Hello,
I am trying to run detect_collinearity_within_gene_families.pl and family_circle_plotter.java to generate a plot highlighting all collinear genes within a gene family. However, only the first line from my gene family input was able to be highlighted.
I have confirmed that the genes listed in the subsequent lines are indeed collinear according to the collinearity file. Moreover, when any of these lines is placed as the first entry in the gene family file, the corresponding genes are correctly highlighted in the visualization. This suggests that the issue may be related to how the program processes entries after the first line.
I am wondering whether this issue could be related to the format of my gene family input file or whether there may be a bug in the Java script. My input file is formatted as follows:
OG0000755 sp1_accession_id1 sp2_accession_id1
OG0001538 sp1_accession_id2 sp2_accession_id2
OG0001301 sp1_accession_id3 sp2_accession_id3
...
in case the program only runs one gene family, i have also tried:
serine_protease sp1_accession_id1 sp2_accession_id1
serine_protease sp1_accession_id2 sp2_accession_id2
serine_protease sp1_accession_id3 sp2_accession_id3
...
and this does not solve the issue. all inputs are tab-delimited.
I would greatly appreciate any suggestions or guidance you may have regarding this issue.
Thank you for your time and assistance.
D
Hello,
I am trying to run detect_collinearity_within_gene_families.pl and family_circle_plotter.java to generate a plot highlighting all collinear genes within a gene family. However, only the first line from my gene family input was able to be highlighted.
I have confirmed that the genes listed in the subsequent lines are indeed collinear according to the collinearity file. Moreover, when any of these lines is placed as the first entry in the gene family file, the corresponding genes are correctly highlighted in the visualization. This suggests that the issue may be related to how the program processes entries after the first line.
I am wondering whether this issue could be related to the format of my gene family input file or whether there may be a bug in the Java script. My input file is formatted as follows:
OG0000755 sp1_accession_id1 sp2_accession_id1
OG0001538 sp1_accession_id2 sp2_accession_id2
OG0001301 sp1_accession_id3 sp2_accession_id3
...
in case the program only runs one gene family, i have also tried:
serine_protease sp1_accession_id1 sp2_accession_id1
serine_protease sp1_accession_id2 sp2_accession_id2
serine_protease sp1_accession_id3 sp2_accession_id3
...
and this does not solve the issue. all inputs are tab-delimited.
I would greatly appreciate any suggestions or guidance you may have regarding this issue.
Thank you for your time and assistance.
D