mlbi-bitool 0.2.2__tar.gz → 0.2.4__tar.gz

{mlbi_bitool-0.2.2 → mlbi_bitool-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mlbi-bitool
-Version: 0.2.2
+Version: 0.2.4
 Summary: Python interface to BioInfo tools for use in Google.Colab
 Author-email: MLBI Lab <syoon@dku.edu>
 License-Expression: MIT

{mlbi_bitool-0.2.2 → mlbi_bitool-0.2.4}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "mlbi-bitool"
-version = "0.2.2"
+version = "0.2.4"
 description = "Python interface to BioInfo tools for use in Google.Colab"
 readme = "README.md"
 authors = [{ name = "MLBI Lab", email = "syoon@dku.edu" }]

{mlbi_bitool-0.2.2 → mlbi_bitool-0.2.4}/src/mlbi_bitool/bistack.py

@@ -228,7 +228,6 @@ apt_pkgs = {
     'samtools':       ("samtools", "samtools", "samtools", _version_samtools),
     'featurecounts':  ("featureCounts(subread)", "subread","featureCounts", _version_featureCounts),
     'stringtie':      ("stringtie","stringtie","stringtie",_version_stringtie),
-    'gffcompare':     ("gffcompare", "gffcompare", "gffcompare", _version_gffcompare),
     'gffread':        ("gffread", "gffread", "gffread", _version_gffread),
     'bcftools':       ("bcftools", "bcftools", "bcftools", _version_bcftools),
     'tabix':          ("tabix", "tabix", "tabix", _version_tabix),
@@ -306,6 +305,7 @@ def _version_gatk():          return _probe_version(["gatk", "--version"])
 conda_pkgs = {
     'rmats':  ('rmats.py', _version_rmats),
     'rsem':   ('rsem-calculate-expression', _version_rsem),
+    'gffcompare': ('gffcompare', _version_gffcompare),
     'ucsc_gtftogenepred': ('gtfToGenePred', _version_gtfToGenePred, 'ucsc-gtftogenepred'),
     'ucsc_genepredtobed': ('genePredToBed', _version_genePredToBed, 'ucsc-genepredtobed'),
 }
@@ -317,7 +317,7 @@ other_pkgs = {
 
 BI_TOOL_PRESETS = {
     "wes": ["bwa", "samtools", "bcftools", "tabix", "bgzip", "gatk", "cnvkit"],
-    "rnaseq": ["star", "samtools", "rsem", "salmon", "stringtie", "gffread", "rmats"],
+    "rnaseq": ["star", "samtools", "rsem", "salmon", "stringtie", "gffcompare", "gffread", "rmats"],
     "ucsc_tools": ["ucsc_gtftogenepred", "ucsc_genepredtobed"],
     "pacbio": ["minimap2", "samtools", "stringtie", "gffcompare", "gffread",
                "ucsc_gtftogenepred", "ucsc_genepredtobed", "rmats"],

{mlbi_bitool-0.2.2 → mlbi_bitool-0.2.4}/src/mlbi_bitool/tasm.py

@@ -1,7 +1,7 @@
 import re, copy, collections
 import numpy as np
 import pandas as pd
-import os, time
+import os, time, glob
 from subprocess import Popen, PIPE
 import shlex, shutil, tempfile, sys
 from typing import Optional, Tuple, Set
@@ -701,11 +701,12 @@ def Stringtie_merge_n_compare( src_dir: str,
                                verbose = True ):
 
     cmd_lst = []
+    if src_dir[-1] == '/':
+        src_dir = src_dir[:-1]
     flst = os.listdir(src_dir)
-    flst = [src_dir + f for f in flst if f.split('.')[-1] == 'gff']
+    flst = [os.path.join(src_dir, f) for f in flst if f.split('.')[-1] == 'gff']
     flst.sort()
 
-    if src_dir[-1] == '/': src_dir = src_dir[:-1]
     if out_dir is None:
         out_dir = src_dir + '_merged_info'
     if not os.path.isdir(out_dir): os.mkdir(out_dir)
@@ -752,7 +753,23 @@ def Stringtie_merge_n_compare( src_dir: str,
     if verbose: print('done.')
 
     if verbose: print('Applying to merged GFF ... ', end = '')
-    df_tmap = pd.read_csv( gffcomp_prefix + '.merged.gff.tmap', sep = '\t' )
+    tmap_file = gffcomp_prefix + '.merged.gff.tmap'
+    if not os.path.isfile(tmap_file):
+        tmap_candidates = sorted(glob.glob(gffcomp_prefix + '*.tmap'))
+        if len(tmap_candidates) == 1:
+            tmap_file = tmap_candidates[0]
+        elif len(tmap_candidates) > 1:
+            tmap_candidates.sort(key=lambda p: ('.merged.gff.tmap' not in p, len(p), p))
+            tmap_file = tmap_candidates[0]
+        else:
+            existing = sorted(glob.glob(gffcomp_prefix + '*'))
+            msg = (
+                "gffcompare did not create a .tmap file. "
+                f"Expected {gffcomp_prefix}.merged.gff.tmap or {gffcomp_prefix}*.tmap. "
+                f"Exit code: {exit_code}. Existing output files: {existing}"
+            )
+            raise FileNotFoundError(msg)
+    df_tmap = pd.read_csv( tmap_file, sep = '\t' )
     df_gff = reflect_gffcompare_res_to_stringtie_res( df_gtf, df_gff, df_tmap, 
                                                       class_code_to_drop = class_code_to_drop, 
                                                       verbose = False )

{mlbi_bitool-0.2.2 → mlbi_bitool-0.2.4}/src/mlbi_bitool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mlbi-bitool
-Version: 0.2.2
+Version: 0.2.4
 Summary: Python interface to BioInfo tools for use in Google.Colab
 Author-email: MLBI Lab <syoon@dku.edu>
 License-Expression: MIT