diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/gsearch.py | 76 |
1 files changed, 40 insertions, 36 deletions
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 8f66f7e9..e541b705 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -92,19 +92,30 @@ class GSearch: if (line[8] != "NULL" and line[8] != "") and (line[9] != 0): this_trait['location_repr'] = 'Chr%s: %.6f' % ( line[8], float(line[9])) - try: - this_trait['mean'] = '%.3f' % line[10] - except: - this_trait['mean'] = "N/A" + this_trait['LRS_score_repr'] = "N/A" + this_trait['additive'] = "N/A" + this_trait['mean'] = "N/A" + if line[11] != "" and line[11] != None: - this_trait['LRS_score_repr'] = '%3.1f' % line[11] + this_trait['LRS_score_repr'] = f"{line[11]:.3f}" + if line[14] != "" and line[14] != None: + this_trait['additive'] = f"{line[14]:.3f}" + if line[10] != "" and line[10] != None: + this_trait['mean'] = f"{line[10]:.3f}" + + locus_chr = line[16] + locus_mb = line[17] + + max_lrs_text = "N/A" + if locus_chr and locus_mb: + max_lrs_text = f"Chr{locus_chr}: {locus_mb}" + this_trait['max_lrs_text'] = max_lrs_text + this_trait['additive'] = "N/A" if line[14] != "" and line[14] != None: this_trait['additive'] = '%.3f' % line[14] this_trait['dataset_id'] = line[15] - this_trait['locus_chr'] = line[16] - this_trait['locus_mb'] = line[17] dataset_ob = SimpleNamespace( id=this_trait["dataset_id"], type="ProbeSet", species=this_trait["species"]) @@ -120,11 +131,6 @@ class GSearch: if permissions['data'] == 'no-access': continue - max_lrs_text = "N/A" - if this_trait['locus_chr'] and this_trait['locus_mb']: - max_lrs_text = f"Chr{str(this_trait['locus_chr'])}: {str(this_trait['locus_mb'])}" - this_trait['max_lrs_text'] = max_lrs_text - trait_list.append(this_trait) self.trait_count = len(trait_list) @@ -230,32 +236,38 @@ class GSearch: 'utf-8', 'replace') else: this_trait['description'] = "N/A" - if line[13] != None and line[13] != "": - this_trait['mean'] = f"{line[13]:.3f}" - else: - this_trait['mean'] = "N/A" this_trait['dataset_id'] = line[14] - this_trait['locus_chr'] = line[15] - this_trait['locus_mb'] = line[16] + + this_trait['LRS_score_repr'] = "N/A" + this_trait['additive'] = "N/A" + this_trait['mean'] = "N/A" + + if line[10] != "" and line[10] != None: + this_trait['LRS_score_repr'] = f"{line[10]:.3f}" + if line[11] != "" and line[11] != None: + this_trait['additive'] = f"{line[11]:.3f}" + if line[13] != "" and line[13] != None: + this_trait['mean'] = f"{line[13]:.3f}" + + locus_chr = line[16] + locus_mb = line[17] + + max_lrs_text = "N/A" + if locus_chr and locus_mb: + max_lrs_text = f"Chr{locus_chr}: {locus_mb}" + this_trait['max_lrs_text'] = max_lrs_text + this_trait['authors'] = line[7] this_trait['year'] = line[8] + this_trait['pubmed_text'] = "N/A" + this_trait['pubmed_link'] = "N/A" if this_trait['year'].isdigit(): this_trait['pubmed_text'] = this_trait['year'] - else: - this_trait['pubmed_text'] = "N/A" if line[9] != "" and line[9] != None: this_trait['pubmed_link'] = webqtlConfig.PUBMEDLINK_URL % line[8] - else: - this_trait['pubmed_link'] = "N/A" if line[12]: this_trait['display_name'] = line[12] + \ "_" + str(this_trait['name']) - this_trait['LRS_score_repr'] = "N/A" - if line[10] != "" and line[10] != None: - this_trait['LRS_score_repr'] = '%3.1f' % line[10] - this_trait['additive'] = "N/A" - if line[11] != "" and line[11] != None: - this_trait['additive'] = '%.3f' % line[11] dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="Publish", species=this_trait["species"]) permissions = check_resource_availability(dataset_ob, this_trait['name']) @@ -266,14 +278,6 @@ class GSearch: if permissions['data'] == 'no-access': continue - this_trait['max_lrs_text'] = "N/A" - if this_trait['dataset'] == this_trait['group'] + "Publish": - try: - if this_trait['locus_chr'] and this_trait['locus_mb']: - this_trait['max_lrs_text'] = f"Chr{str(this_trait['locus_chr'])}: {str(this_trait['locus_mb'])}" - except: - this_trait['max_lrs_text'] = "N/A" - trait_list.append(this_trait) self.trait_count = len(trait_list) |