Skip to content
Snippets Groups Projects
Commit 23333d25 authored by Amandine  PERRIN's avatar Amandine PERRIN
Browse files

Write absolute path for annotate_path in LSTINFO file

parent 874291a0
Branches
Tags
No related merge requests found
...@@ -484,16 +484,13 @@ def write_lstinfo(list_file, genomes, outdir): ...@@ -484,16 +484,13 @@ def write_lstinfo(list_file, genomes, outdir):
""" """
_, name_lst = os.path.split(list_file) _, name_lst = os.path.split(list_file)
outlst = os.path.join(outdir, "LSTINFO-" + ".".join(name_lst.split(".")[:-1]) + ".lst") outlst = os.path.join(outdir, "LSTINFO-" + ".".join(name_lst.split(".")[:-1]) + ".lst")
with open(outlst, "w") as outf: with open(outlst, "w") as outf:
outf.write("\t".join(["gembase_name", "orig_name", "to_annotate", "gsize", outf.write("\t".join(["gembase_name", "orig_name", "to_annotate", "gsize",
"nb_conts", "L90"]) + "\n") "nb_conts", "L90"]) + "\n")
for genome, values in sorted(genomes.items(), key=sort_genomes_byname_l90_nbcont): for genome, values in sorted(genomes.items(), key=sort_genomes_byname_l90_nbcont):
gembase, _, to_annote, gsize, nbcont, l90 = [str(x) for x in values] gembase, _, to_annote, gsize, nbcont, l90 = [str(x) for x in values]
to_annote_file = os.path.basename(to_annote) outf.write("\t".join([gembase, genome, to_annote, gsize, nbcont, l90]) + "\n")
outf.write("\t".join([gembase, genome, to_annote_file, gsize, nbcont, l90]) + "\n")
def sort_genomes_by_name(x): def sort_genomes_by_name(x):
""" """
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment