From 2b904c197cf1acf3a5b91a64dd099822ba77ae22 Mon Sep 17 00:00:00 2001
From: gregdenay <gregoire.denay@cvua-rrw.de>
Date: Thu, 25 Jul 2024 10:33:32 +0200
Subject: [PATCH] attempt fix blast report

---
 workflow/envs/blast.yaml        |  2 +-
 workflow/rules/blast.smk        |  1 -
 workflow/scripts/blast_stats.py | 16 ++++++++--------
 3 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/workflow/envs/blast.yaml b/workflow/envs/blast.yaml
index 093c60c..ade741e 100644
--- a/workflow/envs/blast.yaml
+++ b/workflow/envs/blast.yaml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - blast=2.16.0
+  - blast=2.12.0
diff --git a/workflow/rules/blast.smk b/workflow/rules/blast.smk
index abddfa7..73aa221 100644
--- a/workflow/rules/blast.smk
+++ b/workflow/rules/blast.smk
@@ -155,7 +155,6 @@ rule blast_otus:
             -qcov_hsp_perc {params.qcov} $masking \
             -outfmt '6 qseqid sseqid evalue pident bitscore sacc staxid length mismatch gaps stitle' \
             -num_threads {threads} \
-            -mt_mode 1 \
         2> {log} 
 
         sed -i '1 i\query\tsubject\tevalue\tidentity\tbitscore\tsubject_acc\tsubject_taxid\talignment_length\tmismatch\tgaps\tsubject_name' {output.report}
diff --git a/workflow/scripts/blast_stats.py b/workflow/scripts/blast_stats.py
index bd7f3f2..7cb1d98 100644
--- a/workflow/scripts/blast_stats.py
+++ b/workflow/scripts/blast_stats.py
@@ -55,7 +55,7 @@ def main(otus_in, blast_in, filtered_in, lca_in, report_out, bit_diff, sample):
         if not os.path.isfile(blast_in) or os.stat(blast_in).st_size == 0:
             with open(report_out, "a") as fo:
                 fo.write("\t".join([
-                    sample,
+                    str(sample),
                     "-",
                     "-",
                     "0",
@@ -82,8 +82,8 @@ def main(otus_in, blast_in, filtered_in, lca_in, report_out, bit_diff, sample):
                 if bhits == 0:
                     with open(report_out, "a") as fo:
                         fo.write("\t".join([
-                            sample,
-                            otu,
+                            str(sample),
+                            str(otu),
                             str(size),
                             "0",
                             "0",
@@ -106,18 +106,18 @@ def main(otus_in, blast_in, filtered_in, lca_in, report_out, bit_diff, sample):
 
                     with open(report_out, "a") as fo:
                         fo.write("\t".join([
-                            sample,
-                            otu,
+                            str(sample),
+                            str(otu),
                             str(size),
                             str(bhits),
                             str(bit_best),
                             str(bit_low),
                             str(bit_thr),
                             str(shits),
-                            cons["Consensus"].values[0],
-                            cons["Rank"].values[0],
+                            str(cons["Consensus"].values[0]),
+                            str(cons["Rank"].values[0]),
                             str(cons["Taxid"].values[0]),
-                            cons["Disambiguation"].values[0],
+                            str(cons["Disambiguation"].values[0]),
                             f"../{blast_in}",
                             f"../{filtered_in}"
                         ])+"\n")