From 014d24735a85795946b3d5ee580351c5e840829d Mon Sep 17 00:00:00 2001
From: Thomas Bigot <thomas.bigot@pasteur.fr>
Date: Wed, 22 Feb 2017 13:31:28 +0100
Subject: [PATCH] Reorganization
---
.../makeAnotations.py | 36 ++++++++++---------
collapse.py => build/collapse.py | 0
fastaHmmr.py => build/fastaHmmr.py | 0
.../makeFastaFromCluster.py | 0
.../nucl2ProtGolden.py | 0
partialBlast.py => build/partialBlast.py | 0
.../partialHmmbuild.py | 0
partialMuscle.py => build/partialMuscle.py | 0
removeDup.py => build/removeDup.py | 0
serialBlast.sh => build/serialBlast.sh | 0
serialGolden.sh => build/serialGolden.sh | 0
serialHmmbuild.sh => build/serialHmmbuild.sh | 0
serialMuscle.sh => build/serialMuscle.sh | 0
13 files changed, 20 insertions(+), 16 deletions(-)
rename makeAnotations.py => annotate/makeAnotations.py (69%)
rename collapse.py => build/collapse.py (100%)
rename fastaHmmr.py => build/fastaHmmr.py (100%)
rename makeFastaFromCluster.py => build/makeFastaFromCluster.py (100%)
rename nucl2ProtGolden.py => build/nucl2ProtGolden.py (100%)
rename partialBlast.py => build/partialBlast.py (100%)
rename partialHmmbuild.py => build/partialHmmbuild.py (100%)
rename partialMuscle.py => build/partialMuscle.py (100%)
rename removeDup.py => build/removeDup.py (100%)
rename serialBlast.sh => build/serialBlast.sh (100%)
rename serialGolden.sh => build/serialGolden.sh (100%)
rename serialHmmbuild.sh => build/serialHmmbuild.sh (100%)
rename serialMuscle.sh => build/serialMuscle.sh (100%)
diff --git a/makeAnotations.py b/annotate/makeAnotations.py
similarity index 69%
rename from makeAnotations.py
rename to annotate/makeAnotations.py
index 5da26cf..6a9728d 100644
--- a/makeAnotations.py
+++ b/annotate/makeAnotations.py
@@ -2,9 +2,9 @@
# -*- coding: utf-8 -*-
import glob,re,argparse
-#from taxadb.schema import *
-#from taxadb import accession
-#from taxadb import taxid
+from taxadb.schema import *
+from taxadb import accession
+from taxadb import taxid
parser = argparse.ArgumentParser()
parser.add_argument("hmmDB", help="hmm file")
@@ -55,20 +55,24 @@ print("\nReading acc number from gathered data")
for currCluster in allHMM.keys():
accs = []
for ca in allHMM[currCluster]["annotations"]:
- print(ca)
- accs.append(ca.split("|")[3].split(".")[0])
- #allHMM[currCluster]["taxid"] = accession.taxid(accs, args.taxadb, Prot)
- allHMM[currCluster]["taxid"] = "1234"
+ accs.append(re.findall("[A-Z0-9\._]{5,10}",ca)[0].split(".")[0])
+ allHMM[currCluster]["taxid"] = []
+ currAcc = 0
+ # proceeding by lots, to avoid `too many SQL variables` issue
+ while currAcc < len(accs):
+ allHMM[currCluster]["taxid"].append(accession.taxid(accs[currAcc:(min(currAcc+50,len(accs)-1))], args.taxadb, Prot))
+ currAcc += 50
# from taxid family
allHMM[currCluster]["families"] = {}
- for ct in allHMM[currCluster]["taxid"]:
- #lineage = taxid.lineage_name(ct[1], args.taxadb)
- lineage = (1234,"ABCD")
- family = lineage[2]
- if family not in allHMM[currCluster]["families"].keys():
- allHMM[currCluster]["families"][family] = 1
- else:
- allHMM[currCluster]["families"][family] += 1
+ # deloting
+ for ctgen in allHMM[currCluster]["taxid"]:
+ for ct in ctgen:
+ lineage = taxid.lineage_name(ct[1], args.taxadb)
+ family = lineage[2]
+ if family not in allHMM[currCluster]["families"].keys():
+ allHMM[currCluster]["families"][family] = 1
+ else:
+ allHMM[currCluster]["families"][family] += 1
print("Done !")
@@ -81,4 +85,4 @@ for currCluster in allHMM.keys():
currAnnot.write("FAMILIES\t" + str(allHMM[currCluster]["families"]) + "\n")
currAnnot.write("FASTA SEQUENCE TITLES:\n")
for currST in allHMM[currCluster]["annotations"]:
- currAnnot.write(currST+"\n")
+ currAnnot.write(currST)
diff --git a/collapse.py b/build/collapse.py
similarity index 100%
rename from collapse.py
rename to build/collapse.py
diff --git a/fastaHmmr.py b/build/fastaHmmr.py
similarity index 100%
rename from fastaHmmr.py
rename to build/fastaHmmr.py
diff --git a/makeFastaFromCluster.py b/build/makeFastaFromCluster.py
similarity index 100%
rename from makeFastaFromCluster.py
rename to build/makeFastaFromCluster.py
diff --git a/nucl2ProtGolden.py b/build/nucl2ProtGolden.py
similarity index 100%
rename from nucl2ProtGolden.py
rename to build/nucl2ProtGolden.py
diff --git a/partialBlast.py b/build/partialBlast.py
similarity index 100%
rename from partialBlast.py
rename to build/partialBlast.py
diff --git a/partialHmmbuild.py b/build/partialHmmbuild.py
similarity index 100%
rename from partialHmmbuild.py
rename to build/partialHmmbuild.py
diff --git a/partialMuscle.py b/build/partialMuscle.py
similarity index 100%
rename from partialMuscle.py
rename to build/partialMuscle.py
diff --git a/removeDup.py b/build/removeDup.py
similarity index 100%
rename from removeDup.py
rename to build/removeDup.py
diff --git a/serialBlast.sh b/build/serialBlast.sh
similarity index 100%
rename from serialBlast.sh
rename to build/serialBlast.sh
diff --git a/serialGolden.sh b/build/serialGolden.sh
similarity index 100%
rename from serialGolden.sh
rename to build/serialGolden.sh
diff --git a/serialHmmbuild.sh b/build/serialHmmbuild.sh
similarity index 100%
rename from serialHmmbuild.sh
rename to build/serialHmmbuild.sh
diff --git a/serialMuscle.sh b/build/serialMuscle.sh
similarity index 100%
rename from serialMuscle.sh
rename to build/serialMuscle.sh
--
GitLab