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tomazc / iCount

iCount, protein-RNA interaction analytics
http://icount.biolab.si
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clusters: Output issue #126

Closed nebo56 closed 7 years ago

nebo56 commented 7 years ago

By running the following command results are printed as "error messages" to stderr 2 output (I need to redirect results by using iCount clusters --dist 25 test.peaks.bed 2> test.clusters.bed command). And repeated columns for merged peaks should be removed.

Executing the following command: iCount clusters --dist 25 test.peaks.bed test.clusters.bed
Input parameters for function 'run' in iCount.analysis.clusters
    sites: test.peaks.bed
    clusters: test.clusters.bed
    dist: 25
Merging cross links form file chr1  20137   20138   WASH7P - WASH7P 1   -
chr1    20139   20140   WASH7P - WASH7P 1   -
chr1    20152   20153   WASH7P - WASH7P 1   -
chr1    20189   20190   WASH7P - WASH7P 1   -
chr1    255855  255856  AP006222.1,AP006222.2 - AP006222.1,AP006222.2   1   -
chr1    255862  255863  AP006222.1,AP006222.2 - AP006222.1,AP006222.2   1   -
chr1    255941  255942  AP006222.1,AP006222.2 - AP006222.1,AP006222.2   1   -
chr1    255948  255949  AP006222.1,AP006222.2 - AP006222.1,AP006222.2   2   -
chr1    569410  569411  OR4F16,RP5-857K21.4,RP5-857K21.5 - OR4F16,RP5-857K21.4,RP5-857K21.5 1   -
chr1    569414  569415  OR4F16,RP5-857K21.4,RP5-857K21.5 - OR4F16,RP5-857K21.4,RP5-857K21.5 2   -
chr1    569415  569416  OR4F16,RP5-857K21.4,RP5-857K21.5 - OR4F16,RP5-857K21.4,RP5-857K21.5 1   -
chr1    569432  569433  OR4F16,RP5-857K21.4,RP5-857K21.5 - OR4F16,RP5-857K21.4,RP5-857K21.5 1   -
chr1    569434  569435  OR4F16,RP5-857K21.4,RP5-857K21.5 - OR4F16,RP5-857K21.4,RP5-857K21.5 1   -
...