3.4

Improved documentation:

  • fix url of test_data thanks to @sonnynguyen

  • Better documentation for pyGenomeTracks / makeTracksFile

  • Documentation of each track

Enhancements:

  • Different bed files format (BED3, BED4, BED5, BED6, BED8, BED9, BED12) is guessed based on the first line and rely not only on number of columns but on the type of each column (string/float etc.). This way, broadPeaks/gappedPeaks and other bed-like formats can be accepted as file_type = bed without preprocessing.

  • gtf has now its own file_type. Warning:file_type = bed for gtf will be no longer supported in a future version.

  • You can use a decreasing x-axis (from larger coordinates to smaller coordinates) with the option --decreasingXAxis in pyGenomeTracks.

  • For bedgraph and bigwig:

    • logScale: To apply a log transformation to your data you can set transform to log1p, log, log2, log10, -log. For others than log1p, you can set a log_pseudocount. By default the y axis values will represent the transformed values and the transformation will be written on the left of the y axis but you can decide to keep the original values by setting y_axis_values = original.

    • operation on files: You can plot the result of an operation on one or two files without preprocessing. To use it, put the operation in operation with the variable file or both variables file and second_file, for example operation = 0.89 * file or operation = max(file, second_file) or operation = file - second_file. In the two later cases, you need to put the path of the second file in second_file. However, this operation can be time consuming if you do it multiple times and you may prefer to convert your files in advance.

    For more examples on these two new features, visit the examples.

  • Both type = line and type = lines are working in bedgraph_matrix

Bugfix:

  • In version 3.3, if you were using a colormap in bed the border_color and color_utr were ignored. Now each one can be set to different color/colormap/bed_rgb.