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Auden Cote-L'Heureux 2023-06-13 14:01:17 -04:00 committed by GitHub
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commit 69844a6d66
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1 changed files with 15 additions and 11 deletions
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26
PTL1/Transcriptomes/Scripts/8_SummaryStats.py
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@ -52,18 +52,20 @@ def aa_comp_lengths(args, gcodes):
for rec in SeqIO.parse(args.input + '/ReadyToGo/ReadyToGo_AA/' + file, 'fasta'): for rec in SeqIO.parse(args.input + '/ReadyToGo/ReadyToGo_AA/' + file, 'fasta'):
r2g_lengths.update({ rec.id : len(str(rec.seq)) * 3 }) r2g_lengths.update({ rec.id : len(str(rec.seq)) * 3 })
fymink = 0; garp = 0; other = 0; total = 0 fymink = 0; garp = 0; other = 0; total = 0; x = 0
for char in str(rec.seq): for char in str(rec.seq):
if char in 'FYMINK': if char in 'FYMINKfymink':
fymink += 1 fymink += 1
elif char in 'GARP': elif char in 'GARPgarp':
garp += 1 garp += 1
elif char in 'Xx':
x += 1
else: else:
other += 1 other += 1
total += 1 total += 1
aa_comp.update({ rec.id : { 'FYMINK' : fymink/total, 'GARP' : garp/total, 'Other' : other/total } }) aa_comp.update({ rec.id : { 'FYMINK' : fymink/total, 'GARP' : garp/total, 'Other' : other/total, 'X' : x} })
recid_by_contig_n.update({ rec.id.split('Contig_')[-1].split('_')[0] : rec.id }) recid_by_contig_n.update({ rec.id.split('Contig_')[-1].split('_')[0] : rec.id })
@ -89,7 +91,7 @@ def get_nuc_comp(args, gcodes):
nuc_comp = { } nuc_comp = { }
for file in tqdm([f for f in os.listdir(args.input + '/ReadyToGo/ReadyToGo_NTD')]): for file in tqdm([f for f in os.listdir(args.input + '/ReadyToGo/ReadyToGo_NTD')]):
if file.endswith('.fasta') and file[:10] in gcodes: if file.endswith('.fasta') and file[:10] in gcodes:
cub_out = CUB.CalcRefFasta(args.input + '/ReadyToGo/ReadyToGo_NTD/' + file, gcodes[file[:10]])[0] cub_out = CUB.CalcRefFasta(args.input + '/ReadyToGo/ReadyToGo_NTD/' + file, gcodes[file[:10]].lower())[0]
for k in cub_out: for k in cub_out:
nuc_comp.update({ k : cub_out[k] }) nuc_comp.update({ k : cub_out[k] })
@ -107,7 +109,7 @@ def per_seq(args, nuc_comp, aa_comp, all_transcripts, r2g_lengths, transcript_id
for taxon in taxa: for taxon in taxa:
with open(args.input + '/PerSequenceStatSummaries/' + taxon + '.csv', 'w') as o: with open(args.input + '/PerSequenceStatSummaries/' + taxon + '.csv', 'w') as o:
o.write('Sequence,Taxon,OG,Transcript,TranscriptLength,CDSLength,AvgLengthOGinHook,AmbiguousCodons,GC-Overall,GC1,GC2,GC3,GC3-Degen,ExpWrightENc,ObsWrightENc_6Fold,ObsWrightENc_No6Fold,ObsWeightedENc_6Fold,ObsWeightedENc_No6Fold,FYMINK,GARP,OtherAA\n') o.write('Sequence,Taxon,OG,Transcript,TranscriptLength,CDSLength,AvgLengthOGinHook,AmbiguousCodons,GC-Overall,GC1,GC2,GC3,GC3-Degen,ExpWrightENc,ObsWrightENc_6Fold,ObsWrightENc_No6Fold,ObsWeightedENc_6Fold,ObsWeightedENc_No6Fold,FYMINK,GARP,OtherAA,N.Xs\n')
for rec in nuc_comp: for rec in nuc_comp:
if rec[:10] == taxon: if rec[:10] == taxon:
o.write(rec + ',' + rec[:10] + ',' + rec[-10:]) o.write(rec + ',' + rec[:10] + ',' + rec[-10:])
@ -124,7 +126,7 @@ def per_seq(args, nuc_comp, aa_comp, all_transcripts, r2g_lengths, transcript_id
ENc = [str(v.expENc), str(v.obsENc_6F), str(v.obsENc_No6F), str(v.SunENc_6F),str(v.SunENc_No6F)] ENc = [str(v.expENc), str(v.obsENc_6F), str(v.obsENc_No6F), str(v.SunENc_6F),str(v.SunENc_No6F)]
o.write(',' + ','.join([str(v.amb_cdn)] + gcs + ENc)) o.write(',' + ','.join([str(v.amb_cdn)] + gcs + ENc))
o.write(',' + str(aa_comp[rec]['FYMINK']) + ',' + str(aa_comp[rec]['GARP']) + ',' + str(aa_comp[rec]['Other']) + '\n') o.write(',' + str(aa_comp[rec]['FYMINK']) + ',' + str(aa_comp[rec]['GARP']) + ',' + str(aa_comp[rec]['Other']) + ',' + str(aa_comp[rec]['X']) + '\n')
def per_tax(args, nuc_comp, aa_comp, all_transcripts, r2g_lengths, gcodes): def per_tax(args, nuc_comp, aa_comp, all_transcripts, r2g_lengths, gcodes):
@ -132,7 +134,7 @@ def per_tax(args, nuc_comp, aa_comp, all_transcripts, r2g_lengths, gcodes):
taxa = list(dict.fromkeys([seq[:10] for seq in nuc_comp])) taxa = list(dict.fromkeys([seq[:10] for seq in nuc_comp]))
with open(args.input + '/PerTaxonSummary.csv', 'w') as o: with open(args.input + '/PerTaxonSummary.csv', 'w') as o:
o.write('Taxon,TranscriptsInput,Median_GCTranscripts,IQR_GCTranscripts,Median_LenTranscripts,IRQ_LenTranscripts,SeqsR2G,OGsR2G,Median_GC3R2G,IQR_GC3R2G,Median_ENcR2G,IQR_ENcR2G,Median_LenR2G,IQR_LenR2G,GeneticCode\n') o.write('Taxon,TranscriptsInput,Median_GCTranscripts,5-95Perc_GCTranscripts,Median_LenTranscripts,IRQ_LenTranscripts,SeqsR2G,OGsR2G,Median_GC3R2G,5Perc_GC3R2G,95Perc_GC3R2G,5-95Perc_GC3R2G,Median_ENcR2G,IQR_ENcR2G,Median_LenR2G,IQR_LenR2G,GeneticCode\n')
for taxon in taxa: for taxon in taxa:
o.write(taxon) o.write(taxon)
@ -146,7 +148,7 @@ def per_tax(args, nuc_comp, aa_comp, all_transcripts, r2g_lengths, gcodes):
transcript_gcs = sorted(transcript_gcs) transcript_gcs = sorted(transcript_gcs)
o.write(',' + str(transcript_gcs[floor(len(transcripts)*0.5)])) o.write(',' + str(transcript_gcs[floor(len(transcripts)*0.5)]))
o.write(',' + str(transcript_gcs[floor(len(transcripts)*0.75)] - transcript_gcs[floor(len(transcripts)*0.25)])) o.write(',' + str(transcript_gcs[floor(len(transcripts)*0.95)] - transcript_gcs[floor(len(transcripts)*0.05)]))
transcript_lens = sorted([len(transcript) for transcript in transcripts]) transcript_lens = sorted([len(transcript) for transcript in transcripts])
o.write(',' + str(transcript_lens[floor(len(transcripts)*0.5)])) o.write(',' + str(transcript_lens[floor(len(transcripts)*0.5)]))
@ -159,7 +161,9 @@ def per_tax(args, nuc_comp, aa_comp, all_transcripts, r2g_lengths, gcodes):
r2g_gc3s = sorted([seq.gc4F for seq in r2g_ntds]) r2g_gc3s = sorted([seq.gc4F for seq in r2g_ntds])
o.write(',' + str(r2g_gc3s[floor(len(r2g_ntds)*0.5)])) o.write(',' + str(r2g_gc3s[floor(len(r2g_ntds)*0.5)]))
o.write(',' + str(r2g_gc3s[floor(len(r2g_gc3s)*0.75)] - r2g_gc3s[floor(len(r2g_gc3s)*0.25)])) o.write(',' + str(r2g_gc3s[floor(len(r2g_gc3s)*0.05)]))
o.write(',' + str(r2g_gc3s[floor(len(r2g_gc3s)*0.95)]))
o.write(',' + str(r2g_gc3s[floor(len(r2g_gc3s)*0.95)] - r2g_gc3s[floor(len(r2g_gc3s)*0.05)]))
r2g_encs = sorted([seq.obsENc_6F for seq in r2g_ntds]) r2g_encs = sorted([seq.obsENc_6F for seq in r2g_ntds])
o.write(',' + str(r2g_encs[floor(len(r2g_encs)*0.5)])) o.write(',' + str(r2g_encs[floor(len(r2g_encs)*0.5)]))
@ -223,7 +227,7 @@ def plot_jf(args, nuc_comp):
if __name__ == "__main__": if __name__ == "__main__":
args = get_args() args = get_args()
valid_codes = ['universal', 'blepharisma', 'chilodonella', 'condylostoma', 'euplotes', 'peritrich', 'vorticella', 'mesodinium', 'tag', 'tga', 'taa', 'none'] valid_codes = ['bleph','blepharisma','chilo','chilodonella','condy', 'condylostoma','none','eup','euplotes','peritrich','vorticella','ciliate','universal','taa','tag','tga','mesodinium']
gcodes = { } gcodes = { }
if os.path.isfile(args.input + '/Intermediate/gcode_output.tsv'): if os.path.isfile(args.input + '/Intermediate/gcode_output.tsv'):