Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms
changeset 16:70f4385534f9 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit c400846f3ef40a5cbaa373d2ca7c93fb05ecd20c-dirty
| author | mvdbeek |
|---|---|
| date | Wed, 03 Feb 2016 09:08:13 -0500 |
| parents | 16d0811f7a09 |
| children | a118d511a27c |
| files | readmap.py readmap.xml smRtools.pyc |
| diffstat | 3 files changed, 31 insertions(+), 1 deletions(-) [+] |
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--- a/readmap.py Tue Feb 02 15:28:12 2016 -0500 +++ b/readmap.py Wed Feb 03 09:08:13 2016 -0500 @@ -66,6 +66,35 @@ filtered_list.append(line) return filtered_list + +def listify_plottable_item(item): + """ + plottable is a list of strings: + 'FBti0020401\t78\t-1.0\tR' + split on tab and return gene, coordinate, count and orientation + """ + gene, coordinate, count, orientation = item.split("\t") + return gene, coordinate, count, orientation + +def lookup_gene_length(gene, readDict): + return readDict[readDict.keys()[0]].instanceDict["size"] + +def handle_start_stop_coordinates(plottable, readDict): + """ + To ensure that the plot area always includes the correct start and end coordinates, + we add an entry at start [coordinate 0] and end [last coordinate] of count 0, if these do not exist. + """ + first_line = plottable[0] + last_line = plottable[-1] + gene, coordinate, count, orientation = listify_plottable_item(first_line) + if not coordinate == "0": + new_line = "\t".join([gene, "0", "0", "F"]) + plottable = new_line + plottable + gene_length = str(lookup_gene_length(gene, readDict)) + if not coordinate == gene_length: + last_line = "\t".join([gene, gene_length, "0", "F"]) + plottable = plottable + last_line + def write_readplot_dataframe(readDict, readmap_file): listoflines = [] with open(readmap_file, 'w') as readmap: @@ -77,6 +106,7 @@ dict=readDict[sample].instanceDict for gene in dict.keys(): plottable = dict[gene].readplot() + handle_start_stop_coordinates(plottable, readDict) for line in plottable: #print >>readmap, "%s\t%s" % (line, sample) listoflines.append ("%s\t%s" % (line, sample))
--- a/readmap.xml Tue Feb 02 15:28:12 2016 -0500 +++ b/readmap.xml Wed Feb 03 09:08:13 2016 -0500 @@ -1,4 +1,4 @@ -<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.1.1"> +<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.1.2"> <description>from sRbowtie aligment</description> <requirements> <requirement type="package" version="0.12.7">bowtie</requirement>