Gabriel Pratt gpratt
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| def calculate_on_target(barcodes, barcode_map, expected): | |
| figsize(4,4) | |
| total = 0 | |
| on_target = 0 | |
| off_target = 0 | |
| no_target = 0 | |
| expected_counts = [] | |
| off_target_counts = [] | |
| expected_names = [] |
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| from itertools import groupby | |
| lst = ['DEAA IP', | |
| 'DEAA Input', | |
| 'FLAG IP', | |
| 'FLAG Input', | |
| 'K498A IP', | |
| 'K498A Input', | |
| 'Wild Type IP', | |
| 'Wild Type Input'] |
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| foo |
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| cisbp_db = pd.read_csv("/nas3/gpratt/projects/cisbp/analysis/RBP_Information.txt", sep="\t") | |
| public_clip_list = pd.read_csv("/nas3/gpratt/projects/public_clip/v1/public_clip_list.csv", index_col=0) | |
| public_clip_list= public_clip_list[public_clip_list['CLIP-seq?'] == "Yes"] | |
| public_clip_list['ensembl'] = public_clip_list.Ensemblid.astype(str).apply(lambda x: x.split(".")[0]) |
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| analysis_dir = "/nas3/gpratt/projects/public_clip/analysis/v5" | |
| experiment_mapping = { | |
| "peaks" : "clipper", | |
| "ripseeker" : "ripseeker", | |
| "pyicoclip" : "pyicoclip", | |
| "piranha" : "piranha", | |
| "bed_notrim_ingenes_clusters_hg1950" : "kasey", | |
| "bed_notrim_ingenes_clusters_mm950" : "kasey", | |
| } |
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| """" | |
| barcode_collapse.py read in a .bam file where the | |
| first 9 nt of the read name | |
| are the barcode and merge reads mapped to the same position that have the same barcode | |
| """ | |
| from collections import Counter, OrderedDict |
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| cisbp_db = pd.read_csv("/nas3/gpratt/projects/cisbp/analysis/RBP_Information.txt", sep="\t") | |
| pwm_locations = "/nas3/gpratt/projects/cisbp/analysis/pwm_locations/" | |
| #where %s is the motif id found in cisbp_db | |
| motif_ids = "%s.txt/fimo_reformated.txt" | |
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| import glob | |
| import pandas as pd | |
| datasets = glob.glob("/nas/nas0/gpratt/projects/upf1/analysis/v3/*.RPKM") | |
| datasets = {os.path.basename(dataset).split(".")[0] : pd.read_csv(dataset, index_col=0, sep="\t").RPKM for dataset in datasets} | |
| clipseq_rpkm_df = pd.concat(datasets, join="outer") | |
| clip_count_df.unstack() |
gpratt
/ test_clipper.ipynb
Last active
August 29, 2015 14:04
— forked from mlovci/test_clipper.ipynb
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| from clipper.src import CLIP_analysis | |
| import os | |
| viz = CLIP_analysis_display.ClipVisualization() | |
| def plot_denovo_motifs(bedtool, fig=None): | |
| root = "/Users/gpratt/bioinformatics/yeolab/iPython_Notebook/fox2/" | |
| out_dir = os.path.join(root, "assigned/") | |
| fasta_dir = os.path.join(root, "fasta/") | |
| cluster_name = os.path.basename(bedtool.fn) |
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