/
report.py
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/
report.py
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#!/usr/bin/env python
from __future__ import print_function
import os
import sys
from . import common
from .tasks import get_maf_gff3_task, \
get_hmmscan_gff3_task, \
get_cmscan_gff3_task, \
get_gff3_merge_task, \
get_crb_gff3_task, \
get_maf_best_hits_task, \
get_annotate_fasta_task
def get_report_tasks(transcriptome, annotator, databases, n_threads=1):
tasks = []
outputs = []
orthodb_best_hits = annotator.orthodb_fn + '.best.csv'
orthodb_gff3 = annotator.orthodb_fn + '.gff3'
tasks.append(
get_maf_best_hits_task(annotator.orthodb_fn,
orthodb_best_hits)
)
tasks.append(
get_maf_gff3_task(orthodb_best_hits,
orthodb_gff3, 'OrthoDB')
)
outputs.append(orthodb_gff3)
if annotator.args.full:
uniref_best_hits = annotator.uniref_fn + '.best.csv'
uniref_gff3 = uniref_best_hits + '.gff3'
tasks.append(get_maf_best_hits_task(annotator.uniref_fn,
uniref_best_hits))
tasks.append(get_maf_gff3_task(uniref_best_hits,
uniref_gff3, 'uniref90'))
outputs.append(uniref_gff3)
pfam_gff3 = annotator.pfam_fn + '.gff3'
tasks.append(
get_hmmscan_gff3_task(annotator.pfam_fn,
pfam_gff3,
'Pfam')
)
outputs.append(pfam_gff3)
rfam_gff3 = annotator.rfam_fn + '.gff3'
tasks.append(
get_cmscan_gff3_task(annotator.rfam_fn,
rfam_gff3,
'Rfam')
)
outputs.append(rfam_gff3)
for db, fn in annotator.user_pep_fn_dict.iteritems():
gff3_fn = fn + '.gff3'
tasks.append(
get_crb_gff3_task(fn, gff3_fn, db)
)
outputs.append(gff3_fn)
outputs.append(annotator.transdecoder_gff3_fn)
merged_gff3 = transcriptome + '.dammit.gff3'
tasks.append(
get_gff3_merge_task(outputs, merged_gff3)
)
outputs.append(merged_gff3)
renamed_transcriptome = transcriptome + '.dammit.fasta'
tasks.append(
get_annotate_fasta_task(transcriptome, merged_gff3,
renamed_transcriptome)
)
outputs.append(renamed_transcriptome)
return outputs, tasks