Merge pull request #22 from maxplanck-ie/wd

allow underscores in fasta headers.
matplotlib pin for tobias

.github/workflows/test_data/motifs_fin.meme

@@ -0,0 +1,77 @@
+MEME version 4
+
+ALPHABET= ACGT
+
+strands: + -
+
+Background letter frequencies
+A 0.25 C 0.25 G 0.25 T 0.25
+
+MOTIF MA0154.4 EBF1
+letter-probability matrix: alength= 4 w= 15 nsites= 45425 E= 0
+ 0.311723  0.195223  0.239758  0.253297
+ 0.251029  0.210325  0.296775  0.241871
+ 0.051778  0.099196  0.121013  0.728013
+ 0.029081  0.763126  0.042267  0.165526
+ 0.012504  0.952251  0.008167  0.027078
+ 0.014265  0.936973  0.009752  0.039009
+ 0.055894  0.873418  0.018976  0.051712
+ 0.764887  0.037578  0.037931  0.159604
+ 0.077094  0.017920  0.852570  0.052416
+ 0.057611  0.010897  0.916918  0.014573
+ 0.033352  0.010017  0.941970  0.014662
+ 0.194959  0.054199  0.721211  0.029631
+ 0.696445  0.139901  0.109125  0.054529
+ 0.247199  0.292768  0.216951  0.243082
+ 0.262036  0.238547  0.201937  0.297479
+URL http://jaspar.genereg.net/matrix/MA0154.4
+
+MOTIF MA1604.1 Ebf2
+letter-probability matrix: alength= 4 w= 13 nsites= 26261 E= 0
+ 0.177868  0.223525  0.292373  0.306234
+ 0.122273  0.274019  0.122577  0.481132
+ 0.007464  0.970907  0.014318  0.007311
+ 0.019535  0.923499  0.009863  0.047104
+ 0.016564  0.957199  0.009215  0.017021
+ 0.732455  0.142569  0.054339  0.070637
+ 0.729409  0.051293  0.138418  0.080880
+ 0.028064  0.009101  0.955904  0.006930
+ 0.048589  0.008377  0.928601  0.014432
+ 0.036975  0.022086  0.918625  0.022314
+ 0.830204  0.054720  0.064773  0.050303
+ 0.269449  0.291992  0.262633  0.175926
+ 0.253875  0.272571  0.184037  0.289517
+URL http://jaspar.genereg.net/matrix/MA1604.1
+
+MOTIF MA1637.1 EBF3
+letter-probability matrix: alength= 4 w= 13 nsites= 22062 E= 0
+ 0.173058  0.233660  0.276584  0.316698
+ 0.115221  0.272323  0.138156  0.474300
+ 0.009927  0.965325  0.016363  0.008385
+ 0.017315  0.937404  0.011830  0.033451
+ 0.015230  0.952633  0.014686  0.017451
+ 0.683936  0.164718  0.065089  0.086257
+ 0.721875  0.052126  0.152933  0.073067
+ 0.023343  0.011785  0.960384  0.004487
+ 0.039933  0.010425  0.933234  0.016408
+ 0.025791  0.023343  0.929879  0.020986
+ 0.755235  0.082449  0.089974  0.072342
+ 0.298568  0.277128  0.262397  0.161907
+ 0.258000  0.248708  0.206962  0.286329
+URL http://jaspar.genereg.net/matrix/MA1637.1
+
+MOTIF MA0143.4 SOX2
+letter-probability matrix: alength= 4 w= 11 nsites= 85754 E= 0
+ 0.339401  0.128752  0.249948  0.281899
+ 0.353091  0.176715  0.200072  0.270122
+ 0.973890  0.005084  0.004874  0.016151
+ 0.015241  0.913730  0.014495  0.056534
+ 0.951408  0.014052  0.006414  0.028127
+ 0.942522  0.020314  0.023346  0.013819
+ 0.056149  0.008536  0.010845  0.924470
+ 0.115750  0.009329  0.855610  0.019311
+ 0.172260  0.073046  0.634536  0.120158
+ 0.336544  0.200084  0.207162  0.256210
+ 0.337710  0.203781  0.186557  0.271952
+URL http://jaspar.genereg.net/matrix/MA0143.4
+

src/AOS/envs/deeptools.yml

@@ -3,4 +3,3 @@ channels:
   - bioconda
 dependencies:
   - deeptools
-  - samtools == 1.13

src/AOS/envs/tobias.yml

@@ -3,6 +3,6 @@ channels:
   - bioconda
 dependencies:
   - tobias >= 0.13.3
-  - pip
-  - pip:
-    - gimmemotifs
+  - cython
+  - gimmemotifs
+  - matplotlib<3.8

src/AOS/preflight.py

@@ -66,6 +66,9 @@ def retabspath(_p):
         self.samples = [os.path.basename(x).replace('.bam', '') for x in glob.glob(
             os.path.join(os.path.abspath(bamdir), '*.bam')
         )]
+        if not self.samples:
+            print("No samples found.")
+            sys.exit()
         self.envs = {
             'seqtools': os.path.join(
                 self.dirs['scriptsdir'], 'envs', 'seqtools.yml'