Mercurial > repos > nanettec > lookup
changeset 1:54200db292a3 draft
Uploaded
| author | nanettec |
|---|---|
| date | Thu, 25 Feb 2016 04:58:58 -0500 |
| parents | eac0e302ab3a |
| children | a777732066cb |
| files | lookup.xml |
| diffstat | 1 files changed, 98 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lookup.xml Thu Feb 25 04:58:58 2016 -0500 @@ -0,0 +1,98 @@ +<tool id="lookup5" name="Lookup table" version="5.0.0"> + <description> for 2cM intervals</description> + <command interpreter="python"> + lookup.py --input1 $input1 --input2 $input2 --input3 $input3 --output1 $output1 --output2 $output2 + </command> + <inputs> + <param label="Markers file" name="input1" type="data" format="tabular" help="Tabular file giving marker positions in cM and bp"></param> + <param label="QTL Cartographer Z file" name="input2" type="data" format="tabular" help="QTL Cartographer output file (.z)"></param> + <param label="Chromosome length file" name="input3" type="data" format="tabular" help="A tabular file giving the length of each chromosome in bp"></param> + </inputs> + <outputs> + <data format="tabular" name="output1" /> + <data format="tabular" name="output2" /> + </outputs> + <requirements> + </requirements> + <tests> + <test> + </test> + </tests> + <help> + +**What it does** + +The information from the Markers file and the QTL Cartographer Z file, are combined to proportionally estimate a base pair position at each 2cM interval. + +The Lookup file can then serve as a lookup table to convert between base pair and centimorgan positions. + +------- + +**Example input files** + +Markers file, each row correspond to a marker (5 columns; only a part of the file is shown):: + + chr marker name cM bp + 1 1 marker1 0 2038278 + 1 2 marker2 7.53 3649871 + 1 3 marker3 18.77 6155281 + 1 4 marker4 38.71 12398322 + 1 5 marker5 44.62 14171692 + 1 6 marker6 48.73 16529505 + +QTL Cartographer Z file, each row correspond to a 2cM interval (the example shows part of the important part of the Z file, the first 3 data columns of the first block). Note: Headers is fine and will be ignored:: + + 1 1 0.0001 … + 1 1 0.0201 … + 1 1 0.0401 … + 1 1 0.0601 … + 1 2 0.0754 … + 1 2 0.0954 … + 1 2 0.1154 … + 1 2 0.1354 … + 1 2 0.1554 … + 1 2 0.1754 … + 1 3 0.1878 … + 1 3 0.2078 … + 1 3 0.2278 … + 1 3 0.2478 … + +Chromosome length file, each row correspond to a chromosome (2 columns; only a part of the file is shown):: + + chr1 301354135 + chr2 237068873 + chr3 232140174 + chr4 241473504 + chr5 217872852 + chr6 169174353 + +------- + +**Example output files** + + +Lookup output file, each row correspond to a 2 cM interval (7 columns; only a part of the file is shown):: + + int.id chr marker int cM bp length_cM + 1 1 1 0.0001 0.0 2038278 2.0 + 2 1 1 0.0201 2.0 2466324 2.0 + 3 1 1 0.0401 4.0 2894370 2.0 + 4 1 1 0.0601 6.0 3322416 1.53 + 5 1 2 0.0754 7.53 3649871 2.0 + 6 1 2 0.0954 9.53 4095673 2.0 + 7 1 2 0.1154 11.53 4541476 2.0 + 8 1 2 0.1354 13.53 4987278 2.0 + +Chromosome summary file, each row correspond to a chromosome (6 columns; only a part of the file is shown). The last row gives the total across the genome:: + + chr markers cM bp int_positions bins + 1 27 324.4 301354135 177 176 + 2 14 169.11 237068873 92 91 + 3 19 221.29 232140174 123 122 + 4 20 188.37 241473504 105 104 + 5 20 203.82 217872852 110 109 + 6 17 195.85 169174353 106 105 + Total 117 1302.84 1399083891 713 707 + + </help> +</tool>