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Changed file names and added annotations to various subject orthologs.
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@dmitrymyl
dmitrymyl committed Oct 29, 2021
1 parent a28e7f1 commit 8027bd5
Showing 1 changed file with 45 additions and 27 deletions.
72 changes: 45 additions & 27 deletions ortho2align/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -884,41 +884,33 @@ def build_orthologs(alignments,
for group in subject_orthologs
for ortholog in group
if ortholog]

query_dropped = list()
subject_dropped = list()
for item in dropped_ranges:
if len(item) != 2:
continue
query_dropped_range, subject_dropped_ranges = item
query_dropped.append(query_dropped_range)
print(query_dropped_range.name)
for grange in subject_dropped_ranges:
print(grange)
subject_lifts = grange.find_neighbours(query_dropped_range.relations['lifted'])
print(subject_lifts)
subject_dropped.append(subject_lifts)
query_dropped = BaseGenomicRangesList(query_dropped)
subject_dropped = BaseGenomicRangesList(srange
for group in subject_dropped
for srange in group).drop_duplicates()
# query_dropped = BaseGenomicRangesList([item[0]
# for item in dropped_ranges
# if item])
# subject_dropped = BaseGenomicRangesList([srange
# for item in dropped_ranges
# if item
# for srange in item[1]])

total_dropped = len(query_dropped)
query_exception_list = BaseGenomicRangesList(query_exception_ranges)

if not os.path.exists(outdir):
os.mkdir(outdir)
query_output_bed12_filename = os.path.join(outdir, 'query_orthologs.bed')
subject_output_bed12_filename = os.path.join(outdir, 'subject_orthologs.bed')
query_output_total_filename = os.path.join(outdir, 'query_orthologs.tsv')
subject_output_total_filename = os.path.join(outdir, 'subject_orthologs.tsv')
query_dropped_filename = os.path.join(outdir, 'query_dropped.bed')
subject_dropped_filename = os.path.join(outdir, 'subject_dropped.bed')
query_output_bed12_filename = os.path.join(outdir, 'significant.query_orthologs.bed')
subject_output_bed12_filename = os.path.join(outdir, 'significant.subject_orthologs.bed')
query_output_total_filename = os.path.join(outdir, 'significant.query_orthologs.tsv')
subject_output_total_filename = os.path.join(outdir, 'significant.subject_orthologs.tsv')
query_dropped_filename = os.path.join(outdir, 'insignificant.query_orthologs.bed')
subject_dropped_filename = os.path.join(outdir, 'insignificant.subject_orthologs.bed')
query_exceptions_filename = os.path.join(outdir, 'query_exceptions.bed')

with open(query_output_bed12_filename, 'w') as outfile:
Expand Down Expand Up @@ -1079,7 +1071,7 @@ def annotate_orthologs(subject_orthologs,

stats_msg = "-----------------------\n" \
f"annotate_orthologs stats:\n" \
f"Recieved {len(subject_orthologs)} orthologs.\n" \
f"Recieved {len(subject_orthologs)} orthologs from {subject_orthologs_filename}.\n" \
f"Distribution of amount of annotations:\n{simple_hist(dist_annot_amounts)}\n" \
f"Reported all annotations for each ortholog.\n" \
"-----------------------"
Expand Down Expand Up @@ -1131,15 +1123,23 @@ def run_pipeline(query_genes,
bg_outdir = os.path.join(outdir, 'bg_files')
align_outdir = os.path.join(outdir, 'align_files')
build_outdir = os.path.join(outdir, 'build_files')
query_orthologs = os.path.join(build_outdir, 'query_orthologs.bed')
query_total_orthologs = os.path.join(build_outdir, 'query_orthologs.tsv')
subject_orthologs = os.path.join(build_outdir, 'subject_orthologs.bed')
subject_total_orthologs = os.path.join(build_outdir, 'subject_orthologs.tsv')
best_query_orthologs = os.path.join(outdir, 'best.query_orthologs.bed')
best_query_total_orthologs = os.path.join(outdir, 'best.query_orthologs.tsv')
best_subject_orthologs = os.path.join(outdir, 'best.subject_orthologs.bed')
best_subject_total_orthologs = os.path.join(outdir, 'best.subject_orthologs.tsv')
annotation_output = os.path.join(outdir, 'best.ortholog_annotation.tsv')
annotation_outdir = os.path.join(outdir, 'annotation_files')
if not os.path.exists(annotation_outdir):
os.mkdir(annotation_outdir)
subject_unaligned_orthologs = os.path.join(align_outdir, 'subject_unaligned.bed')
query_orthologs = os.path.join(build_outdir, 'significant.query_orthologs.bed')
query_total_orthologs = os.path.join(build_outdir, 'significant.query_orthologs.tsv')
subject_orthologs = os.path.join(build_outdir, 'significant.subject_orthologs.bed')
subject_total_orthologs = os.path.join(build_outdir, 'significant.subject_orthologs.tsv')
subject_insignificant_orthologs = os.path.join(build_outdir, 'insignificant.subject_orthologs.bed')
best_query_orthologs = os.path.join(outdir, 'bestSignificant.query_orthologs.bed')
best_query_total_orthologs = os.path.join(outdir, 'bestSignificant.query_orthologs.tsv')
best_subject_orthologs = os.path.join(outdir, 'bestSignificant.subject_orthologs.bed')
best_subject_total_orthologs = os.path.join(outdir, 'bestSignificant.subject_orthologs.tsv')
unaligned_annotation_output = os.path.join(annotation_outdir, 'unaligned.annotation.tsv')
insignificant_annotation_output = os.path.join(annotation_outdir, 'insignificant.annotation.tsv')
significant_annotation_output = os.path.join(annotation_outdir, 'significant.annotation.tsv')
best_annotation_output = os.path.join(annotation_outdir, 'bestSignificant.annotation.tsv')
stats_filename = os.path.join(outdir, 'stats.txt')

bg_from_shuffled_ranges(genes_filename=subject_annotation,
Expand Down Expand Up @@ -1204,9 +1204,27 @@ def run_pipeline(query_genes,
outfile_subject=best_subject_orthologs,
outfile_subject_total=best_subject_total_orthologs)
if annotate:
annotate_orthologs(subject_orthologs=subject_unaligned_orthologs,
subject_annotation=subject_annotation,
output=unaligned_annotation_output,
subject_name_regex=subject_name_regex,
stats_filename=stats_filename,
float_precision=float_precision)
annotate_orthologs(subject_orthologs=subject_insignificant_orthologs,
subject_annotation=subject_annotation,
output=insignificant_annotation_output,
subject_name_regex=subject_name_regex,
stats_filename=stats_filename,
float_precision=float_precision)
annotate_orthologs(subject_orthologs=subject_orthologs,
subject_annotation=subject_annotation,
output=significant_annotation_output,
subject_name_regex=subject_name_regex,
stats_filename=stats_filename,
float_precision=float_precision)
annotate_orthologs(subject_orthologs=best_subject_orthologs,
subject_annotation=subject_annotation,
output=annotation_output,
output=best_annotation_output,
subject_name_regex=subject_name_regex,
stats_filename=stats_filename,
float_precision=float_precision)
Expand Down

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