[med-svn] [Git][med-team/umis][upstream] New upstream version 1.0.7

[Steffen Möller]

Steffen Möller pushed to branch upstream at Debian Med / umis


Commits:
2e267bd4 by Steffen Moeller at 2020-05-19T15:01:18+02:00
New upstream version 1.0.7
- - - - -


8 changed files:

- HISTORY.md
- + examples/tagcount/tagcount-example.csv
- setup.py
- test.sh
- + tests/correct/test25.mtx
- + tests/correct/test25.mtx.colnames
- + tests/correct/test25.mtx.rownames
- umis/umis.py


Changes:

=====================================
HISTORY.md
=====================================
@@ -1,3 +1,7 @@
+## 1.0.7
+- Ensure headers are not written when writing out a Series, to make us compatible with pandas > 0.24.
+- Fix for deprecated .ix call, .loc is the new replacement. Thanks to @naumenko-sa.
+
 ## 1.0.6
 - Fix for the python3 fix.
 


=====================================
examples/tagcount/tagcount-example.csv
=====================================
@@ -0,0 +1,3 @@
+gene,GATAACCATA-GTTACCGC,GATAACCATC-GTTACCGC
+ENSDART00000163675.1,1,2
+ENSDART00000163675.2,0,0


=====================================
setup.py
=====================================
@@ -8,7 +8,7 @@ def read(fname):
 
 setup(
         name='umis',
-        version='1.0.6',
+        version='1.0.7',
         description='Package for estimating UMI counts in Transcript Tag Counting data.',
         packages=find_packages(),
         install_requires=['click', 'pysam>=0.8.3', 'pandas', 'regex', 'scipy', 'toolz'],


=====================================
test.sh
=====================================
@@ -190,6 +190,7 @@ umis demultiplex_cells \
 --out_dir tests/results \
 examples/Klein-inDrop/test_cell_demultiplex.fq
 
+umis sparse examples/tagcount/tagcount-example.csv tests/results/test25.mtx
 
 # only display diff output if there are differences
 if [[ $(diff -rq tests/results tests/correct) ]]; then


=====================================
tests/correct/test25.mtx
=====================================
@@ -0,0 +1,5 @@
+%%MatrixMarket matrix coordinate integer general
+%
+2 2 2
+1 1 1
+1 2 2


=====================================
tests/correct/test25.mtx.colnames
=====================================
@@ -0,0 +1,2 @@
+GATAACCATA-GTTACCGC
+GATAACCATC-GTTACCGC


=====================================
tests/correct/test25.mtx.rownames
=====================================
@@ -0,0 +1,2 @@
+ENSDART00000163675.1
+ENSDART00000163675.2


=====================================
umis/umis.py
=====================================
@@ -24,7 +24,7 @@ import numpy as np
 import scipy.io, scipy.sparse
 import click
 
-VERSION = "1.0.6"
+VERSION = "1.0.7"
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
@@ -653,7 +653,7 @@ def tagcount(sam, out, genemap, output_evidence_table, positional, minevidence,
         genes = pd.Series(index=set(gene_map.values()))
         genes = genes.sort_index()
         # Now genes is assigned to a DataFrame
-        genes = expanded.ix[genes.index]
+        genes = expanded.loc[genes.index]
 
     elif gene_tags:
         expanded.sort_index()
@@ -949,8 +949,8 @@ def sparse(csv, sparse):
     '''
     import pandas as pd
     df = pd.read_csv(csv, index_col=0, header=0)
-    pd.Series(df.index).to_csv(sparse + ".rownames", index=False)
-    pd.Series(df.columns.values).to_csv(sparse + ".colnames", index=False)
+    pd.Series(df.index).to_csv(sparse + ".rownames", index=False, header=False)
+    pd.Series(df.columns.values).to_csv(sparse + ".colnames", index=False, header=False)
     with open(sparse, "w+b") as out_handle:
         scipy.io.mmwrite(out_handle, scipy.sparse.csr_matrix(df))
 



View it on GitLab: https://salsa.debian.org/med-team/umis/-/commit/2e267bd488c0a4e4865c450f83c08d6e56fccb4c

-- 
View it on GitLab: https://salsa.debian.org/med-team/umis/-/commit/2e267bd488c0a4e4865c450f83c08d6e56fccb4c
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