Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

FIX: gtf.cds.gff is now created when --chunks options is used #341

Merged
merged 1 commit into from
Oct 11, 2024
Merged

FIX: gtf.cds.gff is now created when --chunks options is used #341

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 16 additions & 7 deletions sqanti3_qc.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -431,7 +431,8 @@ def get_corr_filenames(args, dir=None):
corrSAM = corrPathPrefix +"_corrected.sam"
corrFASTA = corrPathPrefix +"_corrected.fasta"
corrORF = corrPathPrefix +"_corrected.faa"
return corrGTF, corrSAM, corrFASTA, corrORF
corrCDS_GTF_GFF = corrPathPrefix + "_corrected.gtf.cds.gff"
return corrGTF, corrSAM, corrFASTA, corrORF, corrCDS_GTF_GFF

def get_isoform_hits_name(args, dir=None):
d = dir if dir is not None else args.dir
Expand Down Expand Up @@ -461,7 +462,7 @@ def correctionPlusORFpred(args, genome_dict):
global corrSAM
global corrFASTA

corrGTF, corrSAM, corrFASTA, corrORF = get_corr_filenames(args)
corrGTF, corrSAM, corrFASTA, corrORF , corrCDS_GTF_GFF = get_corr_filenames(args)
p = os.path.splitext(os.path.basename(corrSAM))[0]
n_cpu = max(1, args.cpus // args.chunks)

Expand Down Expand Up @@ -1856,7 +1857,7 @@ def run(args):
global isoform_hits_name
global badstrandGTF

corrGTF, corrSAM, corrFASTA, corrORF = get_corr_filenames(args)
corrGTF, corrSAM, corrFASTA, corrORF , corrCDS_GTF_GFF = get_corr_filenames(args)
badstrandGTF = args.dir + "/unknown_strand.gtf"
outputClassPath, outputJuncPath = get_class_junc_filenames(args)

Expand Down Expand Up @@ -2365,7 +2366,7 @@ def combine_split_runs(args, split_dirs):
Combine .faa, .fasta, .gtf, .classification.txt, .junctions.txt
Then write out the PDF report
"""
corrGTF, corrSAM, corrFASTA, corrORF = get_corr_filenames(args)
corrGTF, corrSAM, corrFASTA, corrORF , corrCDS_GTF_GFF = get_corr_filenames(args)
outputClassPath, outputJuncPath = get_class_junc_filenames(args)

if not args.skipORF:
Expand All @@ -2374,9 +2375,10 @@ def combine_split_runs(args, split_dirs):
f_gtf = open(corrGTF, 'w')
f_class = open(outputClassPath, 'w')
f_junc = open(outputJuncPath, 'w')
f_cds_gtf_gff = open(corrCDS_GTF_GFF, 'w')

for i,split_d in enumerate(split_dirs):
_gtf, _sam, _fasta, _orf = get_corr_filenames(args, split_d)
_gtf, _sam, _fasta, _orf , _CDS_GTF_GFF = get_corr_filenames(args, split_d)
_class, _junc = get_class_junc_filenames(args, split_d)
if not args.skipORF:
with open(_orf) as h: f_faa.write(h.read())
Expand All @@ -2394,11 +2396,18 @@ def combine_split_runs(args, split_dirs):
else:
h.readline()
f_junc.write(h.read())
with open(_CDS_GTF_GFF) as h:
if i == 0: # This if condition checks if its the first file to write the header or not in the final file
f_cds_gtf_gff.write(h.readline())
else:
h.readline()
f_cds_gtf_gff.write(h.read())

f_fasta.close()
f_gtf.close()
f_class.close()
f_junc.close()
f_cds_gtf_gff.close()
if not args.skipORF:
f_faa.close()

Expand Down Expand Up @@ -2579,7 +2588,7 @@ def main():
if args.chunks == 1:
run(args)
if args.isoAnnotLite:
corrGTF, corrSAM, corrFASTA, corrORF = get_corr_filenames(args)
corrGTF, corrSAM, corrFASTA, corrORF , corrCDS_GTF_GFF = get_corr_filenames(args)
outputClassPath, outputJuncPath = get_class_junc_filenames(args)
run_isoAnnotLite(corrGTF, outputClassPath, outputJuncPath, args.output, args.gff3)
else:
Expand All @@ -2588,7 +2597,7 @@ def main():
SPLIT_ROOT_DIR = get_split_dir(args)
shutil.rmtree(SPLIT_ROOT_DIR)
if args.isoAnnotLite:
corrGTF, corrSAM, corrFASTA, corrORF = get_corr_filenames(args)
corrGTF, corrSAM, corrFASTA, corrORF , corrCDS_GTF_GFF = get_corr_filenames(args)
outputClassPath, outputJuncPath = get_class_junc_filenames(args)
run_isoAnnotLite(corrGTF, outputClassPath, outputJuncPath, args.output, args.gff3)

Expand Down