diff options
| -rwxr-xr-x | scripts/maintenance/readProbeSetSE_v7.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/plink_mapping.py | 4 |
2 files changed, 3 insertions, 3 deletions
diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py index 7b2fee87..2700a8ef 100755 --- a/scripts/maintenance/readProbeSetSE_v7.py +++ b/scripts/maintenance/readProbeSetSE_v7.py @@ -223,7 +223,7 @@ while line: line2 = list(map(string.strip, line2)) CellId = line2[0] - if not ProbeNameId.has_key(CellId): + if CellId not in ProbeNameId: ferror.write(CellId + " doesn't exist\n") else: DataId = ProbeNameId[CellId] diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index 9571015e..38ef7190 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -111,7 +111,7 @@ def parse_plink_output(output_filename, species): line_list = build_line_list(line=line) # only keep the records whose chromosome name is in db - if species.chromosomes.chromosomes.has_key(int(line_list[0])) and line_list[-1] and line_list[-1].strip()!='NA': + if int(line_list[0]) in species.chromosomes.chromosomes and line_list[-1] and line_list[-1].strip()!='NA': chr_name = species.chromosomes.chromosomes[int(line_list[0])] snp = line_list[1] @@ -121,7 +121,7 @@ def parse_plink_output(output_filename, species): if p_value < threshold_p_value: p_value_dict[snp] = float(p_value) - if plink_results.has_key(chr_name): + if chr_name in plink_results: value_list = plink_results[chr_name] # pvalue range is [0,1] |