From 2257202a2116f8f72e3e77f178e2b3ac3e4c88ac Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Thu, 2 Dec 2021 16:41:52 +0100
Subject: [PATCH] remove a bug in MitoZ biopython gbf parsing
---
tools/mitoz_annotate/mitoz_annotate.yaml | 3 ++-
tools/mitoz_assemble/mitoz_assemble.yaml | 4 +++-
tools/mitoz_filter/mitoz_filter.yaml | 4 +++-
tools/mitoz_findmitoscaf/mitoz_findmitoscaf.yaml | 4 +++-
4 files changed, 11 insertions(+), 4 deletions(-)
diff --git a/tools/mitoz_annotate/mitoz_annotate.yaml b/tools/mitoz_annotate/mitoz_annotate.yaml
index b17ec9fd..54df5173 100755
--- a/tools/mitoz_annotate/mitoz_annotate.yaml
+++ b/tools/mitoz_annotate/mitoz_annotate.yaml
@@ -158,7 +158,8 @@
"python3 -c \"from ete3 import NCBITaxa;ncbi = NCBITaxa();ncbi.update_taxonomy_database()\"",
"sed -i 's/^ yield rec/ try:\n yield rec/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ",
"sed -i 's/^ raise StopIteration/ except:\n raise StopIteration/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ",
- "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior"
+ "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior ",
+ "sed 's/#return re.sub(pos_old, pos_new, str(pos))/return pos_new/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py"
],
ncbi_tools: [ #tbl2asn
"apt-get install -y ncbi-tools-bin"
diff --git a/tools/mitoz_assemble/mitoz_assemble.yaml b/tools/mitoz_assemble/mitoz_assemble.yaml
index c761795d..0f7fc4b3 100755
--- a/tools/mitoz_assemble/mitoz_assemble.yaml
+++ b/tools/mitoz_assemble/mitoz_assemble.yaml
@@ -177,7 +177,9 @@
"python3 -c \"from ete3 import NCBITaxa;ncbi = NCBITaxa();ncbi.update_taxonomy_database()\"",
"sed -i 's/^ yield rec/ try:\n yield rec/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ",
"sed -i 's/^ raise StopIteration/ except:\n raise StopIteration/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ",
- "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior"
+ "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior",
+ "sed 's/#return re.sub(pos_old, pos_new, str(pos))/return pos_new/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py"
+
]
},
citations: {
diff --git a/tools/mitoz_filter/mitoz_filter.yaml b/tools/mitoz_filter/mitoz_filter.yaml
index dda48cdf..07b72619 100755
--- a/tools/mitoz_filter/mitoz_filter.yaml
+++ b/tools/mitoz_filter/mitoz_filter.yaml
@@ -186,7 +186,9 @@
"python3 -c \"from ete3 import NCBITaxa;ncbi = NCBITaxa();ncbi.update_taxonomy_database()\"",
"sed -i 's/^ yield rec/ try:\n yield rec/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ",
"sed -i 's/^ raise StopIteration/ except:\n raise StopIteration/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ",
- "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior"
+ "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior",
+ "sed 's/#return re.sub(pos_old, pos_new, str(pos))/return pos_new/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py"
+
]
},
citations: {
diff --git a/tools/mitoz_findmitoscaf/mitoz_findmitoscaf.yaml b/tools/mitoz_findmitoscaf/mitoz_findmitoscaf.yaml
index cae4a16c..d166c890 100755
--- a/tools/mitoz_findmitoscaf/mitoz_findmitoscaf.yaml
+++ b/tools/mitoz_findmitoscaf/mitoz_findmitoscaf.yaml
@@ -106,7 +106,9 @@
"python3 -c \"from ete3 import NCBITaxa;ncbi = NCBITaxa();ncbi.update_taxonomy_database()\"",
"sed -i 's/^ yield rec/ try:\n yield rec/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ",
"sed -i 's/^ raise StopIteration/ except:\n raise StopIteration/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ",
- "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior"
+ "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior",
+ "sed 's/#return re.sub(pos_old, pos_new, str(pos))/return pos_new/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py"
+
]
},
citations: {
--
GitLab