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Commit 24e6d5d5 authored by Amandine PERRIN's avatar Amandine PERRIN
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get_contigs returned in the wrong way

parent 5b1c37b0
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with 8 additions and 4 deletions
PanACoTA/utils.py
+ 8
− 4
View file @ 24e6d5d5
...@@ -1133,8 +1133,10 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile): ...@@ -1133,8 +1133,10 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
# - write header ("<contig name> <size>") to replicon file # - write header ("<contig name> <size>") to replicon file
if prev_cont: if prev_cont:
cont = "\t".join([prev_cont, str(cont_size)]) + "\n" cont = "\t".join([prev_cont, str(cont_size)]) + "\n"
sizes[prev_cont] = cont_size prevcont_nohead = "".join(prev_cont.split(">")[1:])
contigs[prev_cont] = prev_orig_name prev_orig_name_nohead = "".join(prev_orig_name.split(">")[1:])
sizes[prevcont_nohead] = cont_size
contigs[prev_orig_name_nohead] = prevcont_nohead
grf.write(cont) grf.write(cont)
grf.write(seq) grf.write(seq)
prev_cont = ">" + gembase_name + "." + str(contig_num).zfill(4) prev_cont = ">" + gembase_name + "." + str(contig_num).zfill(4)
...@@ -1148,8 +1150,10 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile): ...@@ -1148,8 +1150,10 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
cont_size += len(line.strip()) cont_size += len(line.strip())
# Write last contig # Write last contig
cont = "\t".join([prev_cont, str(cont_size)]) + "\n" cont = "\t".join([prev_cont, str(cont_size)]) + "\n"
sizes[prev_cont] = cont_size prevcont_nohead = "".join(prev_cont.split(">")[1:])
contigs[prev_cont] = prev_orig_name prev_orig_name_nohead = "".join(prev_orig_name.split(">")[1:])
contigs[prev_orig_name_nohead] = prevcont_nohead
sizes[prevcont_nohead] = cont_size
grf.write(cont) grf.write(cont)
grf.write(seq) grf.write(seq)
return contigs, sizes return contigs, sizes
......
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