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SpatialTranscriptomicsResearch / st_pipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
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Adjust script to work with the new output format from ST aligner webtool #47

Closed Alexander-Stuckey closed 7 years ago

Alexander-Stuckey commented 7 years ago

I have adjusted the script so that it is compatible with the new output format from the ST aligner webtool.

The new format is as follows:

x   y   new_x   new_y   pixel_x pixel_y 
29  5   29.07901925541002   5.114512925737359   13105   1902
5   6   4.849305172444476   6.087884452905548   4392    2257
...

I also round the new x and y positions to 2 dp, as I don't think that more than that is needed.

There is also a new flag to specify the output format of array or pixel position, and it defaults to array if not specified.