From 197ebed48e55f047d8a06834f7a4cbbd4388948e Mon Sep 17 00:00:00 2001
From: oboulle <olivier.boulle@inria.fr>
Date: Thu, 18 Aug 2022 09:28:09 +0200
Subject: [PATCH] select random fragments
---
cluster_consensus.py | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/cluster_consensus.py b/cluster_consensus.py
index e614c15..047a5f3 100755
--- a/cluster_consensus.py
+++ b/cluster_consensus.py
@@ -5,6 +5,7 @@ import sys
import networkx as nx
import time
import argparse
+import random
# used to get the consensus fragments from a directory of fragments clusters
@@ -124,7 +125,6 @@ def fragConsensus(frag_list, frag_length):
if len(cluster) != 0:
clusters_list.append(cluster)
kmers_positions[kmer] = clusters_list
-
# construct a list of pkmers
# a pkmer is an object containing a kmer & his average_position & weight
# example: ACCTGAGT:23:10
@@ -222,13 +222,15 @@ def consensusOnFragDir(frag_dir_path, output_path, frag_length, n_reads):
cluster_file.close()
if n_reads is not None:
- frag_list = frag_list[:n_reads]
+ frag_list = random.sample(frag_list, min(len(frag_list), n_reads))
consensus_sequence = fragConsensus(frag_list, frag_length)
#if len(consensus_sequence) >= 2*frag_length/3:
-
+
consensus_file.write(">consensus_of_"+cluster_filename+"\n")
consensus_file.write(consensus_sequence+"\n")
+ #if len(consensus_sequence) < 2*frag_length/3:
+ #print(cluster_filename)
computed_consensus += 1
consensus_file.close()
--
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