In [1]:

    

%run ../../shared_setup.ipynb


    

    




docker image cggh/biipy:v1.6.0






    

In [2]:

    

callsets = load_callsets(COMBINED_CALLSET_FN_TEMPLATE, 
                         variant_filter='FILTER_PASS',
                         call_filter=combined_conf_calls,
                         sample_exclusions=excessive_recomb_samples)


    

    




2016-03-08 22:36:25.762772 :: loading /data/plasmodium/pfalciparum/pf-crosses/data/public/20141022/3d7_hb3.combined.final.npz
2016-03-08 22:36:26.033269 :: filter variants: excluding 157 (0.4%) retaining 42087 (99.6%) of 42244 variants
2016-03-08 22:36:26.072474 :: filter calls: excluding 2439 (0.3%) retaining 881388 (99.7%) of 883827 calls
2016-03-08 22:36:26.073773 :: loading /data/plasmodium/pfalciparum/pf-crosses/data/public/20141022/hb3_dd2.combined.final.npz
2016-03-08 22:36:26.432508 :: filter variants: excluding 450 (1.2%) retaining 36461 (98.8%) of 36911 variants
2016-03-08 22:36:26.458679 :: filter samples: excluding ['SC01/PG0025-C/ERR019045'] including ['HB3/PG0004-CW/ERR012788', 'DD2/PG0008-CW/ERR012840', '1BB5/PG0023-C/ERR015449', '3BA6/PG0022-Cx/ERR126027', '3BD5/PG0024-C/ERR019053', '7C101/PG0074-C/ERR019048', '7C111/PG0038-C/ERR015457', '7C12/PG0035-Cx/ERR037704', '7C126/PG0047-C/ERR015452', '7C140/PG0039-C/ERR015454', '7C159/PG0040-Cx/ERR107475', '7C16/PG0036-C/ERR015455', '7C170/PG0041-C/ERR015446', '7C183/PG0042-C/ERR015448', '7C188/PG0030-C/ERR019046', '7C20/PG0037-C/ERR015451', '7C3/PG0034-C/ERR019047', '7C408/PG0031-C/ERR015458', '7C421/PG0043-C/ERR015459', '7C424/PG0044-C/ERR019043', '7C46/PG0046-Cx/ERR107476', '7C7/PG0048-C/ERR019049', 'B1SD/PG0015-C/ERR019044', 'B4R3/PG0018-C/ERR019042', 'CH3_116/PG0032-Cx/ERR037703', 'CH3_61/PG0033-Cx/ERR175544', 'D43/PG0029-Cx/ERR107474', 'GC03/PG0021-C/ERR015447', 'GC06/PG0028-C/ERR015456', 'QC01/PG0017-C/ERR019050', 'QC13/PG0016-C/ERR012895', 'QC23/PG0045-C/ERR012892', 'QC34/PG0026-C/ERR015453', 'SC05/PG0019-C/ERR019051', 'TC05/PG0027-C/ERR015450', 'TC08/PG0020-C/ERR019052']
2016-03-08 22:36:26.531364 :: filter calls: excluding 28934 (2.2%) retaining 1283662 (97.8%) of 1312596 calls
2016-03-08 22:36:26.533164 :: loading /data/plasmodium/pfalciparum/pf-crosses/data/public/20141022/7g8_gb4.combined.final.npz
2016-03-08 22:36:26.888840 :: filter variants: excluding 304 (0.9%) retaining 34471 (99.1%) of 34775 variants
2016-03-08 22:36:26.910323 :: filter samples: excluding ['D2/PG0094-CW/ERR045632'] including ['7G8/PG0083-C/ERR027099', 'GB4/PG0084-C/ERR027100', 'AL2/PG0103-CW/ERR045627', 'AUD/PG0112-C/ERR029406', 'AUD/PG0112-CW/ERR045639', 'DAN/PG0098-C/ERR027110', 'DEV/PG0081-CW/ERR045633', 'JB12/PG0099-C/ERR029146', 'JB8/PG0087-C/ERR029091', 'JC3/PG0077-CW/ERR045636', 'JC9/PG0111-C/ERR029409', 'JC9/PG0111-CW/ERR045634', 'JE11/PG0100-C/ERR029404', 'JE11/PG0100-CW/ERR045630', 'JF6/PG0079-C/ERR027102', 'JF6/PG0079-CW/ERR045637', 'JON/PG0107-C/ERR029408', 'KA6/PG0091-C/ERR027117', 'KB8/PG0104-C/ERR029148', 'KB8/PG0104-CW/ERR045642', 'KH7/PG0088-C/ERR027111', 'LA10/PG0086-C/ERR029090', 'LA10/PG0086-CW/ERR045629', 'NF10/PG0096-C/ERR027108', 'NIC/PG0095-C/ERR027107', 'NIC/PG0095-CW/ERR045631', 'QF5/PG0078-C/ERR029092', 'QF5/PG0078-CW/ERR045638', 'TF1/PG0080-C/ERR027103', 'WC4/PG0082-C/ERR029093', 'WE2/PG0085-C/ERR027101', 'WF12/PG0097-C/ERR027109', 'XB3/PG0093-C/ERR029105', 'XD8/PG0105-C/ERR029144', 'XD8/PG0105-CW/ERR045628', 'XE7/PG0106-C/ERR029407', 'XF12/PG0102-C/ERR029143', 'XF12/PG0102-CW/ERR045635', 'XG10/PG0109-C/ERR029405']
2016-03-08 22:36:26.997425 :: filter calls: excluding 19937 (1.5%) retaining 1324432 (98.5%) of 1344369 calls

In [3]:

    

tbl_conversion_tracts = etl.frompickle(os.path.join(PUBLIC_DIR, 'tbl_conversion_tracts.pickle'))
tbl_conversion_tracts.gt('tract_length_min', 15000)


    

    
Out[3]:







0|sample
1|cross
2|chrom
3|tract_start_min
4|tract_start_mid
5|tract_start_max
6|tract_stop_min
7|tract_stop_mid
8|tract_stop_max
9|tract_length_min
10|tract_length_mid
11|tract_length_max
12|tract_support
13|tract_is_complex
14|tract_blocks
15|co_pos_mid
16|co_pos_min
17|co_pos_max
18|co_pos_range
19|tract_type




3BD5/PG0024-C/ERR019053
hb3_dd2
b'Pf3D7_10_v3'
1308754
1309392
1310031
1330511
1330807
1331104
20480
21415
22350
39
True
3
None
None
None
None
NCO


3BD5/PG0024-C/ERR019053
hb3_dd2
b'Pf3D7_10_v3'
1341344
1342132
1342921
1361560
1361995
1362430
18639
19863
21086
32
True
6
1351887
1341344
1362430
21086
CO


7C3/PG0034-C/ERR019047
hb3_dd2
b'Pf3D7_08_v3'
1202631
1203122
1203613
1227264
1227421
1227578
23651
24299
24947
44
True
5
None
None
None
None
NCO


C04/PG0061-C/ERR019059
3d7_hb3
b'Pf3D7_14_v3'
2891817
2892879
2893941
2922794
2923016
2923239
28853
30137
31422
77
True
9
None
None
None
None
NCO


JC3/PG0077-CW/ERR045636
7g8_gb4
b'Pf3D7_08_v3'
1207822
1208720
1209619
1228966
1229286
1229606
19347
20566
21784
42
True
10
1218714
1207822
1229606
21784
CO



...

In [4]:

    

fig = plt.figure(figsize=(10, .4))
plot_inheritance(plt.gca(), callsets['3d7_hb3'], 'Pf3D7_14_v3', start=2870000, stop=2990000, sample_indices=[9])


    

In [5]:

    

fig = plt.figure(figsize=(10, .4))
plot_variants_locator(plt.gca(), callsets['3d7_hb3'], 'Pf3D7_14_v3', start=2870000, stop=2990000, step=1)


    

In [6]:

    

fig = plt.figure(figsize=(10, 1))
plot_genes(plt.gca(), 'Pf3D7_14_v3', start=2870000, stop=2990000, label_named=True, width=.25, label_ytextpad=0.05)


    

In [7]:

    

def fig_recom(cross, sample_indices, chrom, start=0, stop=None, 
              figsize=(8, 3), height_ratios=[2, 1, 2], title=None, filename=None):
    fig = plt.figure(figsize=figsize)
    if title is not None:
        fig.suptitle(title, fontsize=10, fontweight='bold')
    gs = GridSpec(3, 1, height_ratios=height_ratios)
    
    ax = fig.add_subplot(gs[0])
    plot_inheritance(ax, callsets[cross], chrom, start=start, stop=stop, sample_indices=sample_indices, alpha=1)
    ax.xaxis.tick_top()
    ax.set_xlabel('variants')
    ax.xaxis.set_label_position('top')
    for i in range(len(sample_indices)):
        ax.axhline(i, color='k', alpha=.6, linewidth=.5)
    
    ax = fig.add_subplot(gs[1])
    plot_variants_locator(ax, callsets[cross], chrom, start=start, stop=stop, step=1)
    ax.set_xticks([])
    ax.set_xlabel('')
    ax.set_ylabel('variant location', rotation=0, ha='right', va='center')
    
    ax = fig.add_subplot(gs[2])
    plot_genes(ax, chrom, start=start, stop=stop, label_named=True, width=.25, label_ytextpad=.05)
    ax.set_xlabel('chromosome %s position (bp)' % chrom)
    ax.set_ylabel('genes', rotation=0, ha='right', va='center')
    
    fig.tight_layout()
    return fig


    

In [8]:

    

cross = '7g8_gb4'
sample_indices = [0, 1, 14, 15]
chrom = 'Pf3D7_11_v3' 
start=1660000
stop=1780000
fig = fig_recom(cross, sample_indices, chrom, start, stop)
fn = '../../artwork/supp/complex_tract_jf6.{dpi}.{fmt}'
for fmt in 'jpeg', 'png':
    for dpi in 120, 300:
        fig.savefig(fn.format(dpi=dpi, fmt=fmt), dpi=dpi, jpeg_quality=100)


    

In [9]:

    

cross = '3d7_hb3'
sample_indices = [0, 1, 9]
chrom = 'Pf3D7_14_v3'
start=2870000
stop=2990000
fig = fig_recom(cross, sample_indices, chrom, start, stop)
fn = '../../artwork/supp/complex_tract_c04.{dpi}.{fmt}'
for fmt in 'jpeg', 'png':
    for dpi in 120, 300:
        fig.savefig(fn.format(dpi=dpi, fmt=fmt), dpi=dpi, jpeg_quality=100)


    

In [10]:

    

cross = 'hb3_dd2'
sample_indices = [0, 1, 4]
chrom = 'Pf3D7_10_v3'
start=1260000
stop=1385000
fig = fig_recom(cross, sample_indices, chrom, start, stop)
fn = '../../artwork/supp/complex_tract_3bd5.{dpi}.{fmt}'
for fmt in 'jpeg', 'png':
    for dpi in 120, 300:
        fig.savefig(fn.format(dpi=dpi, fmt=fmt), dpi=dpi, jpeg_quality=100)


    

In [ ]: