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Update to Virannot 0.1.0 #6308

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merged 7 commits into from
Sep 8, 2024
Merged

Update to Virannot 0.1.0 #6308

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50e14a9
Add OTU new feature
marieBvr Sep 4, 2024
9929b14
Update OTU data
marieBvr Sep 4, 2024
3104350
Change use of BLASTXML query-id to query
marieBvr Sep 4, 2024
24c2446
Increment tool version
marieBvr Sep 4, 2024
f99b91f
Update RPS test data
marieBvr Sep 6, 2024
ae94fe6
Reduce test data size
marieBvr Sep 6, 2024
714770c
Delete old data test and switch to python 'with open'
marieBvr Sep 6, 2024
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78 changes: 43 additions & 35 deletions tools/virAnnot/otu.py
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Original file line number Diff line number Diff line change
Expand Up @@ -186,6 +186,8 @@ def _align_sequences(options, hits_collection):
os.mkdir(cdd_output)
if os.path.exists(cdd_output + "/seq_to_align.fasta"):
os.remove(cdd_output + "/seq_to_align.fasta")
if os.path.exists(cdd_output + "/seq_nucc.fasta"):
os.remove(cdd_output + "/seq_nucc.fasta")
file_seq_to_align = cdd_output + "/seq_to_align.fasta"
file_color_config = cdd_output + "/color_config.txt"
f = open(file_seq_to_align, "a")
Expand Down Expand Up @@ -298,6 +300,7 @@ def _get_stats(options, hits_collection):
cdd_output = options.output + "/" + hits_collection[cdd_id]["short_description"].replace(" ", "_")
worksheet = workbook.add_worksheet(hits_collection[cdd_id]["short_description"]) # add a worksheet
file_cluster = cdd_output + '/otu_cluster.csv'
file_fasta_nucc = cdd_output + '/representative_nucc.fasta'
with open(file_cluster, 'r') as clust:
otu_reader = csv.reader(clust, delimiter=',')
samples_list = []
Expand Down Expand Up @@ -342,6 +345,8 @@ def _get_stats(options, hits_collection):
if sample not in ['contigs_list', 'global_taxonomy']:
total_nb_read = 0
for contig in otu_collection[otu][sample]:
if otu_collection[otu][sample][contig]['nb'] == '':
otu_collection[otu][sample][contig]['nb'] = 0
total_nb_read += int(otu_collection[otu][sample][contig]['nb'])
otu_collection[otu][sample]['total_nb_read'] = total_nb_read
row = 0
Expand All @@ -355,26 +360,30 @@ def _get_stats(options, hits_collection):
worksheet.write(row, column + 2, 'contigs_list')
row = 1
# column = 0
for otu in otu_collection:
if isinstance(otu_collection[otu], dict):
column = 0
worksheet.write(row, column, otu)
# prepare table with 0 in each cells
for sample in otu_collection[otu]:
column = 1
for samp in samples_list:
worksheet.write(row, column, 0)
column += 1
# fill in table with nb of read for each sample and each OTU
for sample in otu_collection[otu]:
column = 1
for samp in samples_list:
if samp == sample:
worksheet.write(row, column, otu_collection[otu][sample]['total_nb_read'])
column += 1
worksheet.write(row, len(samples_list) + 1, otu_collection[otu]['global_taxonomy'].replace(';', ' '))
worksheet.write(row, len(samples_list) + 2, ",".join(otu_collection[otu]['contigs_list']))
row += 1
with open(file_fasta_nucc, "w+") as f_nucc:
for otu in otu_collection:
log.info(otu)
if isinstance(otu_collection[otu], dict):
column = 0
worksheet.write(row, column, otu)
# prepare table with 0 in each cells
for sample in otu_collection[otu]:
column = 1
for samp in samples_list:
worksheet.write(row, column, 0)
column += 1
# fill in table with nb of read for each sample and each OTU
for sample in otu_collection[otu]:
column = 1
for samp in samples_list:
if samp == sample:
worksheet.write(row, column, otu_collection[otu][sample]['total_nb_read'])
column += 1
worksheet.write(row, len(samples_list) + 1, otu_collection[otu]['global_taxonomy'].replace(';', ' '))
worksheet.write(row, len(samples_list) + 2, ",".join(otu_collection[otu]['contigs_list']))
row += 1
f_nucc.write(">" + cdd_id + "_" + otu + "_" + otu_collection[otu]['contigs_list'][0] + "\n")
f_nucc.write(str(hits_collection[cdd_id][otu_collection[otu]['contigs_list'][0]]['nuccleotide']) + "\n")
workbook.close()
read_file = pd.ExcelFile(file_xlsx)
for sheet in read_file.sheet_names:
Expand All @@ -392,21 +401,20 @@ def _create_html(options, hits_collection):
if os.path.exists(map_file_path):
os.remove(map_file_path)

map_file = open(map_file_path, "w+")
headers = ['#cdd_id', 'align_files', 'tree_files', 'cluster_files', 'cluster_nb_reads_files', 'pairwise_files', 'description', 'full_description\n']
map_file.write("\t".join(headers))
for cdd_id in hits_collection:
cdd_output = hits_collection[cdd_id]["short_description"].replace(" ", "_")
short_description = cdd_output
file_seq_aligned = cdd_output + '/seq_aligned.final_tree.fa'
tree_file = cdd_output + '/tree.dnd.png'
file_cluster = cdd_output + '/otu_cluster.csv'
file_matrix = cdd_output + "/identity_matrix.csv"
cluster_nb_reads_files = cdd_output + "/cluster_nb_reads_files.tab"
map_file.write(cdd_id + "\t" + file_seq_aligned + "\t" + tree_file + "\t")
map_file.write(file_cluster + "\t" + cluster_nb_reads_files + "\t" + file_matrix + "\t")
map_file.write(short_description + "\t" + hits_collection[cdd_id]["full_description"] + "\n")
map_file.close()
with open(map_file_path, "w+") as map_file:
headers = ['#cdd_id', 'align_files', 'tree_files', 'cluster_files', 'cluster_nb_reads_files', 'pairwise_files', 'description', 'full_description\n']
map_file.write("\t".join(headers))
for cdd_id in hits_collection:
cdd_output = hits_collection[cdd_id]["short_description"].replace(" ", "_")
short_description = cdd_output
file_seq_aligned = cdd_output + '/seq_aligned.final_tree.fa'
tree_file = cdd_output + '/tree.dnd.png'
file_cluster = cdd_output + '/otu_cluster.csv'
file_matrix = cdd_output + "/identity_matrix.csv"
cluster_nb_reads_files = cdd_output + "/cluster_nb_reads_files.tab"
map_file.write(cdd_id + "\t" + file_seq_aligned + "\t" + tree_file + "\t")
map_file.write(file_cluster + "\t" + cluster_nb_reads_files + "\t" + file_matrix + "\t")
map_file.write(short_description + "\t" + hits_collection[cdd_id]["full_description"] + "\n")
log.info("Writing HTML report")
html_cmd = os.path.join(options.tool_path, 'rps2tree_html.py') + ' -m ' + map_file_path + ' -o ' + options.output
log.debug(html_cmd)
Expand Down
2 changes: 1 addition & 1 deletion tools/virAnnot/rps2tsv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ def _read_xml(options):
hsp["evalue"] = hit_evalue
hsp["startQ"] = hit_startQ
hsp["endQ"] = hit_endQ
hsp["query_id"] = blast_record.query_id
hsp["query_id"] = blast_record.query
hsp["cdd_id"] = aln.hit_def.split(",")[0]
hsp["hit_id"] = aln.hit_id
hsp["query_length"] = blast_record.query_length # length of the query
Expand Down
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