Example MID Project Script

3.6.1

# Create the project

create project /data/ampProjects/MID_CLI_Example \

    -name MID_CLI_Example \

    -annotation ""

# Load the references from a tab-delimited file

# containing data lines for each reference

# following  the format of the header below

# (which should be included at the top of the file):

# "Name"     "Annotation"     "Sequence"

# For this example, ref1-ref6 should be defined.

create reference -file referencesFile.txt

# Load the amplicons from a tab-delimited file

# containing data lines for each amplicon

# following  the format of the header below

# (which should be included at the top of the file):

# "Name"     "Annotation"     "Reference"     "Primer1"     "Primer2"     "Start"     "End"

# For this example, amp1-amp6 should be defined

# (where amp1 is from ref1, amp2 is from ref2, etc.).

create amplicon -file ampliconsFile.txt

# For this example, the following samples need to be created.

create sample -file - << HERE_TERMINATOR

"Name"

"A001"

"B_1_and_1"

"B_1_and_2"

"B_1_and_3"

"B_1_and_4"

"B_2_and_1"

"B_2_and_2"

"B_2_and_3"

"B_2_and_4"

"B_3_and_1"

"B_3_and_2"

"B_3_and_3"

"B_3_and_4"

"B_4_and_1"

"B_4_and_2"

"B_4_and_3"

"B_4_and_4"

"E_5_or_5"

"E_6_or_6"

"E_7_or_8"

"E_8_or_7"

"P1_9"

"P1_10"

"P1_11"

"P2_12"

"P2_13"

"P2_14"

HERE_TERMINATOR

# Create a readGroup for the readData.

create readGroup -name "96Plex_Both_Data"

# Load the readData from a tab-delimited file

# containing data lines for each readData set

# following  the format of the header below

# (which should be included at the top of the file):

# "SffDir"     "SffName"     "ReadGroup"     "SymLink"     "Name"

# For this example, two sff files named

# ESS716O01 and ESS716O02 are being loaded.

load -file readDataFile.txt

# Use the utility execute command to run the

# default script that loads a project with

# the 454Standard group of 14 MIDs.

utility execute %libDir/create454StandardMIDs.ava

# For the sake of demonstrating functionality,

# this example assumes that you want to replace

# Mid9-Mid14 from the 454Standard group with

# your own custom set of 6 new MIDs.

# To simplify project, optionally remove the

# the 454Standard MIDs that are being replaced.

# Note: specifying the OfMidGroup option isn't

# technically necessary as the MID Names are unique

# in the project.

remove mid -file - << HERE_TERMINATOR

"Name"      "OfMidGroup"

"Mid9"      "454Standard"

"Mid10"     "454Standard"

"Mid11"     "454Standard"

"Mid12"     "454Standard"

"Mid13"     "454Standard"

"Mid14"     "454Standard"

HERE_TERMINATOR

# Create a midGroup for the new MIDs.

create midGroup -name "CustomMids"

# Load the custom MID sequences from a tab-delimited file

# containing data lines for each MID

# following  the format of the header below

# (which should be included at the top of the file):

# "Name"     "Annotation"     "Sequence"     "MidGroup"

# For this example, 6 MIDs are being defined

# with the names CMid9-CMid14.

create mid -file customMidFile.txt

# Create the four different multiplexers

# being used in the project.

create multiplexer -file - << HERE_TERMINATOR

"Name"     "Annotation"     "Encoding"

"MultiplexerBoth"     ""     "both"

"MultiplexerEither"   ""     "either"

"MultiplexerP1"       ""     "primer1"

"MultiplexerP2"       ""     "primer2"

HERE_TERMINATOR

# Set up the association of MIDs to samples

# in each of the multiplexers.

# Note: specifying the OfPrimer1MidGroup and OfPrimer2MidGroup

# options isn't technically necessary as the MID Names are unique

# in the project.

assoc -file - << HERE_TERMINATOR

"Multiplexer"  "Primer1Mid"  "OfPrimer1MidGroup"  "Primer2Mid"  "OfPrimer2MidGroup"  "Sample"

"MultiplexerBoth"  "Mid1"  "454Standard"  "Mid1"  "454Standard"  "B_1_and_1"

"MultiplexerBoth"  "Mid1"  "454Standard"  "Mid2"  "454Standard"  "B_1_and_2"

"MultiplexerBoth"  "Mid1"  "454Standard"  "Mid3"  "454Standard"  "B_1_and_3"

"MultiplexerBoth"  "Mid1"  "454Standard"  "Mid4"  "454Standard"  "B_1_and_4"

"MultiplexerBoth"  "Mid2"  "454Standard"  "Mid1"  "454Standard"  "B_2_and_1"

"MultiplexerBoth"  "Mid2"  "454Standard"  "Mid2"  "454Standard"  "B_2_and_2"

"MultiplexerBoth"  "Mid2"  "454Standard"  "Mid3"  "454Standard"  "B_2_and_3"

"MultiplexerBoth"  "Mid2"  "454Standard"  "Mid4"  "454Standard"  "B_2_and_4"

"MultiplexerBoth"  "Mid3"  "454Standard"  "Mid1"  "454Standard"  "B_3_and_1"

"MultiplexerBoth"  "Mid3"  "454Standard"  "Mid2"  "454Standard"  "B_3_and_2"

"MultiplexerBoth"  "Mid3"  "454Standard"  "Mid3"  "454Standard"  "B_3_and_3"

"MultiplexerBoth"  "Mid3"  "454Standard"  "Mid4"  "454Standard"  "B_3_and_4"

"MultiplexerBoth"  "Mid4"  "454Standard"  "Mid1"  "454Standard"  "B_4_and_1"

"MultiplexerBoth"  "Mid4"  "454Standard"  "Mid2"  "454Standard"  "B_4_and_2"

"MultiplexerBoth"  "Mid4"  "454Standard"  "Mid3"  "454Standard"  "B_4_and_3"

"MultiplexerBoth"    "Mid4"  "454Standard"  "Mid4"  "454Standard"  "B_4_and_4"

"MultiplexerEither"  "Mid5"  "454Standard"  "Mid5"  "454Standard"  "E_5_or_5"

"MultiplexerEither"  "Mid6"  "454Standard"  "Mid6"  "454Standard"  "E_6_or_6"

"MultiplexerEither"  "Mid7"  "454Standard"  "Mid8"  "454Standard"  "E_7_or_8"

"MultiplexerEither"  "Mid8"  "454Standard"  "Mid7"  "454Standard"  "E_8_or_7"

"MultiplexerP1"      "CMid9"  "CustomMids"  ""  ""  "P1_9"

"MultiplexerP1"      "CMid10"  "CustomMids"  ""  ""  "P1_10"

"MultiplexerP1"      "CMid11"  "CustomMids"  ""  ""  "P1_11"

"MultiplexerP2"      ""  ""  "CMid12"  "CustomMids"  "P2_12"

"MultiplexerP2"      ""  ""  "CMid13"  "CustomMids"  "P2_13"

"MultiplexerP2"      ""  ""  "CMid14"  "CustomMids"  "P2_14"

HERE_TERMINATOR

# Associate the non-MID sample directly

# with its amplicon and read data.

assoc -readData ESS716O02 -sample "A001" -amplicon "amp6" -ofRef "ref6"

# Associate the multiplexers with

# their read data and amplicons.

assoc -file - << HERE_TERMINATOR

"Multiplexer"        "readData"  "amplicon"  "ofRef"

"MultiplexerBoth"    "ESS716O01"  "amp1"  "ref1"

"MultiplexerP1"      "ESS716O01"  "amp4"  "ref4"

"MultiplexerEither"  "ESS716O02"  "amp2"  "ref2"

"MultiplexerEither"  "ESS716O02"  "amp3"  "ref3"

"MultiplexerP2"      "ESS716O02"  "amp5"  "ref5"

HERE_TERMINATOR

save