8.74 59.03 1.22 1.96 57.65 +B10 1329 11.6 73.06 0.68 2.04 58.75 +B11 2533 7.31 47.06 3.83 3.01 95.3 +B12 2712 9.31 61.98 2.06 2.49 75.2 +B13 1824 10.83 68.42 1.54 2.45 80.09 +B14 2718 7.68 49.74 4.01 2.54 81.37 +B15 2443 10.4 68.81 1.02 2.64 91.33 +B16 2061 11.82 77.1 0.39 2.53 87.74 +B17 2088 10.83 70.69 0.62 2.22 74.12 +B18 2730 10.36 70.4 0.81 2.39 78.69 +B19 2279 8.09 54.28 1.14 1.98 61.28 +B20 2371 12.37 78.28 0.25 2.23 78.36 +B21 2114 10.49 71.85 0.85 2.32 73.66 +B22 2355 9.84 66.71 0.72 2.04 64.63 +B23 1154 11.75 72.1 0.35 2.35 65.16 +B24 1646 7.49 50.12 1.82 2.11 64.74 +C01 2356 9.67 64.43 1.02 2.07 61.55 +C02 2680 10.27 67.57 0.82 2.03 60.64 +C03 2305 8.51 55.88 1.56 1.87 56.38 +C04 2510 9.55 63.55 1 2.02 58.22 +C05 2650 10.23 67.96 0.3 1.95 59.48 +C06 2918 9.76 64.98 0.69 2.21 65.35 +C07 2618 8.28 55.39 1.26 2.42 68.98 +C08 2654 9.56 65.3 1.09 2.52 75.17 +C09 2828 8.44 57.39 1.34 2.21 63.59 +C10 2877 9.48 64.75 1.32 2.59 77.38 +C11 2441 9.78 65.38 1.47 2.38 73.63 +C12 2870 7.1 47.04 3.69 2.87 88.54 +C13 3202 9.02 59.93 1.72 2.43 78.2 +C14 2619 8.63 57.43 2.1 2.93 95.11 +C15 2716 8.82 58.73 1.18 2.46 78.45 +C16 2413 10.72 71.07 0.33 2.62 84.52 +C17 2893 8.18 56.14 1.52 2.8 83.32 +C18 2669 9.82 66.62 0.67 2.26 70.88 +C19 2272 10.81 71.79 0.79 2.1 68.8 +C20 2161 9.42 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