From 4db9e5f0a250e14e9bffe96bd5883b633a491029 Mon Sep 17 00:00:00 2001 From: Anton Korobeynikov Date: Fri, 1 Mar 2019 15:37:32 +0300 Subject: [PATCH] Trash cleanup --- assembler/wrapped_bin_spades.py | 41 --------------------------------- 1 file changed, 41 deletions(-) delete mode 100755 assembler/wrapped_bin_spades.py diff --git a/assembler/wrapped_bin_spades.py b/assembler/wrapped_bin_spades.py deleted file mode 100755 index 305d2d5004..0000000000 --- a/assembler/wrapped_bin_spades.py +++ /dev/null @@ -1,41 +0,0 @@ -#!/usr/bin/env python - -import os -import sys -cur_d = os.path.dirname(os.path.realpath(__file__)) - -bin = os.path.join(cur_d, "bin/spades") - -if len(sys.argv) < 2 or len (sys.argv) > 3: - print "Usage: " + sys.argv[0] + " config file " -dir = "" -K = "" -if len (sys.argv) == 2: - os.system (bin + " " + sys.argv[1] + " " + os.path.join(cur_d, "configs/debruijn/mda_mode.info") + " " + os.path.join(cur_d, "configs/debruijn/meta_mode.info") + " " + os.path.join(cur_d, "configs/debruijn/plasmid_mode.info")) -for line in open(sys.argv[1], 'r'): - arr = line.split() - if len(arr) >= 2: - if arr[0] == "K": - K = "K" + arr[1] - if arr[0] == "output_base": - dir = arr[1] -dir = dir + "/" + K -res = dir + "/final_contigs_cat.fasta" -res_f = open(res, "w") -for file in os.listdir(dir): - farr = file.split('.') - if farr[-1] != "fasta": - continue - if farr[-2] != "circular": - continue - arr = farr[-3].split("_") - if len(arr) < 2: - continue - cov = arr[-1] - - # for line in open(os.path.join(dir,file), "r"): - for line in open(file, "r"): - line = line.strip() - if len(line) > 0 and line[0] == ">": - line += "_cutoff_" + cov - res_f.write(line+ "\n")