Merge pull request #346 from CGATOxford/AH-CGATScriptsPy36

py36 compatibility
CGATOxford · Aug 21, 2017 · 0968e30 · 0968e30
2 parents 6acb3ee + 012f162
commit 0968e30
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Showing 6 changed files with 70 additions and 58 deletions.
diff --git a/CGAT/scripts/_bam2bam.pyx b/CGAT/scripts/_bam2bam.pyx
@@ -133,12 +133,15 @@ def filter_bam(AlignmentFile input_samfile,
             raise ValueError("require another bam file for mismatch filtering" )
 
         # L = 1 byte (unsigned char)
-        def _gen(): return array.array('B') 
+        def _gen():
+            return array.array('B')
+
         index = collections.defaultdict(_gen)
 
         while ret > 0:
-            ret = bam_read1(hts_get_bgzfp(reference_samfile.htsfile),
-                            b)
+            ret = bam_read1(
+                hts_get_bgzfp(reference_samfile.htsfile),
+                b)
             if ret > 0:
                 # ignore unmapped reads
                 if b.core.flag & 4:
@@ -151,7 +154,6 @@ def filter_bam(AlignmentFile input_samfile,
                 else:
                     nm = 0
                 index[qname].append(nm)
-
         E.info( "built index for %i reads" % len(index))
         bam_destroy1(b)
 
@@ -167,8 +169,7 @@ def filter_bam(AlignmentFile input_samfile,
     for read in input_samfile:
 
         ninput += 1
-        # if ninput > 10000: break
-
+
         # remove unmapped reads
         if read._delegate.core.flag & 4:
             if c_remove_unmapped:

diff --git a/CGAT/scripts/bam2bam.py b/CGAT/scripts/bam2bam.py
@@ -354,8 +354,11 @@ def main(argv=None):
     bamfiles = []
 
     if options.stdin != sys.stdin:
+        from_stdin = True
         bamfiles.append(options.stdin.name)
-
+    else:
+        from_stdin = False
+
     if options.inplace:
         bamfiles.extend(args)
         if len(bamfiles) == 0:
@@ -369,6 +372,8 @@ def main(argv=None):
     if len(bamfiles) == 0:
         bamfiles = ["-"]
 
+    to_stdout = False
+
     for bamfile in bamfiles:
 
         E.info('processing %s' % bamfile)
@@ -383,8 +388,8 @@ def main(argv=None):
 
         # reading bam from stdin does not work with only the "r" tag
         pysam_in = pysam.AlignmentFile(bamfile, "rb")
-
-        if bamfile == "-":
+        if bamfile == "-" or (from_stdin and bamfile == options.stdin.name):
+            to_stdout = True
             if options.output_sam:
                 pysam_out = pysam.AlignmentFile("-", "wh", template=pysam_in)
             else:
@@ -397,7 +402,8 @@ def main(argv=None):
             tmpfile.close()
 
             E.debug("writing temporary bam-file to %s" % tmpfile.name)
-            pysam_out = pysam.AlignmentFile(tmpfile.name, "wb",
+            pysam_out = pysam.AlignmentFile(tmpfile.name,
+                                            "wb",
                                             template=pysam_in)
 
         if "filter" in options.methods:
@@ -431,7 +437,12 @@ def main(argv=None):
                 remove_mismatches=remove_mismatches,
                 colour_mismatches=colour_mismatches)
 
-            options.stdlog.write("category\tcounts\n%s\n" % c.asTable())
+            if pysam_ref:
+                pysam_ref.close()
+
+            # do not write to stdlog in the middle of a SAM/BAM stdout stream.
+            if options.stdlog != options.stdout:
+                E.info("category\tcounts\n%s\n" % c.asTable())
         else:
 
             # set up the modifying iterators
@@ -610,8 +621,8 @@ def keep_first_base(i):
             for read in it:
                 pysam_out.write(read)
 
-            pysam_in.close()
-            pysam_out.close()
+        pysam_in.close()
+        pysam_out.close()
 
         if options.inplace:
             # set date and file permissions according to original

diff --git a/conda/environments/scripts-nosetests.yml b/conda/environments/scripts-nosetests.yml
@@ -15,7 +15,7 @@ dependencies:
 # bioinformatics tools
 - ucsc-wigtobigwig
 # python deps
-- python=3.5
+- python
 - biopython
 - cython
 - alignlib-lite

diff --git a/install-CGAT-tools.sh b/install-CGAT-tools.sh
@@ -193,8 +193,8 @@ if [[ $INSTALL_SCRIPTS ]] ; then
    conda create -q -n ${CONDA_INSTALL_ENV} cgat-scripts --override-channels -c bioconda -c conda-forge -c defaults -y
 else
    # to-update once we merge to master:
-   # wget -O env.yml https://raw.githubusercontent.com/CGATOxford/cgat/conda/environments/${CONDA_INSTALL_TYPE}
-   wget -O env.yml https://raw.githubusercontent.com/CGATOxford/cgat/SLV-update-install/conda/environments/${CONDA_INSTALL_TYPE}
+   # wget -O env.yml https://raw.githubusercontent.com/CGATOxford/cgat/master/conda/environments/${CONDA_INSTALL_TYPE}
+   wget -O env.yml https://raw.githubusercontent.com/CGATOxford/cgat/${TRAVIS_BRANCH}/conda/environments/${CONDA_INSTALL_TYPE}
    conda env create -f env.yml
 fi
 

diff --git a/tests/counts2counts.py/counts_rowspikes_logfold.tsv b/tests/counts2counts.py/counts_rowspikes_logfold.tsv
@@ -1,29 +1,29 @@
 spike	wt-N-1	wt-N-2	wt-N-3	wt-P-1	wt-P-2	wt-P-3
-spike-in_6.5_2.5_0	96	98	144	889	758	519
-spike-in_5.5_8.5_1	51	30	42	14505	16477	14570
-spike-in_5.5_1.5_2	77	44	66	131	197	163
-spike-in_7.5_4.5_3	186	172	218	3660	4986	4420
-spike-in_5.5_6.5_4	51	40	47	6449	4275	3019
-spike-in_7.5_1.5_5	56	60	332	372	306	244
-spike-in_3.5_1.5_6	11	3	14	29	32	44
-spike-in_9.5_4.5_7	873	733	934	39474	14358	11350
-spike-in_5.5_7.5_8	40	34	35	10374	9391	7415
-spike-in_0.5_6.5_9	2	1	0	107	184	186
-spike-in_7.5_3.5_10	175	167	251	2595	2949	2272
-spike-in_5.5_5.5_11	39	33	41	1334	1472	1256
-spike-in_4.5_5.5_12	23	20	15	618	696	645
-spike-in_6.5_6.5_13	109	83	95	7453	10100	8401
-spike-in_6.5_1.5_14	98	90	67	204	292	224
-spike-in_6.5_3.5_15	178	76	56	1193	1105	654
-spike-in_5.5_2.5_16	48	73	61	278	317	248
-spike-in_4.5_3.5_17	32	27	22	317	473	394
-spike-in_9.5_3.5_18	744	701	791	6962	11651	9331
-spike-in_6.5_0.5_19	147	91	123	150	191	160
-spike-in_1.5_6.5_20	1	2	2	216	295	289
+spike-in_0.5_6.5_0	2	1	0	107	184	186
+spike-in_1.5_6.5_1	1	2	2	216	295	289
+spike-in_2.5_3.5_2	7	6	7	107	133	77
+spike-in_3.5_1.5_3	11	3	14	29	32	44
+spike-in_3.5_2.5_4	12	9	12	56	78	74
+spike-in_4.5_3.5_5	32	27	22	317	473	394
+spike-in_4.5_5.5_6	23	20	15	618	696	645
+spike-in_5.5_0.5_7	52	60	67	120	89	69
+spike-in_5.5_1.5_8	77	44	66	131	197	163
+spike-in_5.5_2.5_9	48	73	61	278	317	248
+spike-in_5.5_5.5_10	39	33	41	1334	1472	1256
+spike-in_5.5_6.5_11	51	40	47	6449	4275	3019
+spike-in_5.5_7.5_12	40	34	35	10374	9391	7415
+spike-in_5.5_8.5_13	51	30	42	14505	16477	14570
+spike-in_6.5_0.5_14	147	91	123	150	191	160
+spike-in_6.5_1.5_15	98	90	67	204	292	224
+spike-in_6.5_2.5_16	96	98	144	889	758	519
+spike-in_6.5_3.5_17	178	76	56	1193	1105	654
+spike-in_6.5_4.5_18	128	104	125	3384	3387	2364
+spike-in_6.5_6.5_19	109	83	95	7453	10100	8401
+spike-in_7.5_1.5_20	56	60	332	372	306	244
 spike-in_7.5_2.5_21	106	169	153	955	1209	848
-spike-in_8.5_1.5_22	423	268	309	157	492	1499
-spike-in_2.5_3.5_23	7	6	7	107	133	77
-spike-in_5.5_0.5_24	52	60	67	120	89	69
-spike-in_6.5_4.5_25	128	104	125	3384	3387	2364
-spike-in_3.5_2.5_26	12	9	12	56	78	74
-spike-in_8.5_4.5_27	398	300	330	7865	9033	8825
+spike-in_7.5_3.5_22	175	167	251	2595	2949	2272
+spike-in_7.5_4.5_23	186	172	218	3660	4986	4420
+spike-in_8.5_1.5_24	423	268	309	157	492	1499
+spike-in_8.5_4.5_25	398	300	330	7865	9033	8825
+spike-in_9.5_3.5_26	744	701	791	6962	11651	9331
+spike-in_9.5_4.5_27	873	733	934	39474	14358	11350
diff --git a/tests/counts2counts.py/counts_rowspikes_relative.tsv b/tests/counts2counts.py/counts_rowspikes_relative.tsv
@@ -1,18 +1,18 @@
 spike	wt-N-1	wt-N-2	wt-N-3	wt-P-1	wt-P-2	wt-P-3
-spike-in_65.0_250.0_0	48	73	61	278	317	248
-spike-in_5.0_50.0_1	7	6	7	107	133	77
-spike-in_15.0_50.0_2	12	9	12	56	78	74
-spike-in_45.0_50.0_3	43	43	39	43	63	39
-spike-in_65.0_150.0_4	77	44	66	131	197	163
-spike-in_115.0_650.0_5	96	98	144	889	758	519
-spike-in_105.0_850.0_6	178	76	56	1193	1105	654
-spike-in_15.0_650.0_7	23	20	15	618	696	645
-spike-in_85.0_150.0_8	98	90	67	204	292	224
-spike-in_55.0_50.0_9	52	60	67	120	89	69
-spike-in_145.0_850.0_10	106	169	153	955	1209	848
-spike-in_5.0_250.0_11	1	2	2	216	295	289
-spike-in_25.0_350.0_12	32	27	22	317	473	394
-spike-in_5.0_150.0_13	2	1	0	107	184	186
+spike-in_5.0_50.0_0	7	6	7	107	133	77
+spike-in_5.0_150.0_1	2	1	0	107	184	186
+spike-in_5.0_250.0_2	1	2	2	216	295	289
+spike-in_15.0_50.0_3	12	9	12	56	78	74
+spike-in_15.0_650.0_4	23	20	15	618	696	645
+spike-in_25.0_350.0_5	32	27	22	317	473	394
+spike-in_45.0_50.0_6	43	43	39	43	63	39
+spike-in_45.0_150.0_7	11	35	81	134	191	180
+spike-in_55.0_50.0_8	52	60	67	120	89	69
+spike-in_65.0_150.0_9	77	44	66	131	197	163
+spike-in_65.0_250.0_10	48	73	61	278	317	248
+spike-in_85.0_150.0_11	98	90	67	204	292	224
+spike-in_105.0_850.0_12	178	76	56	1193	1105	654
+spike-in_115.0_650.0_13	96	98	144	889	758	519
 spike-in_125.0_50.0_14	147	91	123	150	191	160
 spike-in_145.0_150.0_15	56	60	332	372	306	244
-spike-in_45.0_150.0_16	11	35	81	134	191	180
+spike-in_145.0_850.0_16	106	169	153	955	1209	848