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ref not source
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@olga24912
olga24912 committed Oct 25, 2018
1 parent 3a423bc commit 8d6b743
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Showing 2 changed files with 29 additions and 26 deletions.
7 changes: 0 additions & 7 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -153,13 +153,6 @@ install(PROGRAMS "${CMAKE_CURRENT_SOURCE_DIR}/UI/scripts/utils.js"
DESTINATION bin/scripts/
COMPONENT runtime)








install(PROGRAMS "${CMAKE_CURRENT_SOURCE_DIR}/UI/scripts/Icon.png"
DESTINATION bin/scripts/
COMPONENT runtime)
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48 changes: 29 additions & 19 deletions sgtk.py
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Original file line number Diff line number Diff line change
Expand Up @@ -151,8 +151,8 @@ def parse_args():
parser.add_argument("--rna-p", dest="rnap", nargs=2, help="paths to RNA-Seq paired reads in SAM/BAM format", type=str, action=StoreArgAction)
parser.add_argument("--rna-s", dest="rnas", nargs=1, help="path to RNA-Seq single reads in SAM/BAM format", type=str, action=StoreArgAction)

parser.add_argument("--ref", dest="ref", nargs=1, help="path to reference genome in FASTA format", type=str, action=StoreArgAction)
parser.add_argument("--refcoord", dest="refcoord", nargs=2, help="path to ref and to alignment of contigs to reference in coord format", type=str, action=StoreArgAction)
parser.add_argument("--ref", dest="ref", nargs=1, help="path to reference genome in FASTA format", type=str, action='append')
parser.add_argument("--refcoord", dest="refcoord", nargs=2, help="path to ref and to alignment of contigs to reference in coord format", type=str, action='append')

parser.add_argument("--gr", nargs=1, dest="graph", help="path to graph in .gr format", type=str, action='append')
parser.add_argument("--scg", nargs=1, dest="scg", help="path to file with connection list", type=str, action=StoreArgAction)
Expand Down Expand Up @@ -819,16 +819,16 @@ def add_conection_to_res_file(f):
f.write("scaffoldedges[" + str(i) + "].info=\"" + extraInfo + "\";\n")

def add_refcoord_to_res_file(contig_file_name, f):
if (len(args.libs["refcoord"]) == 0):
if (len(args.refcoord) == 0):
return

lib = args.libs["refcoord"][0]
lib = args.refcoord[0]

chrid = {}
chrlen = []
chrlist = []
chralig = []
fasta_seq = SeqIO.parse(open(lib.path[0]), 'fasta')
fasta_seq = SeqIO.parse(open(lib[0]), 'fasta')
curid = 0

for fasta in fasta_seq:
Expand All @@ -850,7 +850,7 @@ def add_refcoord_to_res_file(contig_file_name, f):
#TODO: del file
g = open("out.coords", "w")

with open(lib.path[1]) as cf:
with open(lib[1]) as cf:
for line in cf:
if ("[S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] | [TAGS]" in line or "====" in line):
continue
Expand Down Expand Up @@ -890,22 +890,19 @@ def getRefFileName(fileName):


def merge_ref_files(ref_libs):
if (len(ref_libs) == 1):
return ref_libs[0]

with open("ref_merge.fasta", "w") as out:
for i in range(len(ref_libs)):
for record in SeqIO.parse(ref_libs[i].path[0], "fasta"):
record.id = getRefFileName(ref_libs[i].path[0]) + "_" + record.id
for record in SeqIO.parse(ref_libs[i], "fasta"):
record.id = getRefFileName(ref_libs[i]) + "_" + record.id
SeqIO.write(record, out, "fasta")

return Lib([os.path.abspath("ref_merge.fasta")], "ref", "ref")

def add_ref_to_res_file(contig_file_name, f):
if (len(args.libs["ref"]) == 0):
if (len(args.ref) == 0):
return

lib = merge_ref_files(args.libs["ref"])
lib = merge_ref_files(args.ref)

prevdir = os.getcwd()
lib_dir = os.path.dirname(os.path.abspath(lib.name) + "/")
Expand All @@ -917,11 +914,11 @@ def add_ref_to_res_file(contig_file_name, f):
global idbyname
global lenbyid

chrnameToId = dict()
chrlist = []
chralig = []

curid = -2
lastname = '-'

chrm_len_by_name = dict()
save_lens_from_sam(chrm_len_by_name, "out.sam")
Expand All @@ -933,23 +930,22 @@ def add_ref_to_res_file(contig_file_name, f):
continue
vid = idbyname[qcont]
lenf = int(chrm_len_by_name[chrname])
if (chrname != lastname):
if (chrname not in chrnameToId):
curid += 2
chrlist.append("new Chromosome(" + str(curid) + ", '" + chrname + "', " + str(lenf) + ")")
chrlist.append("new Chromosome(" + str(curid + 1) + ", '" + chrname + "-rev', " + str(lenf) + ")")
chralig.append([])
chralig.append([])
lastname = chrname
chrnameToId[chrname] = curid

if ((max(rq, lq) - min(rq, lq)) * 100 < lenbyid[vid]):
continue

if (lq > rq):
vid ^= 1


chralig[curid].append("new Alignment(" + str(l) + ", " + str(r) + ", " + str(curid) + ", " + str(vid) + ")")
chralig[curid + 1].append("new Alignment(" + str(lenf - r) + ", " + str(lenf - l) + ", " + str(curid + 1) + ", " + str(vid^1) + ")")
chralig[chrnameToId[chrname]].append("new Alignment(" + str(l) + ", " + str(r) + ", " + str(chrnameToId[chrname]) + ", " + str(vid) + ")")
chralig[chrnameToId[chrname] + 1].append("new Alignment(" + str(lenf - r) + ", " + str(lenf - l) + ", " + str(chrnameToId[chrname] + 1) + ", " + str(vid^1) + ")")

for i in range(len(chrlist)):
f.write("chromosomes.push(" + chrlist[i] + ");\n")
Expand Down Expand Up @@ -1040,6 +1036,16 @@ def run(args):
for i in range(len(args.graph)):
args.graph[i] = os.path.abspath(args.graph[i][0])

if args.ref != None:
for i in range(len(args.ref)):
args.ref[i] = os.path.abspath(args.ref[i][0])

if args.refcoord != None:
for i in range(len(args.refcoord)):
args.refcoord[i][0] = os.path.abspath(args.refcoord[i][0])
args.refcoord[i][1] = os.path.abspath(args.refcoord[i][1])


out_dir = main_out_dir + "tmp/"
log.log("OUTPUT DIR: " + out_dir)
directory = os.path.dirname(out_dir)
Expand Down Expand Up @@ -1091,7 +1097,11 @@ def run(args):
add_conection_to_res_file(f)
if 'libs' in args:
save_scaffolds(contig_file_name, args, f)

if args.ref != None:
add_ref_to_res_file(contig_file_name, f)

if args.refcoord != None:
add_refcoord_to_res_file(contig_file_name, f)

f.write("var scaffoldgraph = new ScaffoldGraph(scaffoldlibs, scaffoldnodes, scaffoldedges);\n")
Expand Down

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