Mercurial > repos > xuebing > sharplabtool
diff tools/indels/indel_sam2interval.xml @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/indels/indel_sam2interval.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,139 @@ +<tool id="indel_sam2interval" name="Extract indels" version="1.0.0"> + <description>from SAM</description> + <command interpreter="python"> + indel_sam2interval.py + --input=$input1 + --include_base=$include_base + --collapse=$collapse + --int_out=$output1 + #if $ins_out.include_ins_out == "true" + --bed_ins_out=$output2 + #else + --bed_ins_out="None" + #end if + #if $del_out.include_del_out == "true" + --bed_del_out=$output3 + #else + --bed_del_out="None" + #end if + </command> + <inputs> + <param format="sam" name="input1" type="data" label="Select dataset to convert" /> + <param name="include_base" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Include the relevant base(s) for each insertion (and a dash (-) for deletions)" /> + <param name="collapse" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Collapse repeated locations onto single line with counts" /> + <conditional name="ins_out"> + <param name="include_ins_out" type="select" label="Include insertions output bed file?"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true" /> + <when value="false" /> + </conditional> + <conditional name="del_out"> + <param name="include_del_out" type="select" label="Include deletions output bed file?"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true" /> + <when value="false" /> + </conditional> + </inputs> + <outputs> + <data format="interval" name="output1" /> + <data format="bed" name="output2"> + <filter>ins_out[ "include_ins_out" ] == "true"</filter> + </data> + <data format="bed" name="output3"> + <filter>del_out[ "include_del_out" ] == "true"</filter> + </data> + </outputs> + <tests> + <test> + <param name="input1" value="indel_sam2interval_in1.sam" ftype="sam"/> + <param name="include_base" value="true"/> + <param name="collapse" value="true"/> + <param name="include_ins_out" value="true" /> + <param name="include_del_out" value="true" /> + <output name="output1" file="indel_sam2interval_out1.interval" ftype="interval"/> + <output name="output2" file="indel_sam2interval_out2.bed" ftype="bed"/> + <output name="output3" file="indel_sam2interval_out3.bed" ftype="bed"/> + </test> + </tests> + <help> + +**What it does** + +Given a SAM file containing indels, converts these to an interval file with a column indicating whether it is an insertion or a deletion, and then also can create a BED file for each type (one for insertions, one for deletions). The interval file can be combined with other like files to create a table useful for analysis with the Indel Analysis Table tool. The BED files can be useful for visualizing the reads. + +----- + +**Example** + +Suppose you have the following mapping results:: + + r327 16 chrM 11 37 8M1D10M * 0 0 CTTACCAGATAGTCATCA -+<2;?@BA@?-,.+4=4 XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:41^C35 + r457 0 chr1 14 37 14M * 0 0 ACCTGACAGATATC =/DF;?@1A@?-,. XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 + r501 16 chrM 6 23 7M1I13M * 0 0 TCTGTGCCTACCAGACATTCA +=$2;?@BA@?-,.+4=4=4A XT:A:U NM:i:3 X0:i:1 X1:i:1 XM:i:2 XO:i:1 XG:i:1 MD:Z:28C36G9 XA:Z:chrM,+134263658,14M1I61M,4; + r1288 16 chrM 8 37 11M1I7M * 0 0 TCACTTACCTGTACACACA /*F2;?@%A@?-,.+4=4= XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:1 MD:Z:2T0T1A69 + r1902 0 chr1 4 37 7M2D18M * 0 0 AGTCTCTTACCTGACGGTTATGA <2;?@BA@?-,.+4=4=4AA663 XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:17^CA58A0 + r2204 16 chrM 9 0 19M * 0 0 CTGGTACCTGACAGGTATC 2;?@BA@?-,.+4=4=4AA XT:A:R NM:i:1 X0:i:2 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T75 XA:Z:chrM,-564927,76M,1; + r2314 16 chrM 6 37 10M2D8M * 0 0 TCACTCTTACGTCTGA <2;?@BA@?-,.+4=4 XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:25A5^CA45 + r3001 0 chrM 13 37 3M1D5M2I7M * 0 0 TACAGTCACCCTCATCA <2;?@BA/(@?-,$& XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:17^CA58A0 + r3218 0 chr1 13 37 8M1D7M * 0 0 TACAGTCACTCATCA <2;?@BA/(@?-,$& XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:17^CA58A0 + r4767 16 chr2 3 37 15M2I7M * 0 0 CAGACTCTCTTACCAAAGACAGAC <2;?@BA/(@?-,.+4=4=4AA66 XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:1 MD:Z:2T1A4T65 + r5333 0 chrM 5 37 17M1D8M * 0 0 GTCTCTCATACCAGACAACGGCAT FB3$@BA/(@?-,.+4=4=4AA66 XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:1 MD:Z:45C10^C0C5C13 + r6690 16 chrM 7 23 20M * 0 0 CTCTCTTACCAGACAGACAT 2;?@BA/(@?-,.+4=4=4A XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 XA:Z:chrM,-568532,76M,1; + r7211 0 chrM 7 37 24M * 0 0 CGACAGAGACAAAATAACATTTAA //<2;?@BA@?-,.+4=442;;6: XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:2 XO:i:1 XG:i:1 MD:Z:73G0G0 + r7899 69 * 0 0 * * 0 0 CTGCGTGTTGGTGTCTACTGGGGT #%#'##$#$##&%#%$$$%#%#'# + r9192 133 * 0 0 * * 0 0 GTGCGTCGGGGAGGGTGCTGTCGG ######%#$%#$$###($###&&% + r9922 16 chrM 4 0 7M3I9M * 0 0 CCAGACATTTGAAATCAGG F/D4=44^D++26632;;6 XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 + r9987 16 chrM 4 0 9M1I18M * 0 0 AGGTTCTCATTACCTGACACTCATCTTG G/AD6"/+4=4426632;;6:<2;?@BA XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 + r10145 16 chr1 16 0 5M2D7M * 0 0 CACATTGTTGTA G//+4=44=4AA XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 + r10324 16 chrM 15 0 6M1D5M * 0 0 CCGTTCTACTTG A@??8.G//+4= XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 + r12331 16 chrM 17 0 4M2I6M * 0 0 AGTCGAATACGTG 632;;6:<2;?@B XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 + r12914 16 chr2 24 0 4M3I3M * 0 0 ACTACCCCAA G//+4=42,. XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 + r13452 16 chrM 13 0 3M1D11M * 0 0 TACGTCACTCATCA IIIABCCCICCCCI XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 + + +The following three files will be produced (Interval, Insertions BED and Deletions BED):: + + chr1 11 13 D - 1 + chr1 21 22 D - 1 + chr1 21 23 D - 1 + chr2 18 19 I AA 1 + chr2 28 29 I CCC 1 + chrM 11 12 I TTT 1 + chrM 13 14 I C 1 + chrM 13 14 I T 1 + chrM 16 17 D - 1 + chrM 16 18 D - 1 + chrM 19 20 D - 1 + chrM 19 20 I T 1 + chrM 21 22 D - 1 + chrM 21 22 I GA 1 + chrM 22 23 D - 1 + + chr2 18 19 + chr2 28 29 + chrM 11 12 + chrM 13 14 + chrM 13 14 + chrM 19 20 + chrM 21 22 + + chr1 11 13 + chr1 21 22 + chr1 21 23 + chrM 16 17 + chrM 16 18 + chrM 19 20 + chrM 21 22 + chrM 22 23 + +For more information on SAM, please consult the `SAM format description`__. + +.. __: http://www.ncbi.nlm.nih.gov/pubmed/19505943 + + + </help> +</tool>