Commit 647a117b authored by Amandine  PERRIN's avatar Amandine PERRIN
Browse files

gff headers with 1 space instead of 2

parent 2c04051c
Pipeline #66649 passed with stages
in 5 minutes and 38 seconds
...@@ -358,7 +358,7 @@ def create_gff(gpath, gff_file, res_gff_file, res_lst_file, contigs, sizes): ...@@ -358,7 +358,7 @@ def create_gff(gpath, gff_file, res_gff_file, res_lst_file, contigs, sizes):
# open lst file to read all information saved from prodigal results # open lst file to read all information saved from prodigal results
with open(gff_file, 'r') as gf, open(res_gff_file, "w") as rgf, open(res_lst_file, "r") as rlf: with open(gff_file, 'r') as gf, open(res_gff_file, "w") as rgf, open(res_lst_file, "r") as rlf:
# Write headers of gff3 file # Write headers of gff3 file
rgf.write("##gff-version 3\n") rgf.write("##gff-version 3\n")
for ori_name, new_name in contigs.items(): for ori_name, new_name in contigs.items():
# Write the list of contigs, with their size # Write the list of contigs, with their size
end = sizes[new_name] end = sizes[new_name]
......
...@@ -411,7 +411,7 @@ def generate_gff(gpath, prokka_gff_file, res_gff_file, res_lst_file, sizes, cont ...@@ -411,7 +411,7 @@ def generate_gff(gpath, prokka_gff_file, res_gff_file, res_lst_file, sizes, cont
with open(prokka_gff_file, "r") as prokf, open(res_lst_file, "r") as lstf, \ with open(prokka_gff_file, "r") as prokf, open(res_lst_file, "r") as lstf, \
open(res_gff_file, "w") as gfff: open(res_gff_file, "w") as gfff:
# Write headers of gff3 file # Write headers of gff3 file
gfff.write("##gff-version 3\n") gfff.write("##gff-version 3\n")
# Write all sequences with their size. Order by name in gembase format # Write all sequences with their size. Order by name in gembase format
for old, new in sorted(contigs.items(), key=lambda items:items[1]): for old, new in sorted(contigs.items(), key=lambda items:items[1]):
end = sizes[new] end = sizes[new]
......
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