diff _modules/seq_processing.py @ 0:69e8f12c8b31 draft

"planemo upload"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/_modules/seq_processing.py	Fri Mar 11 15:06:20 2022 +0000
@@ -0,0 +1,95 @@
+##@file seq_processing.py
+#
+# This file contains functions that are used when running phageterm on multiple machines on a calculation cluster.
+# @param DR_Path directory path where to put DR content.
+from __future__ import print_function
+
+from time import gmtime, strftime
+import os
+import numpy as np
+from _modules.utilities import checkReportTitle
+from _modules.readsCoverage_res import loadRCRes
+from _modules.common_readsCoverage_processing import processCovValuesForSeq
+#from SeqStats import SeqStats
+def sum_readsCoverage_for_seq(dir_cov_res,idx_refseq,nb_pieces,inDArgs,fParms,inRawDArgs,dir_seq_res,DR_path):
+    if os.path.exists(DR_path):
+        if not (os.path.isdir(DR_path)):
+            raise RuntimeError("DR_path must point to a directory")
+    else:
+        os.mkdir(DR_path)
+    DR = {"Headful (pac)": {}, "COS (5')": {}, "COS (3')": {}, "COS": {}, "DTR (short)": {}, "DTR (long)": {},
+          "Mu-like": {}, "UNKNOWN": {}, "NEW": {}}
+    print("going to load ",nb_pieces," files for sequence ",idx_refseq)
+    print(strftime("%a, %d %b %Y %H:%M:%S +0000", gmtime()))
+    for i in range(0,nb_pieces):
+        fic_name = os.path.join(dir_cov_res, "coverage" + str(idx_refseq) + "_" + str(i)+".npz")
+        print("loading file: ",fic_name)
+        print(strftime("%a, %d %b %Y %H:%M:%S +0000", gmtime()))
+        partial_res=loadRCRes(fic_name)
+        #npzfile=np.load(fic_name)
+        if i == 0:
+            termini_coverage = partial_res.termini_coverage
+            whole_coverage = partial_res.whole_coverage
+            paired_whole_coverage = partial_res.paired_whole_coverage
+            phage_hybrid_coverage = partial_res.phage_hybrid_coverage
+            host_hybrid_coverage = partial_res.host_hybrid_coverage
+            host_whole_coverage = partial_res.host_whole_coverage
+            list_hybrid = partial_res.list_hybrid
+            insert = partial_res.insert
+            paired_missmatch = partial_res.paired_mismatch
+            reads_tested = partial_res.reads_tested
+        else:
+            termini_coverage += partial_res.termini_coverage
+            whole_coverage += partial_res.whole_coverage
+            paired_whole_coverage += partial_res.paired_whole_coverage
+            phage_hybrid_coverage += partial_res.phage_hybrid_coverage
+            host_hybrid_coverage += partial_res.host_hybrid_coverage
+            host_whole_coverage += partial_res.host_whole_coverage
+            list_hybrid += partial_res.list_hybrid
+            insert += partial_res.insert
+            paired_missmatch += partial_res.paired_mismatch
+            reads_tested += partial_res.reads_tested
+
+    # fic_name = os.path.join(dir_seq_res, "coverage" + str(idx_refseq))
+    # np.savez(fic_name, termini_coverage=termini_coverage, whole_coverage=whole_coverage,
+    #          paired_whole_coverage=paired_whole_coverage, \
+    #          phage_hybrid_coverage=phage_hybrid_coverage, host_hybrid_coverage=host_hybrid_coverage, \
+    #          host_whole_coverage=host_whole_coverage, list_hybrid=list_hybrid, insert=insert,
+    #          paired_missmatch=np.array(paired_missmatch))
+    termini_coverage = termini_coverage.tolist()
+    whole_coverage = whole_coverage.tolist()
+    paired_whole_coverage = paired_whole_coverage.tolist()
+    phage_hybrid_coverage = phage_hybrid_coverage.tolist()
+    host_hybrid_coverage = host_hybrid_coverage.tolist()
+    host_whole_coverage = host_whole_coverage.tolist()
+    list_hybrid = list_hybrid.tolist()
+
+    if sum(termini_coverage[0]) + sum(termini_coverage[1]) == 0:
+        no_match_file="no_natch"+str(idx_refseq)
+        f=open(os.path.join(dir_seq_res,no_match_file),"w")
+        f.write((checkReportTitle(seq_name[idx_refseq])))
+        f.close()
+
+    print("finished sum, calling processCovValuesForSeq")
+    print(strftime("%a, %d %b %Y %H:%M:%S +0000", gmtime()))
+    # TODO: having so many values in input and returned is ugly and bad for readibility and maintanability. Group those who are related in structures.
+    refseq = inDArgs.refseq_liste[idx_refseq]
+    S_stats=processCovValuesForSeq(refseq, inDArgs.hostseq, inDArgs.refseq_name, inDArgs.refseq_liste, fParms.seed,
+                            inRawDArgs.analysis_name, inRawDArgs.tot_reads, \
+                            idx_refseq, fParms.test_run, inRawDArgs.paired, fParms.edge, inRawDArgs.host,
+                            fParms.test, fParms.surrounding, \
+                            fParms.limit_preferred, fParms.limit_fixed, fParms.Mu_threshold, termini_coverage,
+                            whole_coverage, \
+                            paired_whole_coverage, phage_hybrid_coverage, host_hybrid_coverage,
+                            host_whole_coverage, insert, list_hybrid, reads_tested, DR,DR_path)
+    #fic_name = os.path.join(dir_seq_res, "seq_stats" + str(idx_refseq))
+    # S_stats.toFile(fic_name) s_stats content is only used in the case where there is only 1 sequence. I'm not interested in this case here since sum_readsCoverage_for_seq will be used for viromes.
+    # so, just drop s_stat and forget it...
+    # Only writing DR content to file is usefuk in the case of a virome processing over several machines on a cluster.
+    print("exit sum_readsCoverage_for_seq")
+    print(strftime("%a, %d %b %Y %H:%M:%S +0000", gmtime()))
+
+
+
+
+