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Small fix to 6_SummaryStats.py

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Auden Cote-L'Heureux 2023-08-21 13:24:42 -04:00 committed by GitHub
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commit 2f334642d3
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1 changed files with 14 additions and 14 deletions
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PTL1/Genomes/Scripts/6_SummaryStats.py
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@ -105,13 +105,13 @@ def get_nuc_comp(args, gcodes):
def per_seq(args, nuc_comp, aa_comp, all_transcripts, r2g_lengths, transcript_id_corr, og_mean_lens): def per_seq(args, nuc_comp, aa_comp, all_transcripts, r2g_lengths, transcript_id_corr, og_mean_lens):
if not os.path.isdir(args.input + '/PerSequenceStatSummaries_' + today): if not os.path.isdir(args.input + '/PerSequenceStatSummaries_' + str(today)):
os.mkdir(args.input + '/PerSequenceStatSummaries_' + today) os.mkdir(args.input + '/PerSequenceStatSummaries_' + str(today))
taxa = list(dict.fromkeys([seq[:10] for seq in nuc_comp])) taxa = list(dict.fromkeys([seq[:10] for seq in nuc_comp]))
for taxon in taxa: for taxon in taxa:
with open(args.input + '/PerSequenceStatSummaries_' + today + '/' + taxon + '.csv', 'w') as o: with open(args.input + '/PerSequenceStatSummaries_' + str(today) + '/' + taxon + '.csv', 'w') as o:
o.write('Sequence,Taxon,OG,OrigName,OrigLength,R2GLength,AvgLengthOGinHook,AmbiguousCodons,GC-Overall,GC1,GC2,GC3,GC3-Degen,ExpWrightENc,ObsWrightENc_6Fold,ObsWrightENc_No6Fold,ObsWeightedENc_6Fold,ObsWeightedENc_No6Fold,FYMINK,GARP,OtherAA,N.Xs\n') o.write('Sequence,Taxon,OG,OrigName,OrigLength,R2GLength,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:
@ -136,7 +136,7 @@ def per_tax(args, nuc_comp, aa_comp, all_transcripts, r2g_lengths, gcodes, og_me
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_' + today + '.csv', 'w') as o: with open(args.input + '/PerTaxonSummary_' + str(today) + '.csv', 'w') as o:
o.write('Taxon,OrigSeqs,Orig_MedianGC,Orig_GCWidth_5-95Perc,Orig_MedianLen,Orig_IQRLen,R2GSeqs,R2GOGs,R2GMedian_GC3,R2G_5Perc_GC3,R2G_95Perc_GC3,R2G_GC3Width_5-95Perc,R2G_MedianENc,R2G_IQRENc,R2G_MedianLen,R2G_IQRLen,R2G_Prop.G1.5_OGAvg,R2G_Prop.L0.5_OGAvg,R2G_MeanXs,GeneticCode\n') o.write('Taxon,OrigSeqs,Orig_MedianGC,Orig_GCWidth_5-95Perc,Orig_MedianLen,Orig_IQRLen,R2GSeqs,R2GOGs,R2GMedian_GC3,R2G_5Perc_GC3,R2G_95Perc_GC3,R2G_GC3Width_5-95Perc,R2G_MedianENc,R2G_IQRENc,R2G_MedianLen,R2G_IQRLen,R2G_Prop.G1.5_OGAvg,R2G_Prop.L0.5_OGAvg,R2G_MeanXs,GeneticCode\n')
for taxon in taxa: for taxon in taxa:
@ -193,11 +193,11 @@ def r2g_jf(args, nuc_comp, gcodes):
#Q: should there be an maximum IQR cutoff at which we do NOT produce a file here? #Q: should there be an maximum IQR cutoff at which we do NOT produce a file here?
if not os.path.isdir(args.input + '/ReadyToGo/ReadyToGo_NTD_JF_' + today): if not os.path.isdir(args.input + '/ReadyToGo/ReadyToGo_NTD_JF_' + str(today)):
os.mkdir(args.input + '/ReadyToGo/ReadyToGo_NTD_JF_' + today) os.mkdir(args.input + '/ReadyToGo/ReadyToGo_NTD_JF_' + str(today))
if not os.path.isdir(args.input + '/ReadyToGo/ReadyToGo_AA_JF_' + today): if not os.path.isdir(args.input + '/ReadyToGo/ReadyToGo_AA_JF_' + str(today)):
os.mkdir(args.input + '/ReadyToGo/ReadyToGo_AA_JF_' + today) os.mkdir(args.input + '/ReadyToGo/ReadyToGo_AA_JF_' + str(today))
for file in os.listdir(args.input + '/ReadyToGo/ReadyToGo_NTD'): for file 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:
@ -206,12 +206,12 @@ def r2g_jf(args, nuc_comp, gcodes):
r2g_ntds = [nuc_comp[seq] for seq in nuc_comp if seq[:10] == taxon] r2g_ntds = [nuc_comp[seq] for seq in nuc_comp if seq[:10] == taxon]
r2g_gc3s = sorted([seq.gc4F for seq in r2g_ntds]) r2g_gc3s = sorted([seq.gc4F for seq in r2g_ntds])
with open(args.input + '/ReadyToGo/ReadyToGo_NTD_JF_' + today + '/' + file.replace('.fasta', '.JF.fasta'), 'w') as o: with open(args.input + '/ReadyToGo/ReadyToGo_NTD_JF_' + str(today) + '/' + file.replace('.fasta', '.JF.fasta'), 'w') as o:
for rec in SeqIO.parse(args.input + '/ReadyToGo/ReadyToGo_NTD/' + file, 'fasta'): for rec in SeqIO.parse(args.input + '/ReadyToGo/ReadyToGo_NTD/' + file, 'fasta'):
if nuc_comp[rec.id].gc4F > r2g_gc3s[floor(len(r2g_gc3s)*0.25)] and nuc_comp[rec.id].gc4F < r2g_gc3s[floor(len(r2g_gc3s)*0.75)]: if nuc_comp[rec.id].gc4F > r2g_gc3s[floor(len(r2g_gc3s)*0.25)] and nuc_comp[rec.id].gc4F < r2g_gc3s[floor(len(r2g_gc3s)*0.75)]:
o.write('>' + rec.id + '\n' + str(rec.seq) + '\n\n') o.write('>' + rec.id + '\n' + str(rec.seq) + '\n\n')
with open(args.input + '/ReadyToGo/ReadyToGo_AA_JF_' + today + '/' + file.replace('.fasta', '.JF.fasta').replace('NTD', 'AA'), 'w') as o: with open(args.input + '/ReadyToGo/ReadyToGo_AA_JF_' + str(today) + '/' + file.replace('.fasta', '.JF.fasta').replace('NTD', 'AA'), 'w') as o:
for rec in SeqIO.parse(args.input + '/ReadyToGo/ReadyToGo_AA/' + file.replace('NTD', 'AA'), 'fasta'): for rec in SeqIO.parse(args.input + '/ReadyToGo/ReadyToGo_AA/' + file.replace('NTD', 'AA'), 'fasta'):
if nuc_comp[rec.id].gc4F > r2g_gc3s[floor(len(r2g_gc3s)*0.25)] and nuc_comp[rec.id].gc4F < r2g_gc3s[floor(len(r2g_gc3s)*0.75)]: if nuc_comp[rec.id].gc4F > r2g_gc3s[floor(len(r2g_gc3s)*0.25)] and nuc_comp[rec.id].gc4F < r2g_gc3s[floor(len(r2g_gc3s)*0.75)]:
o.write('>' + rec.id + '\n' + str(rec.seq) + '\n\n') o.write('>' + rec.id + '\n' + str(rec.seq) + '\n\n')
@ -219,8 +219,8 @@ def r2g_jf(args, nuc_comp, gcodes):
def plot_jf(args, nuc_comp): def plot_jf(args, nuc_comp):
if not os.path.isdir(args.input + '/GC3xENc_Plots_' + today): if not os.path.isdir(args.input + '/GC3xENc_Plots_' + str(today)):
os.mkdir(args.input + '/GC3xENc_Plots_' + today) os.mkdir(args.input + '/GC3xENc_Plots_' + str(today))
taxa = list(dict.fromkeys([rec[:10] for rec in nuc_comp])) taxa = list(dict.fromkeys([rec[:10] for rec in nuc_comp]))
@ -235,7 +235,7 @@ def plot_jf(args, nuc_comp):
plt.scatter(np.array([val[0] for val in comp_data]), np.array([val[1] for val in comp_data]), s = 1) plt.scatter(np.array([val[0] for val in comp_data]), np.array([val[1] for val in comp_data]), s = 1)
plt.xlabel("GC content (3rd pos, 4-fold sites)") plt.xlabel("GC content (3rd pos, 4-fold sites)")
plt.ylabel("Observed Wright ENc (6 Fold)") plt.ylabel("Observed Wright ENc (6 Fold)")
plt.savefig(args.input + '/GC3xENc_Plots_' + today + '/' + taxon + '.png') plt.savefig(args.input + '/GC3xENc_Plots_' + str(today) + '/' + taxon + '.png')
if __name__ == "__main__": if __name__ == "__main__":
args = get_args() args = get_args()